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Tuesday, September 24
 

10:00am HST

Workshop: Specialty Crop Community Databases and Breeding Data Management Tools
Tuesday September 24, 2024 10:00am - 12:00pm HST
Coral 2
In this interactive workshop, participants will be provided training on how to use Rosaceae (GDR, www.rosaceae.org), Vaccinium (GDV, www.vaccinoum.org) and Citrus (www.citrusgenomedb.org) specialty crop databases resources, as well as the Breeding Data Management tools, BIMS (www.breedwithbims.org), and the Field Book App for phenotype data collection. Using a case-study approach we will focus on how to use these integrated resources most efficiently for research and crop improvement efforts, how to apply FAIR data principles to sharing and submitting research data to these databases at the time of publication and facilitate a robust dialogue between researcher, breeders and the development team on needed improvements and long-term sustainability options for these resources.

This interactive workshop will bring together researchers and breeders to accelerate research and crop improvement in specialty crops. It will provide training and feedback on how to most effectively use the NIFA SCRI and National Research Support project 10 (NRSP10) funded Rosaceae, Citrus, and Vaccinium specialty crop databases and breeding data management resources (BIMS and Field Book), learn how to follow FAIR data principles, foster better two-way communication for increased feedback from researchers on further development of these resources, and continue to build a robust community around these research and crop improvement tools. The trainers include users and developers of these resources, ranging from early career to well-known and respected research enabling resource generators.

The Genome Database for Rosaceae (GDR), Genome Database for Vaccinium, and Citrus Genome Database (CGD) offer critical resources and tools to enable genomic, genetic, and breeding research for fruit, nut, and ornamental crops of great economic importance to the U.S. In addition, BIMS (BreedwithBIMS.org) and the Field Book APP provide widely used tools for managing plant breeding program data. While these resources are heavily used worldwide, many researchers are unaware of the full potential of using them and how they can contribute their own data for wider recognition and reuse. This interactive workshop aims to bridge this knowledge gap by providing hands-on training for specialty crop researchers on how to best use these resources and contribute their data. The workshop will also solicit ideas from participants on how to improve these databases and discuss the various options to make them sustainable in the long term. The workshop will bolster the utilization of integrated big data, promote future data sharing, and ensure that data is FAIR (Findable, Accessible, Interoperable, and Reusable).

The workshop aims to bring together researchers to accelerate research by more effective use of specialty crop databases and breeding data management resources, encouraging data submission at the time of publication, and gaining feedback from researchers. Through hands-on training, participants will become more familiar with the database resources and breeding data management tools, learn how to submit their data, and provide essential input for improving these databases and their long-term sustainability.

Coordinator(s)
  • Dorrie Main, Washington State University, Pullman, WA, United States
Moderator(s)
  • Cameron Peace, Washington State University, Horticulture, Pullman, WA, United States

Speaker/Participant(s)
  • Dorrie Main, Washington State University, Pullman, WA, United States
Introduction to the Workshop and Specialty Crop Research Databases (15 mins)

  • Jodi Humann, Washington State University, Horticulture, Pullman, WA, United States
How to efficiently use integrated genomics data and tools for research (20 mins)

  • Sook Jung, Washington State University, Horticulture, Pullman, WA, United States
    How to efficiently use integrated genetics data and tools for research (20 mins)

  • Nahla Bassil, USDA ARS, National Clonal Germplasm Repository, Corvallis, OR, United States
    How to efficiently use integrated germplasm and genotype data for research (15 mins)
    Summary:

  • Trevor Rife, Clemson University, Plant and Environmental Sciences Department, Florence, SC, United States
    How to use the Field Book App for phenotypic data collection (15 mins)
  • Sushan Ru, Auburn University, Auburn, United States
    How to use the Breeding Information Management System, BIMS, for Crop Improvement (20 mins)
  • Cameron Peace, Washington State University, Horticulture, Pullman, WA, United States


Moderator
CP

Cameron Peace

Washington State University
Speakers
avatar for Dorrie Main

Dorrie Main

Professor, Washington State University
I am a member of the Pullman Charter School Initiative team and am particularly interested in how to set up and maintain a thriving Washington State Charter School to serve the needs of Eastern Washington students.
SR

Sushan Ru

Auburn University
JH

Jodi Humann

Washington State University
SJ
NB
TR
Tuesday September 24, 2024 10:00am - 12:00pm HST
Coral 2
  Interactive Workshop

11:59am HST

Genetics and Germplasm 1 (GG 1)
Tuesday September 24, 2024 11:59am - 1:10pm HST
South Pacific 2
Chromosome Level Assemblies of Phoenix dactylifera L. 'Medjool' and 'Deglet Noor' - Yoko Hiraoka
Development of Haplotype-Phased, Chromosome-scale Genomes for Pomegranate - Alexander Schaller
In Planta Transformation Efficiency Assessment of Different Agrobacterium Strains and Explant Types in Catharanthus rose - Ting Hsuan Huang
Native Southern Red Aroniaberry (Aronia arbutifolia) Response to Chill Hours in Georgia - Leynar Leyton
Enhancing Ornamental Traits through Induced Polyploidy in Hibiscus hamabo: A Cytomolecular Analysis - Hamidou Sakhanokho
Insights into the Genetic Diversity and Population Structure of Wild and Cultivated Spinach - Gehendra Bhattarai
Population Analysis of Wild-type Venezuelan Sabadilla - Luke Czerwinski

Moderator
HS
Tuesday September 24, 2024 11:59am - 1:10pm HST
South Pacific 2
  Poster Session, Genetics and Germplasm 1

12:00pm HST

GG 1 - Chromosome Level Assemblies of Phoenix dactylifera L. 'Medjool' and 'Deglet Noor'
Tuesday September 24, 2024 12:00pm - 12:10pm HST
South Pacific 2
Date palm (Phoenix dactylifera L.) is one of the oldest cultivated perennial woody plant species with significant agricultural and economic importance. Date has its center of origin in the Middle East, spreading in ancient times to North Africa and South Asia and later to other hot, arid areas. Dates are a strict dioecious evergreen, obligate outcrossing, and highly heterozygous monocot species that are typically vegetatively propagated. ‘Medjool’ and ‘Deglet Noor’ are the most widely grown date cultivars in the United States and are also important at the global level. Despite their economic values, genomic studies have been hampered due to lack of available assembled genomes. To facilitate future genomic studies, genomes for ‘Medjool’ and ‘Deglet Noor’ were assembled using Dovetail® HiFi and Omni-C® technologies. ‘Medjool’ had a total length of 757 Mb comprising 899 scaffolds (L50 : 7, N50 : 37 Mb) with a BUSCO completeness score of 97.65 %, and ‘Deglet Noor’ had a total length of 772 Mb comprising 1287 scaffolds (L50 : 9, N50 : 33 Mb) with a BUSCO completeness score of 97.65 %.
Speakers
YH

Yoko Hiraoka

University of California Riverside/USDA-ARS
Co-authors
RK

Robert Krueger

United States Department of Agriculture
NA
Tuesday September 24, 2024 12:00pm - 12:10pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

12:10pm HST

GG 1 - Development of Haplotype-Phased, Chromosome-scale Genomes for Pomegranate
Tuesday September 24, 2024 12:10pm - 12:20pm HST
South Pacific 2
Pomegranates (Punica granatum L.) are a significant fruit crop globally, gaining traction due to their high nutritional value and many uses outside of consumption. Despite increasing interest, genetic resources for pomegranates lag behind other crops. Developing these resources can enhance breeding efficiency and deepen genomic understanding. To address this, we sequenced the genomes of two cultivars: 'Azadi', known for its robust fruit rot resistance, and 'Peppy Le Pom', a dwarf variety with short juvenility. Using the PacBio Revio Platform, we generated HiFi reads with 30x coverage and employed Hi-C for sequencing. Leveraging hifiasm's Hi-C integrated assembly method, we assembled two haplotypes for the genome of each cultivar. For 'Peppy Le Pom', we utilized 10.03 Gb of PacBio HiFi reads and 30 Gb of Hi-C data and constructed two haplotypes with eight chromosome-length scaffolds each, totaling 304.9 Mb and 318.7 Mb, with a BUSCO score of 90.3% and 92.3%, respectively. For 'Azadi', we utilized 10.08 Gb of Pacbio HiFi reads and 30 Gb of Hi-C data and assembled two haplotypes with eight chromosome-length scaffolds, measuring 305.5 Mb and 318.1 Mb, with a BUSCO score of 91.0% and 92.6%, respectively. Chromosome sizes of these pomegranate cultivars range from 27.1 Mb to 62.4 Mb. Notably, these results closely align with the previously published draft genome of the 'Tunisia' cultivar. These phased, chromosome-scale genomes will facilitate further exploration of traits of interest for pomegranate breeding, such as disease resistance, dwarfing, and short juvenility. The genomic resources established here pave the way for accelerated advancements in pomegranate research and breeding.
Speakers
AS

Alexander Schaller

University of Florida
Co-authors
JC

John Chater

University of Florida
ZD

Zhanao Deng

University of Florida
Tuesday September 24, 2024 12:10pm - 12:20pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

12:20pm HST

GG 1 - In Planta Transformation Efficiency Assessment of Different Agrobacterium Strains and Explant Types in Catharanthus rose
Tuesday September 24, 2024 12:20pm - 12:30pm HST
South Pacific 2
Catharanthus roseus (L.) G. Don is a common ornamental crop worldwide due to its high tolerance to drought and heat. The researches on Agrobacterium-mediated transformation of C. roseus are few, and mostly focus on the production of secondary metabolites in roots. Furthermore, the organogenesis from callus to plantlet is frequently unstable which limits the study on entire plant, especially on flowering. The objective of this study is to evaluate the in planta transformation survival rate in different explants and Agrobacterium strains. C. roseus ‘Cora XDR White’ seeds were cultivated in vitro till the cotyledon expanded. Plantlets and cotyledonary nodes were respectively inoculated with two Agrobacterium strains, GV3101 or LBA4404 harboring the binary vector pHEE401E. Explants were co-cultivated in 1/2 MS medium for three days. After washing with sterile water and cefotaxime, the explants were first placed in a medium containing cefotaxime, then were transferred to a same medium that was further added hygromycin. During the elimination and selection, each cotyledonary node turned brown. In the process of subculture, necrotic parts were removed. Result showed that the survival rate of plantlets was 5% in GV3101 treatment. However, LBA4404 ones eventually got brown.
Speakers
TH

Ting Hsuan Huang

Department of Horticultural Science, National Chiayi University
Co-authors
RS

Rong Show Shen

National Chiayi University
NA
YH

Yang Hsin Hsu

National Chiayi University
NA
YC

Yi Chien Lu

National Chiayi University
Tuesday September 24, 2024 12:20pm - 12:30pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

12:30pm HST

GG 1 - Native Southern Red Aroniaberry (Aronia arbutifolia) Response to Chill Hours in Georgia
Tuesday September 24, 2024 12:30pm - 12:40pm HST
South Pacific 2
Aroniaberry or chokeberry (Aronia sp., Rosaceae) is an attractive deciduous tree-like shrub. Native to eastern and central United States, red aroniaberry (A. arbutifolia) is more predominant in the southern part of the distribution. Bright red fruits, proliferous white flowers in spring, and attractive fall color, make A. arbutifolia a native shrub with ornamental potential. Most of the aroniaberry ornamental varieties available in the market are selections or hybrids of black aroniaberry (A. melanocarpa), they produce black fruit, and do not perform well in sub-tropical climates. We collected triploid and tetraploid A. arbutifolia from five different locations in South Georgia and evaluated their flowering period, fruit production, and response to chill hours in Griffin, GA (Zone 8a, Piedmont region). Plants were exposed to 1000, 800, 600, 400, or 0 chill hours and planted in the field in April of 2023. Flowering timing had a strong correlation with chill hours; plants with chill hours below 600 hrs. presented less flowers and flowering was not uniform.
Speakers
LL

Leynar Leyton

University of Florida
Co-authors
BP

Bodie Pennisi

University of Georgia
NA
CR

Carol Robacker

University of Georgia
NA
Tuesday September 24, 2024 12:30pm - 12:40pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

12:40pm HST

GG 1 - Enhancing Ornamental Traits through Induced Polyploidy in Hibiscus hamabo: A Cytomolecular Analysis
Tuesday September 24, 2024 12:40pm - 12:50pm HST
South Pacific 2
The Hibiscus genus, encompassing roughly 300 species across 10 sections, presents a diverse and economically significant range of industrial, ornamental, and medicinal properties. Polyploidy, whether occurring spontaneously or induced through external agents, such as chemicals like colchicine and oryzalin, plays a crucial role in plant breeding. It enhances various attributes including flower size, resilience, and metabolite production. Among the species in this genus, Hibiscus hamabo is noted for its salt tolerance and its attractive yellow flowers in summer and golden-yellow or burnt orange leaves in fall. However, H. hamabo typically has small and sparse flowers, which led to our efforts to enhance its ornamental value through induced polyploidy. In our study, we treated germinating seeds of H. hamabo with three concentrations of colchicine (0, 0.125, and 0.25% v/v) for varying durations (6, 12, or 24 hours). The most effective conversion was achieved with seeds treated with 0.25% v/v colchicine for 24 hours. This treatment produced solid polyploids (4n = 184) and mixed-polyploids (2n 4n). The 4n plants exhibited a 2C-DNA content of 8.50 pg, compared to 4.23 pg in the untreated (2n = 92) plants. We evaluated the impact of induced polyploidy on several morphological traits including leaf color, shape, size, trichome density, and plant height. Significant differences were observed between the polyploid plants and the control plants. Additionally, we explored the cytomolecular analysis of induced polyploidy, particularly focusing on the distribution and organization of rDNA. In 2n plants, one locus of 5S and four loci of 35S rDNA (two major and two minor) were identified. The 5S site is pericentromeric, while one of the major 35S sites is sub-terminal, and the others are at terminal locations. In 4n plants, the number of 5S and 35S sites was exactly duplicated, confirming the polyploidization at the genetic level. Our results proved that colchicine can be used to induce polyploidy in germinating H. hamabo seeds, paving the way for the improvement of this species through this method.
Speakers
HS
Co-authors
BJ
NI
Tuesday September 24, 2024 12:40pm - 12:50pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

12:50pm HST

GG 1 - Insights into the Genetic Diversity and Population Structure of Wild and Cultivated Spinach
Tuesday September 24, 2024 12:50pm - 1:00pm HST
South Pacific 2
The wealth of genetic and phenotypic diversity in plant species serves as the primary source of novel traits in plant breeding and crop improvement efforts. Spinach (Spinacia oleracea) has a long cultivation history across diverse environments and geographic regions, which has resulted in adaptation to diverse conditions. This adaptation has been influenced further by human preferences for distinct leaf shapes, tastes, flavors, and nutrition, constituting a rich reserve of genetic and phenotypic diversity within Spinacia germplasm. Moreover, wild species (S. tetrandra and S. turkestanica) offer valuable resources, particularly for traits of commercial significance, such as resistance to prevalent pathogens and pests. Therefore, understanding the genetic variations that underlie phenotypic traits is crucial to enable effective gene introgression and the development of novel spinach varieties. We recently investigated the genetic diversity and population structure of a panel of over 500 cultivated and wild germplasm obtained from the Centre for Genetic Resources, the Netherlands (CGN) at Wageningen University and Research (WUR). This panel, complemented with material from other sources, comprised 49 S. tetrandra and 86 S. turkestanica accessions. Our findings revealed the presence of significant genetic diversity within these panels of accessions, which were categorized into multiple distinct population groups. We evaluate this Spinacia panel for several horticulturally important traits to identify SNP markers and candidate gene regions associated with commercially important traits. Our objectives are to share novel insights into the genetic diversity of spinach and provide valuable molecular markers for improving cultivated spinach production.
Speakers
GB

Gehendra Bhattarai

University of Arkansas
Co-authors
avatar for Ainong Shi

Ainong Shi

Associate Professor, University of Arkasnas
Dr. Ainong Shi is a faculty member in the Department of Horticulture at the University of Arkansas. His research laboratory specializes in plant breeding and genetics, particularly focusing on vegetable crops such as arugula, cowpea, and spinach for cultivar and germplasm development... Read More →
CK

Chris Kik

Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research
NA
LD

Lindsey du Toit

Mount Vernon Northwestern Washington Research and Extension Center, Washington State University
NA
RV

Rob van Treuren

Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research
NA
SG

Sanjaya Gyawali

Sakata Seed America Inc.
NA
Tuesday September 24, 2024 12:50pm - 1:00pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

1:00pm HST

GG 1 - Population Analysis of Wild-type Venezuelan Sabadilla
Tuesday September 24, 2024 1:00pm - 1:10pm HST
South Pacific 2
Schoenocaulon officinale, also known by the common name of sabadilla, is a species of plant belonging to the family Liliaceae. It is thought to be endemic to Mexico; at some point in history, it was spread throughout other parts of South America. Sabadilla is a geophytic perennial bulb plant that is not frost tolerant. Due to the environmental factors where sabadilla grows, it is also hypothesized to be a heliophyte. It is estimated to live, while continuously flowering, for up to 8 years. Sabadilla will normally reach its mature stage at around year 2-3. The seeds of sabadilla contain two insecticidally active chemical compounds known as veratridine and cevadine. The normal compositional range that these compounds make up in the seeds is anywhere from 0.5-5%. The mode of action is similar to that of pyrethrins; these compounds will attach to sodium channels on the insects and cause continuous overactivation until the insect is knocked. It is not yet known which specific sodium channel these compounds act on. Sabadilla has been used by people for thousands of years for its insecticidal properties and alleged homeopathic benefits. However, sabadilla is a relatively untouched and unstudied plant. Due to this, almost no biological, physiological, or genetic work has been done on the plant. The purpose of this research was to delve deeper into population differences of plants that were collected from different environments in Venezuela. In 2019, seeds were collected from 7 distinct geographic locations in Venezuela. They were collected from two different sites (The Ávila National Park
Speakers
LC
Tuesday September 24, 2024 1:00pm - 1:10pm HST
South Pacific 2
  Poster presentation (individual talk), Genetics and Germplasm 1

4:00pm HST

Interest Group Session: Restoration and Utilization Efforts of Germplasms and Wild Crop Relatives at the USDA
Tuesday September 24, 2024 4:00pm - 6:00pm HST
Kahili
Leveraging the inherent genetic diversity conserved in plant resource collections is key to new crops, new cultivars, and adapted germplasm with improved traits that provide food security for a growing population, remain productive amidst rapid climate change, meet shifting consumer demands, and enhance sustainability and efficiency. The USDA National Plant Germplasm System manages large and genetically diverse plant collections representing crop plant species and many of crop wild relatives (CWR) that have significant impacts on crop production. In this Special Topic Session hosted by the Federal Partners Interest Group, scientists of the Agricultural Research Service (ARS) will discuss the current efforts and future perspectives on the restoration and utilization of germplasms and CWR at the USDA with a special focus on fruit, nut, and beverage crops.

Coordinator(s)
  • Lisa Tang, USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, United States
Moderator(s)
  • Lisa Tang, USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, United States
  • Matthew Mattia, USDA-ARS U. S. Horticultural Research Laboratory, Fort Pierce, FL, United States
Speaker/Participant(s)
  • Lisa Tang, USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, United States
    Introduction of the Federal Partners special session (5 mins)
  • Gayle Volk, USDA, Fort Collins, Colorado, United States
    The USDA-ARS National Plant Germplasm System Strategic Plan: A roadmap to conserve and utilize U. S. plant genetic resources (15 mins)
    Summary: The USDA-ARS National Plant Germplasm System (NPGS) conserves more than 620, 000 accessions of plant genetic resources of crops and crop wild relatives which annually distribute 200, 000+ samples globally. As directed by the 2018 Farm Bill, an NPGS Strategic Plan was developed to address the backlogs in maintenance, characterization, and to enhance utilization. This presentation will provide information about the impacts of the NPGS and details about the NPGS Strategic Plan, which, when funded, will result in: 1) More plant germplasm maintained disease-free, securely backed up, and readily available; 2) Expanded knowledge of the intrinsic genetic variation and high-value traits in NPGS collections; and 3) New plant germplasm with valuable traits acquired, safeguarded and developed. This presentation is authored by Gayle M. Volk (USDA), Marilyn L. Warburton (USDA), Moira Sheehan (Cornell University), Christina Walters (USDA), Stacey Estrada (USDA), Glenn Hanes (USDA), Jim McFerson (USDA), and Peter K. Bretting (USDA-retired).
  • Chris Gottschalk, USDA-ARS Appalachian Fruit Research Station, Kearneysville, WV, United States
    Into the wild: utilization of wild crop relatives the USDA ARS apple pre-breeding program (15 mins)
    Summary:
  • Nahla Bassil, USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, United States
    Crop wild relatives of temperate fruits at the Corvallis Genebank: Uses and prospects (10 mins)
    Summary:
  • Michael Hardigan, USDA-ARS, Corvallis, OR, United States
    Crop wild relatives of temperate fruits at the Corvallis Genebank: Uses and prospects (10 mins)
    Summary:
  • Tracie Matsumoto, USDA-ARS Daniel K. Inouye Pacific Basin Agricultural Research Center, Tropical Plant Genetic Resources and Disease Research Unit, Hilo, HI, United States
    Sub-Tropical/tropical Fruit, Nut, and Beverage Clonal Repository in Hilo, Hawaii (15 mins)
    Summary: The National Clonal Germplasm Repository for Tropical Fruit, Nut and Beverage Crops is located in Hilo, Hawaii and is a part of the National Germplasm Repository System and USDA ARS DKI PBARC Tropical Plant and Genetic Resources Unit. The repository is responsible for collecting, maintaining, evaluating, and distributing germplasm of tropical/subtropical fruit and nut crops. Crops include Pineapple (Ananas), Breadfruit (Artocarpus), Starfruit (Averrhoa), Peach palm (Bactris), Pili nut (Canarium), Papaya (Carica and Vasconcellea), Coffee (Coffea) Longan (Dimocarpus), Litchi (Litchi), Macadamia (Macadamia), Acerola (Malpighia), Rambutan and Pulasan (Nephelium), and Guava (Psidium). In addition to the field and greenhouse collections, we are actively investigating new methods to propagate and effectively manage the collections. We work to characterize the collection for resistance to pest and diseases and genetically characterize the germplasm to determine potential gaps for future collections.
  • Qingyi Yu, USDA-ARS Daniel K. Inouye Pacific Basin Agricultural Research Center, Tropical Plant Genetic Resources and Disease Research Unit, Hilo, HI, United States
    Exploring germplasm diversity to understand the domestication process of papaya (15 mins)
    Summary: Papaya (Carica papaya L.), originating and domesticated in southern Mexico and Central America, is widely cultivated in tropical and subtropical regions due to its nutritional benefits and the commercially significant proteolytic enzyme, papain. While wild papaya yields small, seedy fruits with minimal edible flesh, domesticated papaya varieties can weigh over five pounds. Wild papaya populations are exclusively dioecious, whereas cultivated papaya is predominantly gynodioecious, although certain dioecious cultivars exist. In this study, we conducted whole-genome resequencing of 86 diverse papaya accessions, comprising 63 cultivars and 23 wild accessions. To identify regions undergoing selection during domestication and improvement, we scanned for areas exhibiting a drastic reduction in nucleotide diversity in cultivars compared to wild accessions. Our results suggest that papaya domestication involved selecting fruit quality traits such as taste and flesh color. Moreover, we re-sequenced the male-specific region of the Y (MSY) in 24 wild males and the hermaphrodite-specific region of the Yh chromosome (HSY) in 12 cultivated hermaphrodites. The Yh sequence is highly similar to one Y haplotype (MSY3), exclusive to wild dioecious populations in the north Pacific region of Costa Rica. The low MSY3-Yh divergence suggests that hermaphrodite papaya resulted from human domestication.

Moderator
MM
LT

Lisa Tang

USDA-ARS Appalachian Fruit Research Station
Speakers
NB
GV
CG

Christopher Gottschalk

USDA ARS
During his Ph.D. studies, Dr. Gottschalk studied the molecular mechanisms that control flowering in apple as they relate to seasonal bloom times and biennial/alternate bearing in diverse apple germplasm, from wild species to cultivated varieties. Moreover, he investigated plant growth... Read More →
MH
TM
QY
Tuesday September 24, 2024 4:00pm - 6:00pm HST
Kahili
  Interest Group Session
 
Wednesday, September 25
 

7:59am HST

Genetics and Germplasm 1 (GG 1)
Wednesday September 25, 2024 7:59am - 9:45am HST
Coral 1
Assembling a Reference Panel of DNA Profiles for U.S. Heirloom Apple Cultivars - Cameron Peace
Rediscovering Lost Heirloom Apple Cultivars with DNA Fingerprinting - Dongyun Lee
Air or Soil Temperature: Understanding the Cues for Dormancy Transition in Peach - Ksenija Gasic
Selection and Evaluation of Citrus Resistobiome for HLB Resistance/Tolerance - Yongping Duan
Population Genetics and Genome-wide Association Studies Provide Insights into the Genetic Basis of Persea Fruit Quality Traits - Gul Ali
Genome Assembly of Persia Americana cv. Simmonds Provides Insights on Genetic Relationships Among Avocado Hybrids Exhibiting Tolerance To Laurel Wilt - Vincent Njung'e Michael
Utilizing Haploid Pollen Grains and Diploid Leaf Tissue Genomic Sequence Data to Phase the ‘Wonderful’ Pomegranate Genome - Giuseppe Lana

Moderator
CP

Cameron Peace

Washington State University
Wednesday September 25, 2024 7:59am - 9:45am HST
Coral 1
  Oral Sessions, Genetics and Germplasm 1

8:00am HST

GG 1 - Assembling a Reference Panel of DNA Profiles for U.S. Heirloom Apple Cultivars
Wednesday September 25, 2024 8:00am - 8:15am HST
Coral 1
Heirloom apple cultivars represent an important specialty crop for producers and a genetic resource for the dessert apple industry. These cultivars are plagued with misidentifications, which hinders utilization and long-term preservation. Phenotypic identification, used for centuries, is unable to distinguish among the thousands of existing U.S. heirlooms. DNA profiling provides an objective basis for cultivar identification. Washington State University’s “MyFruitTree” (myfruittree.org), built upon the RosBREED project and with international collaborations, has accumulated a DNA profile dataset of thousands of apple individuals focused on the U.S. genepool. Users submit leaf samples for trees of interest, and MyFruitTree’s cost-recovery research opportunity determines the cultivar identity (or reveals their uniqueness and pedigree position). However, a common and valid question is, “How do you know that is the correct identity?” The core panel of robustly identified cultivars was based on public breeding germplasm, modern cultivars, and their ancestors, which were DNA profiled in the RosBREED project last decade. Since then, examined trees from collections in the U.S. and abroad have greatly expanded the number of DNA profiles with cultivar labels. But those labels are not always correct, especially when a tree is derived from only a single source. Therefore, a system was derived for assigning confidence to the cultivar labels associated with DNA profiles. Cultivar name evidence is assembled in the categories of provenance, phenotype, and genotype for both the DNA-profiled tree and the historically named cultivar, and congruence is examined. This system is applied at two levels: streamlined and comprehensive. The streamlined approach for the current DNA profile dataset efficiently determined whether each individual belongs confidently in the “Reference Panel” or is relegated to “Accessory Profiles” pending further evidence. A Reference Panel was assembled of hundreds of U.S. heirlooms (and more than a thousand close relatives from other regions). The comprehensive approach involves attention from a transdisciplinary tribunal of experts who carefully weigh evidence that an apple individual – often a proposed new discovery of an otherwise lost heirloom – is indeed a historically named cultivar. As MyFruitTree accumulates more DNA profiles submitted by cultivar collection managers and apple enthusiasts nationwide, the cultivar name assignment system is being applied to unidentified trees with strong provenance evidence of cultivar status. Establishing accurate cultivar identities of valued trees via DNA profiling is providing the critical foundation for a coordinated national effort to sustain preservation and utilization of apple crop diversity.
Speakers
CP

Cameron Peace

Washington State University
Co-authors
DL

Dongyun Lee

Washington State University
Wednesday September 25, 2024 8:00am - 8:15am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

8:15am HST

GG 1 - Rediscovering Lost Heirloom Apple Cultivars with DNA Fingerprinting
Wednesday September 25, 2024 8:15am - 8:30am HST
Coral 1
U.S. heirloom apple cultivars are an underutilized and threatened resource, that DNA fingerprinting can help save and remobilize. These heirlooms are old cultivars that were named, clonally propagated, and distributed more than a century ago. Many heirloom cultivars have great historical value, some are still grown commercially, and others could be reintroduced to enhance rural prosperity and diversify options for consumers. While some heirloom cultivars are ancestors of modern cultivars, many others could be valuable for future breeding. However, most heirlooms have been long neglected, and thousands once documented are already extinct. Before more heirlooms disappear forever, mystery trees need to be distinguished from known cultivars, identified, and adequately preserved. Leaf samples for more than 2000 apple trees in collections, national heritage sites, old orchards, and backyards across the U.S. were crowdsourced from about 150 “MyFruitTree” submitters and DNA fingerprinted using KASP genotyping with 48 SNPs. The cultivar identity or uniqueness of each tree was determined by comparing obtained DNA profiles to a previously developed dataset of several thousand apple cultivars and individuals. Trees with replicates were prioritized into five categories according to several criteria for likelihood of representing heirloom cultivars. After removing duplicate samples, poor genotypic data, and non-apple samples, about 60% (1202) of samples were identified as cultivars and most were heirlooms. Of the unidentified samples, 85% (665) were unique, and 15% (118) of the samples represented replicated trees. We found five “Priority 1” trees (filled cultivar pedigree gaps or from three U.S. regions) and four “Priority 2” trees (detected in two regions). Hundreds more trees likely representing unknown heirlooms were also identified in single regions. Collaborators across the country, including historians and citizen scientists, can now closely examine the highest priority trees to uncover their historic cultivar names, while ensuring they are propagated so that they are preserved and valued once again. As more old apple trees are DNA fingerprinted, it is expected that current “unique” DNA profiles will be replicated in the same or other regions. Replicated trees must represent propagated, valued, and likely named cultivars, increasing the opportunities to rediscover lost heirlooms.
Speakers
DL

Dongyun Lee

Washington State University
Co-authors
AD

Amy Dunbar-Wallis

University of Colorado
NA
CP

Cameron Peace

Washington State University
JB

John Bunker

Maine Heritage Orchard
NA
RM

Rebecca McGee

USDA-ARS Pullman
NA
TL

Todd Little-Siebold

College of the Atlantic
NA
Wednesday September 25, 2024 8:15am - 8:30am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

8:30am HST

GG 1 - Air or Soil Temperature: Understanding the Cues for Dormancy Transition in Peach
Wednesday September 25, 2024 8:30am - 8:45am HST
Coral 1
Peach trees require quantitative exposure to winter chilling (chilling requirement, CR) for spring bloom. The chill accumulation time points are determined using weather data of air temperatures between 32 and 45 ºF, using various calculation methods such as the simple chill hour (CH) method or more sophisticated methods like Utah and Chill portions (CP) that account for negations of chilling due to warm weather during the dormancy. All these methods rely on air temperature and do not consider the soil temperature during the dormancy and its effect on the tree’s perception and account for chill accumulation. Peach flowers and developing fruit are highly sensitive to freezing temperatures and are killed following even a limited exposure. In the past decade, mild winters and early spring frosts have significantly reduced or eliminated the annual peach production in the southeast U.S. Low-chill winters have become increasingly common in the southeastern peach-producing regions, and when followed by warm springs, result in early bud break and early flowering, increasing the risk of crop loss to frost. Due to a replant issue caused by Armillaria root rot, almost all acreage under the new peach orchards in the southeast, including South Carolina, are planted on berms adopting root collar excavation as a method to extend the life of orchards on infested soil. We observed significant differences between the air temperature and temperature of undisrupted soil and soil within berms at various depths (3, 6, 12 and 18 in) during dormancy. The effect of observed temperature differences on ‘Cresthaven’ tree chill accumulation calculation and transition between endo- and eco-dormancy stages was investigated by collecting vegetative bud and root tissue from all four depths at six chill hour time points (400, 500, 600, 700, 800 and 900). Preliminary data show significant gene expression differences between bud and root tissue and different gene expression profiles related to the chill accumulation in each tissue. Detailed analyses of the gene expression profiles between the tissues at the different chill accumulation stages and their effect on chilling and heat accumulation, bloom time, and the transition between the dormancy stages in peaches will be discussed.
Speakers
avatar for Ksenija Gasic

Ksenija Gasic

Clemson University
Co-authors
CS

Christopher Saski

Clemson University
NA
JL

John Lawton

Clemson University
NA
SP

Stephen Parris

Clemson University
ZL

Zhigang Li

Clemson University
NA
Wednesday September 25, 2024 8:30am - 8:45am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

8:45am HST

GG 1 - Selection and Evaluation of Citrus Resistobiome for HLB Resistance/Tolerance
Wednesday September 25, 2024 8:45am - 9:00am HST
Coral 1
Since no Huanglongbing (HLB)-resistant citrus cultivar is available in the world, selection of elite natural mutants of commercial citrus for HLB-resistance/tolerance becomes a much more appealing breeding approach, especially in HLB-epidemic regions. In this study, we have selected and evaluated more than 30 citrus mutants from commercial citrus varieties in the past eight years in Florida. After greenhouse and field trials with high HLB disease pressure, we have identified several citrus lines with improved HLB-resistance/tolerance, which can be released or used for large scale of field trials. Our analyses of these lines have revealed that citrus resistobiome plays a role in the HLB resistance/tolerance, which involves a plant virus that can enhance plant resistance and illustrated the pursuit of breeding for biocontrol and a healthy microbiome. Meanwhile, we revealed that transposons have driven the selection and diversification of sweet orange (SWO). We identified six transposon families with up to 8900-fold activity increases in modern sweet orange cultivars tracing back to a common ancestor ~500 years ago. Notably, these six families of transposons contribute significantly to the formation of major cultivar groups, with frequent independent activations or accelerations observed in the breeding history of SWO. We will discuss the molecular mechanisms underlying the improved HLB-resistance, especially how the resistobiome plays a role in the improved HLB resistance/tolerance, and how to implement this new approach by utilizing and expanding the breeding of citrus resistobiome for the control of citrus HLB.
Speakers
YD

Yongping Duan

USDA ARS
NA
Co-authors
BW

Bo Wu

Clemson University
NA
DZ

Desen Zheng

USDA ARS
NA
FL

Feng Luo

Clemson University
NA
ZD

Zhanao Deng

University of Florida
Wednesday September 25, 2024 8:45am - 9:00am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

9:00am HST

GG 1 - Population Genetics and Genome-wide Association Studies Provide Insights into the Genetic Basis of Persea Fruit Quality Traits
Wednesday September 25, 2024 9:00am - 9:15am HST
Coral 1
Avocado (Persea americana) is renowned for its high nutritional value and its global consumption is steadily increasing. Currently, only a few cultivars with limited genetic variability are cultivated, and there is a need for developing new avocado cultivars with enhanced horticultural, fruit quality and nutritional traits as well as resistance to diseases and pests. Application of marker assisted selection can significantly accelerate breeding new avocado varieties, which can take 15 - 20 years using traditional breeding methods. Towards the application of molecular markers in avocado breeding, in this report, genome-wide association studies (GWAS) of nine fruit quality traits of a diversity panel of 110 avocado accessions were explored using 4,706 high-quality single nucleotide polymorphisms (SNPs) using multiple models. In addition, genetic diversity and population structure were also investigated, which unveiled three main populations corresponding to the three major avocado botanical races representing Mexican, West Indian, and Guatemalan ecotypes. Phylogenetic study and quantitative genetic analyses suggested a closer relationship between the Guatemalan and West Indian races compared to the Mexican race. Genome-wide association study revealed twelve markers distributed over eleven genomic regions strongly associated with fruit quality traits including fruit color, shape, taste, and skin texture. Annotation analyses of these genomic regions revealed candidate genes affecting these traits. These findings contribute to a comprehensive understanding of the genetic composition of avocado germplasm, which will be useful for identifying genes governing fruit quality traits as well as for accelerating breeding and parent selection efforts in the avocado breeding pipeline.
Speakers
GA

Gul Ali

Geneticist/Lead Scientist, USDA ARS Subtropical Horticulture Research Station
Co-authors
BF

Barbie Freeman

USDA ARS Subtropical Horticulture Research Station
NA
JL

Jin Li

USDA ARS Subtropical Horticulture Research Station
NA
SE

Shamseldeen Eltaher

USDA ARS Subtropical Horticulture Research Station
NA
Wednesday September 25, 2024 9:00am - 9:15am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

9:15am HST

GG 1 - Genome Assembly of Persia Americana cv. Simmonds Provides Insights on Genetic Relationships Among Avocado Hybrids Exhibiting Tolerance To Laurel Wilt
Wednesday September 25, 2024 9:15am - 9:30am HST
Coral 1
Avocado (Persea americana) is the major fruit cultivated in southern Florida counties with a value exceeding 20 million dollars annually. While production in other regions is dominated by the Hass cultivar, south Florida is unique in production of the increasingly popular, green-skinned varieties. Recently, the avocado industry in South Florida has been devastated by laurel wilt (LW), an insect-disease complex spread by Raffaelea lauricola (Rf), a fungal symbiont of redbay ambrosia beetle (Xyleborus glabratus Eichhoff). Current management practices including prophylactic fungicide injections, tree rejuvenation and ambrosia beetle population reduction are costly and onerous . Unfortunately, no mature avocado trees tolerant to LW are available to growers and genetic mechanism of LW tolerance observed in some avocado seedlings is unknown. In this study, a chromosomal genome of avocado cv. ‘Simmonds’, a ‘West Indian’ (Lowland) ecotype was assembled from Pacific Biosciences HiFi reads. The genome assembly contained 451 scaffolds spanning 98.89% of the avocado genome, a N50 of 82.34MB and a BUSCO score of 95%. This assembly served as a reference genome to generate 9198 genome wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS) reads of a germplasm collection comprising 80 accessions of three avocado ecotypes (Mexican, Guatemalan and West Indian) and 18 novel hybrids exhibiting seedling tolerance to LW. Phylogentic analyses revealed three major clusters with majority of LW tolerant seedlings clustering amongst Hass derived hybrids as well as cultivars belonging to Mexican and Guatemalan ecotypes such as 'Winter Mexican', and 'Ettinger'. This work provides genomic resources for characterization of genetic tolerance of LW in avocado germplasm collections and is a significant step in developing LW tolerant hybrids to support local avocado industry.
Speakers
VN

Vincent Njung'e Michael

University of Florida
Co-authors
AH
JH

Jonathan H Crane

University of Florida, TREC
RG

Romina Gazis

University of Florida
NA
XW

Xingbo Wu

Chair 2023-2024, University of Florida
NA
Wednesday September 25, 2024 9:15am - 9:30am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

9:30am HST

GG 1 - Utilizing Haploid Pollen Grains and Diploid Leaf Tissue Genomic Sequence Data to Phase the ‘Wonderful’ Pomegranate Genome
Wednesday September 25, 2024 9:30am - 9:45am HST
Coral 1
The scientific and commercial interest in pomegranate (Punica granatum L.) cultivation has increased noticeably during the last two decades. Because of the high concentration of bioactive compounds and its nutraceutical properties, pomegranate has been defined as a super food. The consumption of pomegranate juice or arils has been related to several possible benefits on human health. Recent studies have highlighted an antioxidant and anti-inflammatory activity of this fruit which seem to prevent cardiovascular, neoplastic, neurological, metabolic, and intestinal disease. The areas of cultivation of this crop are exposed to current and future challenges like long term-drought conditions and invasive pests and diseases. Increasing the biodiversity of pomegranate has been proposed has the main strategy to reduce the risk of food system vulnerability related to monoculture and the valorization of marginal land. In order to develop advanced genetic tools to improve pomegranate breeding program efficiency we present the de novo sequencing of the ‘Wonderful’ pomegranate genome. DNA isolated from diploid leaf tissues was sequenced using long read sequencing technology (PacBio), while DNA extracted from haploid pollen grains was sequenced using short reads (Illumina). Genomic data from single haploid gamete cells were analyzed using the R package called ‘Hapi’. This allowed to infer chromosomal haplotypes obtaining a higher resolution for DNA variants detection and investigating recombination events in single gametes. Although ‘Wonderful’ represents the industry standard in the United States, several cultivars with desirable traits, such as low acidity and soft seednesses, have been identified in the national germplasm. The results of this study will provide the genomic data required to investigate differences among cultivars and create trait-gene associations. This will allow breeders to facilitate the integration of desired quality traits into new germplasm resources.
Speakers
GL

Giuseppe Lana

University of Florida
Co-authors
DS

Danelle Seymour

UC-Riverside
NA
DM

Donald Merhaut

UC-Riverside
NA
HQ

Han Qu

UC-Riverside
NA
JC

John Chater

University of Florida
MR

Mikeal Roose

UC-Riverside
NA
RT

Ryan Traband

UC- Riverside
NA
SP
TB

Taylor Beaullieau

UC-Riverside
NA
ZJ

Zhenyu Jia

UC-Riverside
NA
Wednesday September 25, 2024 9:30am - 9:45am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 1

2:14pm HST

Genetics and Germplasm 2 (GG 2)
Wednesday September 25, 2024 2:14pm - 3:45pm HST
South Pacific 1
Updates on Curation and Standardization of Phenotypic and Genotypic Data for Horticultural Databases - Jill Bushakra
Identification Of Branched-Chain Amino Acid Derived Volatile Loci In Tomato (Solanum Lycopersicum) Using GWAS And WGCNA - Austin hart
Genomic Characterization of Cultivated and Wild Fragaria Species to Inform Germplasm Conservation and Breeding Practices - Alexander Sandercock
From 'Agawam' to 'Zinfandel': Fruit Quality And Metabolite Diversity In The USDA Grapevine Repository - Victoria Meakem
Moving Beyond Montmorency: Exploring the Genetic Diversity of Tart Cherry - Benjamin Gutierrez
Population affects growth and plant architecture in wild-collected Hydrangea quercifolia - Lisa Alexander
Moderator
BG
Wednesday September 25, 2024 2:14pm - 3:45pm HST
South Pacific 1
  Oral Sessions, Genetics and Germplasm 2

2:15pm HST

GG 2 - Updates on Curation and Standardization of Phenotypic and Genotypic Data for Horticultural Databases
Wednesday September 25, 2024 2:15pm - 2:30pm HST
South Pacific 1
The Genome Database for Rosaceae (GDR, https://www.rosaceae.org/) and the Genome Database for Vaccinium (GDV, https://www.vaccinium.org/), are databases that support genomics, genetics and breeding in under-represented crops like small fruits. These fruit crops include Fragaria (strawberry), Rubus (red raspberry, black raspberry, and blackberry) in GDR, and Vaccinium (blueberry and cranberry) in GDV. Data include curated genome sequences, genetic maps, markers, QTL, genes, transcripts, germplasm, and publications, made accessible to browse, query and download through easy-to-use web interfaces and tools. One of the objectives of a 2022-funded SCRI- project ‘Advanced National Database Resources for Specialty Crop Research and Improvement’ is to collect, curate, and integrate all types of genomics, genetics, and breeding big data in easy-to-use and robust crop-specific databases. In this presentation, we summarize our progress towards curating and making available phenotype and genotype data for strawberry. We also present a strawberry Crop Ontology we have developed with input from crop researchers and breeders from North America and Europe. Public availability of phenotypic and genotypic data in GDR, GDV, and GRIN-GLOBAL will allow easy access to this data to use in genome-wide association studies. Crop Ontology will enable digital capture and trait data integration across locations and projects.
Speakers
avatar for Jill Bushakra
Co-authors
CH

Chun Huai Cheng

Washington State University
NA
DM

Doreen Main

Washington State University
JY

Jing Yu

Washington State University
NA
JH

Jodi Humann

Washington State University
KB

Katheryn Buble

Washington State University
NA
NB

Nahla Bassil

USDA-ARS
NA
PZ

Ping Zheng

Washington State University
NA
SJ

Sook Jung

Washington State University
NA
TL

Taein Lee

Washington State University
NA
Wednesday September 25, 2024 2:15pm - 2:30pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2

2:30pm HST

GG 2 - Identification Of Branched-Chain Amino Acid Derived Volatile Loci In Tomato (Solanum Lycopersicum) Using GWAS And WGCNA
Wednesday September 25, 2024 2:30pm - 2:45pm HST
South Pacific 1
A major focus in plant breeding has been the improvement of crops through various traits that affect disease resistance and yield. However, the focus on productivity has led to an inattentiveness to other traits that specifically affect produce quality. An example of a critical fruit quality trait is its flavor, contributing to our perception of aromatic volatiles. Even at nanomolar concentrations, aromatic volatiles can be perceived by the olfactory system and influence the liking of the fruit. The focus of this study was to investigate the genetic aspect of the branched-chain amino acid (BCAA) volatiles, derived from L-valine, L-isoleucine and L-leucine, in tomato fruits. It is generally considered that these BCAA-derived volatiles contribute positively to overall liking, because these are essential amino acids required by the human diet. To identify quantitative trait loci (QTLs) affecting the biosynthetic pathway for 11 BCAA-derived volatiles, a Genome-Wide Association Study (GWAS) was conducted using a diverse and unique panel of 167 tomato accessions. The GWAS was run using the FarmCPU model in GAPIT-R, with a total of 21,893,681 SNPs, 2,735,297 INDELs, and 154 structural variants across the genome. Furthermore, a weighted gene co-expression network analysis (WGCNA) was conducted in parallel to identify modules of co-expressed genes that cluster with known genes that affect the BCAA-derived volatile pathway. A total of 113 QTLs were identified from GWAS and 3024 co-expressed genes were identified from the WGCNA. Candidate genes were screened based on annotated biochemical function, overlap within the GWAS QTLs, and gene expression in the red-ripe fruits. This led to the identification of two candidate genes, one on the long arm of chromosome 1 and another on the long arm of chromosome 11. These genes are being knocked-out using CRISPR-Cas9, and current progress is aimed to confirm the validity and function of these genes in the near-future.
Speakers
AH

Austin Hart

University of Georgia
Co-authors
DT

Denise Tieman

University of Florida
EV

Esther van der Knaap

Institute of Plant Breeding, Genetics, and Genomics, University of Georgia
NA
MS

Manoj Sapkota

University of Georgia
NA
Wednesday September 25, 2024 2:30pm - 2:45pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2

2:45pm HST

GG 2 - Genomic Characterization of Cultivated and Wild Fragaria Species to Inform Germplasm Conservation and Breeding Practices
Wednesday September 25, 2024 2:45pm - 3:00pm HST
South Pacific 1
Understanding the genetic composition and diversity of plant collections is crucial for their effective management and utilization in breeding programs. Cultivated strawberry (Fragaria x ananassa) is a significant global crop, contributing substantially to the U.S. agricultural economy with more than $3 billion in production value. The USDA-ARS National Clonal Germplasm Repository (NCGR) maintains a collection of cultivated and wild Fragaria accessions, which provide a valuable source of disease-resistance and other quality traits for the improvement of cultivated strawberry. Despite the recognized importance of genetic diversity, an in-depth assessment of genetic relationships within the USDA-ARS collection remains incomplete. To address these gaps, we genotyped 1,876 cultivated and wild Fragaria accessions from NCGR using a strawberry 5K DArTag marker panel. The evaluation of microhaplotype-based missing data rates revealed an increase in percent of missing data with an increased distance from the cultivated strawberry. This trend is expected because the 5K panel was developed based on the octoploid cultivated strawberries. Among the species studied, the higher ploidy accessions representing F. x vescana, F. x ananassa, F. virginiana, F. cascadensis, and F. chiloensis exhibited the least missing data, with percentages of 2.6%, 5.0%, 7.5%, 10.2%, 14.7%, respectively. Conversely, diploid accessions mostly Asian F. daltoniana, F. nubicola, F. viridis (Eurasian), F. pentaphylla, and F. nilgerrensis displayed the highest percentages of missing data, with 87.1%, 82.5%, 80.2%, 80.2%, 79.9%, respectively. Utilizing the microhaplotypes derived from the 5K panel, a total of 17,925 SNPs were identified after quality filtering, which were then used to assess the ancestry and genomic diversity of the Fragaria species housed within the USDA-ARS collection. We performed PCA and UPGMA analyses, and found distinct species clusters for each putative taxonomic assignment, suggesting high concordance between sample genotype and species identity. Finally, species-specific loci were then identified and genomic diversity analyses were performed for species represented with more than five accessions. Our findings clarified the identity and diversity of Fragaria within the USDA-ARS germplasm collection, aiding in germplasm conservation efforts and informing future breeding initiatives.
Speakers
AS

Alexander Sandercock

Cornell University
Co-authors
CB

Craig Beil

Cornell University
NA
DZ

Dongyan Zhao

Cornell University
NA
MS

Manoj Sapkota

Cornell University
NA
ML

Meng Lin

Cornell University
NA
MH

Michael Hardigan

USDA-ARS Horticultural Crops Research Unit
NA
MS

Moira Sheehan

Cornell University
NA
NB

Nahla Bassil

USDA-ARS National Clonal Germplasm Repository
NA
RK

Ryan King

USDA-ARS National Clonal Germplasm Repository
NA
SC

Shufen Chen

Cornell University
NA
Wednesday September 25, 2024 2:45pm - 3:00pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2

3:00pm HST

GG 2 - From 'Agawam' to 'Zinfandel': Fruit Quality And Metabolite Diversity In The USDA Grapevine Repository
Wednesday September 25, 2024 3:00pm - 3:15pm HST
South Pacific 1
The USDA National Plant Germplasm System is a network of germplasm repositories dedicated to conserving genetic diversity of crops and their wild relatives. The USDA grapevine (Vitis) repository contains 5000 unique accessions representing 36 species, and is divided between two locations: Davis, CA and Geneva, NY. While this material is available for distribution to researchers and breeders, there is currently limited characterization data to help requestors identify accessions with unique and valuable traits, particularly for fruit quality. Thus, we began a germplasm screening project to measure fruit quality traits of 481 unique accessions from both locations spanning three years (2022-2024). Fruit samples were juiced, filtered through cheesecloth, and analyzed for Brix, titratable acidity, and available nitrogen. Additionally, composition of phenolic compounds was assessed using liquid chromatography-mass spectrometry (LC-MS), and aromas were detected using solid phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS). Overall, there was a wide range of diversity in fruit quality traits across the collection. Brix values ranged from 8.5 to 30.1 (average=17.8), and titratable acidity ranged from 2.7 to 25.6 g mol-1 Tartaric acid equivalents (average=8.2). The phenolic compounds commonly detected in grape juice included the anthocyanins malvidin 3-O-glucoside and peonidin 3-O-glucoside, the hydroxycinnamic acid caftaric acid, and the flavonols quercetin 3-O-glucuronide and isoquercetin. Analysis of aromatic compounds revealed accessions that contained higher amounts of linalool, β-myrcene, and geraniol, which are associated with a “Muscat” flavor profile, while others contained methyl anthranilate, which is associated with a “Foxy” flavor profile. We hope this fruit quality dataset not only proves to be a valuable asset to researchers utilizing the USDA Vitis repository, but may also open new directions of exploration into improved grape flavor, nutrition, and quality.
Speakers
VM

Victoria Meakem

USDA ARS
NA
Co-authors
BG
EG
GZ

Gan-yuan Zhong

USDA-ARS
NA
Wednesday September 25, 2024 3:00pm - 3:15pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2

3:15pm HST

GG 2 - Moving Beyond Montmorency: Exploring the Genetic Diversity of Tart Cherry
Wednesday September 25, 2024 3:15pm - 3:30pm HST
South Pacific 1
Genetic diversity is invaluable to the sustainability of American horticulture. In the case of tart cherry, production in the United States is precariously reliant on a single cultivar, ‘Montmorency.’ Our research explores diverse genetic resources in tart cherry to promote utilization of high quality and locally adapted cultivars for plant breeding and improved production. Tart cherry nutritional quality is of particular interest to consumers. The United States Department of Agriculture Tart Cherry collection in Geneva, New York maintains 100 cultivars of tart cherry, including their wild relatives. Over a five-year period, we assayed fruit quality traits, including Brix, titratable acidity, and phenolic content. Total soluble solids (TSS) ranged from 10.9 to 20.7% (average=14.8%) and acidity (TA) ranged from 5.3 to 32.1 g/L (average=16.3%). The sugar/acid ratio ranged from 3.7 to 27.6 (average=10.2). Individual fruit weight ranged from 0.2 to 8.6 g (average of 5.0 g) and pit weight percentage ranged from 6-32% (average=11%). Total anthocyanin content varied from 75.2 to 3760.0 μg/g, with an average of 771.4 μg. We also evaluated bloom phenology over a three-year period. The distribution of bloom ranged from 56.7 to 134.4 GDD, with an average value of 86.0 Growing Degree Days (GDD ). ‘Montmorency’ bloom was above average with values around 95.8 GDD. Sweet cherries (63.5 – 90.6 GDD) tended to bloom much earlier than tart cherries (64.9 –118.0 GDD) and P. fruticosa, the wild progenitor of the tart cherry, bloomed the latest with a range of 85.3 to 134.4 GDD. For Brix, acidity, and phenolic content, ‘Montmorency’ falls significantly below average, though it has a balanced sugar/acid ratio. ‘Montmorency’ is lacking in anthocyanin content which is increasingly relevant for the juice industry. It tends to bloom later than other tart cherries evaluated, though there are some more extreme late bloomers. This data will be available through GRIN-Global, the USDA germplasm database to facilitate future research and breeding.
Speakers
BG
Co-authors
VM

Victoria Meakem

USDA ARS
NA
Wednesday September 25, 2024 3:15pm - 3:30pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2

3:30pm HST

GG 2 - Population affects growth and plant architecture in wild-collected Hydrangea quercifolia
Wednesday September 25, 2024 3:30pm - 3:45pm HST
South Pacific 1
Hydrangea quercifolia, oakleaf hydrangea, a flowering shrub native to woodlands of the southeastern United States. Oakleaf hydrangea has immense ornamental potential with four-season interest, including traits like showy panicles, striking foliage textures, red fall color, and exfoliating bark. Cultivars are often derived from wild selections either directly or only a few generations removed. Full genetic and phenotypic variation has not been evaluated for the species, and little is known about the diversity in horticulturally important traits for oakleaf hydrangea. For this study, growth and plant architecture of wild-collected oakleaf hydrangea seedlings were observed at the Otis L. Floyd Nursery Research Center in McMinnville Tennessee over a 3-year period. Seedlings from 14 populations of oakleaf hydrangea spanning the species’ native range were planted in a randomized complete block design containing six blocks and nine replications per block. Two-way ANOVA was used to partition variation in height, width, growth rate, and number of stems into sources attributable to block, population, and block × population. There were significant differences among populations for growth rate, size, and number of stems in all years. Southern populations were smaller than northern populations and showed a slower growth rate. Genetic and phenotypic variation shown among populations will guide conservation efforts and supplement breeding efforts for oakleaf hydrangea.
Speakers
avatar for Lisa Alexander

Lisa Alexander

Research Geneticist, USDA-ARS U.S. National Arboretum
Co-authors
AS

A. Sherwood

USDA-ARS, Agricultural Research Service, North Central Regional Plant Introduction Station
CJ

C. Jennings

Tennessee State University
SH

S.C. Hokanson

University of Minnesota
Wednesday September 25, 2024 3:30pm - 3:45pm HST
South Pacific 1
  Oral presentation (Individual talk), Genetics and Germplasm 2
 
Thursday, September 26
 

10:00am HST

Specialty Crops Collaboration Session
Thursday September 26, 2024 10:00am - 11:00am HST
Coral 4
A forum for discussion of potential collaborations with regards to specialty crops – i.e. hemp, herbs, medicinal plants, and tropicals, breeding, production, etc.
Thursday September 26, 2024 10:00am - 11:00am HST
Coral 4
  Hort Theater & Collaboration Center

12:14pm HST

Genetics and Germplasm 2 (GG 2)
Thursday September 26, 2024 12:14pm - 1:25pm HST
Nautilus 1
Exploration of Salt-Tolerant Germplasm to Increase Specialty Rice Production in South Carolina - Gursewak Singh
Independent Domestication of Cucumber (Cucumis sativus L.) Fruit Revealed by Cucurbitacin and Volatile Compound Profiling - Eun Jin Lee
Evaluation of watermelon and Citrullus crop wild relatives for resistance to whiteflies and whitefly transmitted viruses - Alexander Luckew
Development of Specialty Pumpkin Cultivars with Potential to be Released for Organic and Conventional Resilient Cropping - Angela Linares Ramirez
SSR Marker Development and Fine Mapping of Linkage Group 2 Eastern Filbert Blight Resistance from ‘Georgian OSU 759.010’ - Brianna Heilsnis
Enhancing the Fruit Set of NJ BP1-1 Beach Plum (Prunus maritima) - Megan Muehlbauer
The wonderful world of worms: Microbiota of rabbit manure vermicompost at different maturities - Amanda Birnbaum
Moderator
GS

Gursewak Singh

Clemson University
Thursday September 26, 2024 12:14pm - 1:25pm HST
Nautilus 1
  Poster Session, Genetics and Germplasm 2

12:15pm HST

GG 2 - Exploration of Salt-Tolerant Germplasm to Increase Specialty Rice Production in South Carolina
Thursday September 26, 2024 12:15pm - 12:25pm HST
Nautilus 1
The significance of Carolina Gold specialty rice in South Carolina's (SC) agricultural history is deeply rooted, dating back to colonial times. Its unique flavor and texture have made it a prized variety among chefs and food enthusiasts. Currently, saltwater intrusion and weed infestation threaten this specialty rice production in SC. Understanding salt tolerance and weed interactions is crucial for ensuring the continued production and quality of this specialty rice. Preliminary experiments assessed the impact of different concentrations of ocean water and native weed pressure on rice plant vigor when cultivated organically under controlled environmental conditions. In brief, we screened rice germplasm under various seawater concentrations (0, 0.375, 0.75, 1.5%, and 3%) in both weed-free and weed competition conditions. In our preliminary greenhouse studies, we observed weed competition reduced the rice plant biomass by 2-3 times and yield up to 5 times at a 3% seawater concentration. M202 and Doble Carolina exhibited the highest salt tolerance and higher photosynthesis rate when compared to local genotypes, Carolina Gold and Santee Gold. The cultivars demonstrating superior performance under these conditions were subsequently subjected to further testing in organic research plots, incorporating supplemental irrigation with tidal ocean water. A field experiment was designed to evaluate and validate the salinity tolerance of six rice genotypes (Carolina Gold, Santee Gold, Doble Carolina, M202, Jupiter, and JN100) under different seawater concentrations (0%, 1.5%, 3%, 6%, and 12%), both in weed-free and weed-competition scenarios. Using a gasoline pump, we collect brackish water from the adjacent marsh in a 4000-gallon-capacity reservoir/pool. The calculated volumes are then pumped into the field plots based on each plot's fresh and seawater volumes. The salinity level of treated plots is monitored by measuring the EC values. The results indicated that M202, Doble Carolina and JN100 showed the highest salt tolerance. Weed competition reduced the rice plant height, number of tillers, panicles, dry root, and shoot weight across the entire salinity gradient. Weed competition led to an approximately 50% reduction in both the aboveground (shoot) and belowground (root) weights of rice plants, as compared to weed-free plots, across the tested salinity levels. Weed biomass, weeding time and regrowth of weeds declined significantly above 3 % seawater concentration when compared to control. Eventually, the most promising cultivars identified are being incorporated into a breeding program to integrate salt-tolerant genes into the Carolina Gold specialty rice.
Speakers
GS

Gursewak Singh

Clemson University
Co-authors
BW

Brian Ward

Clemson University
JR

Jai Rohila

USDA-ARS
NA
MC
MM

Michael Marshall

Clemson University
NA
RK

Raghupathy Karthikeyan

Clemson University
NA
SW

Sarah White

Clemson University
NA
Thursday September 26, 2024 12:15pm - 12:25pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

12:25pm HST

GG 2 - Independent Domestication of Cucumber (Cucumis sativus L.) Fruit Revealed by Cucurbitacin and Volatile Compound Profiling
Thursday September 26, 2024 12:25pm - 12:35pm HST
Nautilus 1
Cucumber (Cucumis sativus L.) fruit has characteristic taste and aroma, the important organoleptic qualities influencing consumer preference and marketability. Profiling of metabolites conferring bitterness and aroma is required to improve cucumber fruit quality and produce preferred fruit. In this study, we profiled cucurbitacins responsible for bitterness and volatile compounds using fruit of 69 cucumber genotypes with different fruit shape, color, and origin and provided qualitative and quantitative information of metabolites involved in the organoleptic quality. Among six types of cucurbitacis (CuA-E, I), only CuC was detected in six inbreds while most genotypes didn’t contain them. It means bitterness has been lost in modern cucumber cultivars with domestication process. The 69 genotypes were classified into four clusters according to the profiles of cucurbitacins and volatile compounds. Clusters 2 and 3 accumulated the highest and lowest volatile contents, respectively. Clusters 1 and 4 were discriminated by minor volatiles rather than major ones, suggesting they have distinct background flavor. Clusters 1 and 4 also showed different phenotypes such as length and color, implying a relationship between fruit phenotype and background flavor. However, the clustering was inconsistent with cultivar types or origins. It suggests independent domestication for bitterness and flavor has been conducted for cultivars in different origins. We further examined hybridization effect on metabolite compositions using 15 F1 hybrids from selected inbreds. Total volatile compound (TVC) content was reduced in the F1 hybrids, especially due to decrease in total alcohol content affecting increase in ratio of aldehyde to TVC. These findings will contribute to improvements of cucumber organoleptic qualities and will provide useful information for selecting cucumber materials to produce preferred fruit.
Speakers
EJ

Eun Jin Lee

Seoul National University
Co-authors
JK

Jeongyun Kim

Dankook University
NA
KM

Kyeonglim Min

Seoul National University
Thursday September 26, 2024 12:25pm - 12:35pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

12:35pm HST

GG 2 - Evaluation of watermelon and Citrullus crop wild relatives for resistance to whiteflies and whitefly transmitted viruses
Thursday September 26, 2024 12:35pm - 12:45pm HST
Nautilus 1
In the Southeastern U.S., cucurbit production is vulnerable to the sweetpotato whitefly Bemisia tabaci and the viruses it transmits. There are limited control methods for the whitefly pest, including mulches, row covers, and spray programs. Unfortunately, none of these practices reduce the whitefly populations to zero, leaving whiteflies behind to transmit viruses. Therefore, host resistance is the best management practice, and the identification of resistant genotypes to whitefly transmitted viruses is a top priority. To aid watermelon breeding for resistance, 21 Citrullus genotypes were evaluated over two field seasons in Tifton, GA in 2022 and 2023. The traits evaluated were viral disease severity (AUDPC), Cucurbit leaf crumple virus (CuLCrV), Cucurbit yellow stunting disorder virus (CYSDV), and Cucurbit chlorotic yellows virus (CCYV) viral loads and in 2022 only, whitefly counts were collected to evaluate whitefly preference. Leaf tissue was collected 5 weeks after transplanting (WAT) in 2022 and 7 WAT in 2023. Total nucleic acids were extracted, and qPCR was performed to determine viral loads. Grif 16444 was the only genotype that had lower adult whitefly counts, indicating non-preference of this genotype. Over the two years there were three consistent genotypes with the statistically lowest AUDPC, two C. mucosospermus (PI 595203 and PI 494528) and one C. ecirrhosus (Grif 16444). In 2022, these three genotypes had significantly lower CuLCrV viral loads than the cultivar checks, however, in 2023 due to low CuLCrV presence there were no significant differences. For CYSDV and CCYV, there were no genotypes with significantly lower viral loads than the cultivar checks in both years. These wild crop relatives provide sources of resistance that can be used by breeders to improve cultivated watermelon.
Speakers
AL

Alexander Luckew

University of Georgia
Thursday September 26, 2024 12:35pm - 12:45pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

12:45pm HST

GG 2 - Development of Specialty Pumpkin Cultivars with Potential to be Released for Organic and Conventional Resilient Cropping
Thursday September 26, 2024 12:45pm - 12:55pm HST
Nautilus 1
Specialty pumpkins, such as the tropical pumpkin or “calabaza” (Cucurbita moschata Duchesne), are widely grown and consumed in Puerto Rico, ranking second among the most important vegetables on the island. This crop is also increasingly becoming a lucrative emerging market in the United States, particularly in communities with a high density of households of Latino/Hispanic and Caribbean heritage. Yield, fruit quality, and disease resistance of 21 genotypes were evaluated under conventional and certified organic management conditions in Puerto Rico at the University of Puerto Rico Lajas Research Station from January to May 2022, and from November 2022 to March 2023. The genotypes were evaluated using a randomized complete block design with three replications. The number of marketable fruits, total fruits per plot, yield (kg ha-1), and incidence of whiteflies, among other variables, were recorded. Overall, the number of fruits per plot and marketable fruits ranged from 2 and 12, while the yield reached 9,229 kg ha-1 to 65,707 kg ha-1. Under organic certified management, the highest yield was obtained by UFTP42 with 46,567 kg ha-1, while UFTP4 obtained the lowest yield with 5,110 kg ha-1. Under conventional conditions, the UFTP34, UFTP80, and ‘Soler’ lines obtained the highest performance, with 66,677; 63,974, and 75,971 kg ha-1, respectively. On the other hand, the genotypes UFTP4, UFTP10, UFTP22, and UFTP46 obtained lower yields with 9,229; 10,881; 17,635, and 15,408 kg ha-1, respectively. Verde Luz, showed the lowest incidence of whiteflies (< 10%), under both management conditions, while the remaining genotypes showed no significantdifferences between them. In summary, UFTP34, UFTP44, UFTP45, and UFTP80 could be released as prospective cultivars for the southern area of Puerto Rico and could be used as parents for breeding purposes under organic and conventional cropping systems.
Speakers
AL

Angela Linares Ramirez

University of Puerto Rico
Co-authors
GM

Geoffrey Meru

University of Florida
NA
JR

Jorge Ruiz Menjivar

University of Florida
MG

Miguel Garcia Carrucini

University of Puerto Rico - SEA
NA
Thursday September 26, 2024 12:45pm - 12:55pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

12:55pm HST

GG 2 - SSR Marker Development and Fine Mapping of Linkage Group 2 Eastern Filbert Blight Resistance from ‘Georgian OSU 759.010’
Thursday September 26, 2024 12:55pm - 1:05pm HST
Nautilus 1
Anisogramma anomala, causal agent of Eastern Filbert Blight (EFB), is endemic to eastern North America and was accidentally introduced to the Pacific Northwest hazelnut (Corylus avellana) growing regions around 1960. A single gene conferring resistance was identified in the pollinizer ‘Gasaway’ by the OSU Hazelnut Breeding Program, and deployed across the Willamette Valley in the majority of cultivars released since 2008. In preparation for a mutation or second accidental new introduction, research has focused on discovering, mapping, and developing useful molecular markers for new sources of resistance. In October 2023, a new isolate of A. anomala was detected in a grower’s orchard in Woodburn, OR, growing on the previously resistant ‘Jefferson’. The results of this study focus on linkage group 2 resistance (LG2), conveyed by ‘Georgian OSU 759.010’. Using two populations from a cross between ‘OSU 1477.047’ with Georgian resistance and ‘Sacajawea’ with quantitative resistance, n=272 recombinant offspring were identified using existing SSR markers. Marker development resulted in 40 new SSR markers covering an 8.5Mbp region, and a linkage map of the resistance region was constructed. Characterization of the 40 new SSR markers is in progress.
Speakers
BH

Brianna Heilsnis

Oregon State University
Co-authors
JS

Jacob Snelling

Oregon State University
NA
SM

Shawn Mehlenbacher

Oregon State University
Thursday September 26, 2024 12:55pm - 1:05pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

1:05pm HST

GG 2 - Enhancing the Fruit Set of NJ BP1-1 Beach Plum (Prunus maritima)
Thursday September 26, 2024 1:05pm - 1:15pm HST
Nautilus 1
Wild plum, Prunus maritima, has a native habitat that ranges from coastal Virginia to Nova Scotia and is well known to be associated with beach communities with sandy soils. Recent trials by Rutgers, New Jersey Agricultural Experiment Station suggests beach plum has the potential to be grown throughout the state where higher clay content, fertile soils contribute to increased vegetative growth leading to a dense bush habit. Crop potential is abundant due to high natural bloom density. However fruit set has been challenging under traditional commercial growing systems, partly due to self-incompatibility. BP1-1 Jersey Jems cultivar was bred and selected by the Rutgers University Plant Breeding program for its high yield, large size and superior flavor in costal locations where there are diverse beach plum pollen clouds. In order to establish clonal orchards of this cultivar, a pollen parent must be identified. In this study, a total of 7 controlled test crosses were made in triplicate on BP 1-1. Fruit yields were collected from BP1-1 and top yielding crosses were noted. The purpose of this study is to find compatible pollen parents, ensuring quality and uniform yield to base future pollen parent recommendations in New Jersey commercial tree fruit orchards.
Speakers
MM

Megan Muehlbauer

Rutgers University
Co-authors
PN

Peter Nitzsche

Rutgers NJAES Cooperative Extension
NA
RM

Rebecca Magorn

Rutgers Cooperative Extension
NA
Thursday September 26, 2024 1:05pm - 1:15pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

1:15pm HST

GG 2 - The wonderful world of worms: Microbiota of rabbit manure vermicompost at different maturities
Thursday September 26, 2024 1:15pm - 1:25pm HST
Nautilus 1
Vermicompost, derived from the processing of organic waste by earthworms, is a beneficial soil amendment known to improve plant and soil health due to the presence of beneficial microorganisms. Vermicompost microbiome can vary radically depending on the starting substrate, environmental conditions, and earthworm species, making it important to characterize the microbial community over time under a variety of vermicomposting conditions. To characterize the microbial community of vermicompost produced from rabbit manure, four samples were collected from vermicomposting bins (Avery Islands, LA) for Nanopore long-read sequencing: one unprocessed manure samples, and samples which had been composting for 1-, 6-, and 12-months. About 135Gb of sequence data with a median quality of Q19 was produced. Relative taxonomic abundance of the microbial community was assessed using Kraken2 and Braken. Manure samples differed in microbiome composition, but were both much less diverse than vermicomposted samples, which had much greater bacterial diversity and were rich in nitrogen-fixing bacteria such as Mesorhizobium and Bradyrhizobium. 1-month old vermicompost more closely resembled 12-month old vermicompost than unprocessed manure, suggesting that a majority of the benefits of vermicomposting are realized within a relatively short period of time.
Speakers
JL
Co-authors
AB
AD

Amit Dhingra

Texas A
NA
Thursday September 26, 2024 1:15pm - 1:25pm HST
Nautilus 1
  Poster presentation (individual talk), Genetics and Germplasm 2

4:00pm HST

Interest Group Session: Crop Germplasm Committees (CGC) – Get Involved in Setting Germplasm Priorities
Thursday September 26, 2024 4:00pm - 6:00pm HST
Kahili
The USDA National Plant Germplasm System (NGPS) is an invaluable resource to researchers and breeders of horticultural crops. Crop Germplasm Committees, with members from academic, private and governmental organizations provide expertise in a variety of topics, including collection priorities and vulnerabilities, identifying important traits for evaluation, and reviewing Plant Exploration and Evaluation grant proposals. The CGCs are a great opportunity for ASHS members to get more involved in setting germplasm related priorities for their crops of interest. This session gives an overview of the activities of the CGC and highlight activities of 3 specific CGCs. The talks will be followed by a 30-minute discussion session on avenues for increased interaction between the ASHS PICs and the CGCs to ensure that germplasm collection priorities are relevant to the needs of stakeholders.


Coordinator(s)
  • Cecilia McGregor, University of Georgia, Athens, GA, United States
Speaker/Participant(s)
  • Gayle Volk, USDA, Fort Collins, Colorado, United States
    Introduction to Crop Germplasm Committees: An Opportunity to have an Impact on Crop Collections in the USDA-ARS National Plant Germplasm System (20 mins)
    Summary: The USDA-ARS National Plant Germplasm System (NPGS) maintains over 620, 000 accessions of more than 200 crops at 22 sites around the United States. Most crop collections have Crop Germplasm Committees (CGC) that provide guidance to the curator with regard to vulnerabilities, acquisitions, maintenance, genotypic characterization, phenotypic evaluations and distribution. CGCs welcome new members to improve the quality and impact of the NPGS collections.
  • Glenn Wright, University of Arizona - Yuma Agriculture Center, Yuma, AZ, United States
    The Rewards and Challenges of Chairing Two Crop Germplasm Committees (20 mins)
    Summary: The Citrus CGC and the Date Palm CGC are both affiliated with the National Clonal Germplasm Repository for Citrus and Dates in Riverside, CA. Membership of both committees include representatives of the federal government, academia, and industry. Activities of both committees include advising the NCGRCD on critical issues, including staffing, infrastructure, threats to the genebank, and germplasm backup, acquisition, sanitation, and distribution. We also advise repository staff on project plans, relevant research, and strategic planning. Finally, the committees comment and approve germplasm evaluation, plant exploration and plant exchange proposals.
  • Kim Shearer, The Morton Arboretum, Lisle, IL, United States
    Seeing the Forest for the Trees (20 mins)
    Summary: The Woody Landscape Plant Crop Germplasm Committee has a somewhat unique task in that the wild crop relatives can include all of the trees and shrubs of all of the forests. As a group, we found that the task of identifying priorities and vulnerabilities limited to specific taxonomic categories seemed insurmountable. How could we predict an event like the introduction of emerald ash borer (Agrilus planipennis) wiping out native floodplain forests and masses of street trees? What can be lost in an uncertain future with the onset of climate change? And how could we communicate this vulnerability in a way that was politically palatable? In this talk, the strategy for developing a new crop vulnerability statement and QUAD will be presented along with some examples of projects that have been funded and implemented for both plant exploration and evaluation.
  • Cecilia McGregor, University of Georgia, Athens, GA, United States
    Crop Germplasm Committees: An Opportunity for Value-added Research (20 mins)
    Summary: The Cucurbit Crop Germplasm Committee (Cucurbit CGC) includes experts from local and global academic institutions and private industries, as well as the federal government. In addition to the routine activities of the CGC, the participation of several Cucurbit CGC members in the federally supported SCRI CucCAP and CucCAP2 projects provided the opportunity for improved coordination and alignment of federally funded academic research and germplasm priorities This contributed to the development of tools and resources that adds value to the existing Cucurbit germplasm collections.
Moderator
CM

Cecilia McGregor

University of Georgia
NA
Speakers
GV
GW
KS
Thursday September 26, 2024 4:00pm - 6:00pm HST
Kahili
  Interest Group Session
 
Friday, September 27
 

9:44am HST

Genetics and Germplasm 3 (GG 3)
Friday September 27, 2024 9:44am - 11:15am HST
Coral 1
Transcriptomic responses underlying host-pathogen interactions between resistant and susceptible Prunus accessions and two Armillaria Root Rot fungi - Stephen Parris
Fine mapping of Linkage Group 7 (LG7) Eastern Filbert Blight (EFB) Resistance in Hazelnut - Rion Mooneyham
Estimation of Breeding Values to Improve Kernel Weight in Almond (Prunus dulcis) - Shashi Goonetilleke
Alternative RNA Splicing Associated with Pecan Dichogamy - Xinwang Wang
Alaska Can Grow More Than Giant Vegetables: The Potential of Rhubarb for Specialty Crop Producers - Carol Miles
Utilization of Germplasm to Improve Illinois Horseradish - Alan Walters
Moderator
SG

Shashi Goonetilleke

The University of Queensland
Friday September 27, 2024 9:44am - 11:15am HST
Coral 1
  Oral Sessions, Genetics and Germplasm 3

9:45am HST

GG 3 - Transcriptomic responses underlying host-pathogen interactions between resistant and susceptible Prunus accessions and two Armillaria Root Rot fungi
Friday September 27, 2024 9:45am - 10:00am HST
Coral 1
Armillaria root rot (ARR) caused by Desarmillaria caespitosa and Armillaria mellea represents the main cause of premature stone fruit and nut tree decline in the United States. A. mellea is a primary concern for almond and peach growers in California, while D. caespitosa threatens peach production in the southeast region of the U.S. These fungi survive as facultative necrotrophs and colonize roots of several agriculturally important crops, including peach, almond, and sweet cherry. This colonization ultimately kills the woody roots and therefore host, severely limiting the tree’s lifespan and ability to provide a return on investment for the grower. Few management options are available to slow down ARR disease progression, and no management practice eliminates ARR fungi presence in an infested field. Additionally, most of the commercially available rootstocks are susceptible to infection, with only two peach/plum hybrid commercial rootstocks (Prunus umbellata × P. persica ‘MP-29’ and P. cerasifera × P. persica ‘Krymsk® 86’) showing partial resistance to ARR. The shared plum genetic background in these hybrids, paired with the lack of ARR resistance observed in peach germplasm suggests the source of resistance originated from plum. In this work, induced genetic responses in one susceptible accession, P. persica ‘Guardian®’, and two resistant accessions, P. cerasifera ’14-4’ and ‘MP-29’, when infected with D. tabescens and A. mellea were analyzed. Additionally, expression of genes encoding effectors and cell wall degrading enzymes (CWDEs) were investigated in the ARR fungi while infecting the three hosts. The results of the infection assays revealed unique responses between each of the three hosts in their progression of disease symptoms over time and in their transcriptomes while under infection by the two ARR fungi. Analysis identified key hub genes expressed by the two resistant Prunus accessions involved in the sensing and enzymatic degradation of chitin and the upregulation of GSTs, oxidoreductases, and transcription factors. Investigation of the ARR fungi transcriptomes similarly identified host-dependent expression of fungal effectors and CWDEs responsible for degrading the cell wall components cellulose, hemicellulose and pectin. Comprehensive analyses considering transcriptomes produced by both the host and pathogen during the infection course provides a deeper understanding of the factors driving resistant and susceptible responses to ARR infection, and their effects on the infecting pathogen’s gene expression.
Speakers
SP

Stephen Parris

Clemson University
Co-authors
CS

Christopher Saski

Clemson University
NA
GS

Guido Schnabel

Clemson University
NA
JW

Jared Weaver

Clemson University
NA
JA

Jeffrey Adelberg

Clemson University
NA
KG

Ksenija Gasic

Clemson University
LC

Lichun Cai

Clemson University
NA
Friday September 27, 2024 9:45am - 10:00am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

10:00am HST

GG 3 - Fine mapping of Linkage Group 7 (LG7) Eastern Filbert Blight (EFB) Resistance in Hazelnut
Friday September 27, 2024 10:00am - 10:15am HST
Coral 1
Eastern filbert blight (EFB) disease caused by the fungal pathogen Anisogramma anomala (Peck) E. Müller is a major threat to Oregon’s hazelnut (Corylus avellana) industry. The Oregon State University (OSU) hazelnut breeding program has used ‘Gasaway’ as a source of resistance in many releases. Cultivars with ‘Gasaway’ resistance mapped to linkage group 6 (LG6) including ‘Jefferson’ and ‘McDonald’ have been extensively planted throughout Oregon’s Willamette Valley over the past decade. However ,‘Jefferson’ and ‘McDonald’ have exhibited small cankers in commercial orchards under high disease pressure. In New Jersey, cultivars with ‘Gasaway’ resistance develop large cankers. Thus, there are concerns about the long-term durability of ‘Gasaway’ resistance and the sustainability of Oregon’s hazelnut industry. The disease is also a main limiting factor to commercial hazelnut production in the eastern USA. New sources of resistance would be interesting, and a few major resistance genes have been mapped to LG7. Four populations were developed for fine mapping the LG7 resistance region using the ‘Ratoli’ (from Spain) and OSU 1166.123 (from Sochi, Russia) resistance sources. SSRs narrowed the resistance region to < 20 cM, and recombinant individuals were identified using 4-5 SSR loci within the region. Recombinants were inoculated with Anisogramma anomala in the greenhouse and in the field, and disease was evaluated 18 months later. A set of 22 new SSR markers were developed from di- and tri-nucleotide repeats between the flanking markers in the ‘Jefferson’ genome (v4). SSR markers were characterized using a diversity panel of 50 hazelnut accessions. To develop KASP/PACE primers for SNPs in the region, an initial set of 3000 SNPs was reduced to 100 using a SNP array. High density genetic linkage maps with new SSR and KASP markers were constructed for all four mapping populations. The results of this study will aid marker-assisted selection and the breeding of EFB-resistant cultivars with these new sources, and facilitate the pyramiding of R-genes in a single clonal selection for more durable resistance.
Speakers
RM

Rion Mooneyham

Oregon State University
Co-authors
JS

Jacob Snelling

Oregon State
NA
SM

Shawn Mehlenbacher

Oregon State University
Friday September 27, 2024 10:00am - 10:15am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

10:15am HST

GG 3 - Estimation of Breeding Values to Improve Kernel Weight in Almond (Prunus dulcis)
Friday September 27, 2024 10:15am - 10:30am HST
Coral 1
Improving nut and kernel quality traits is a high priority in almond breeding programs around the world. Almond has a long juvenile period and phenotypic selection for nut and kernel traits can only be conducted after three years from planting. In early stages of planting, individuals with desirable nut and kernel traits can be identified by marker-trait associations (MTAs) using molecular markers. Currently, MTAs are identified by quantitative trait locus (QTL) mapping using progeny from bi-parental crosses or association mapping panels. However, the efforts of identifying MTAs using current QTL detection methods are hampered either by unavailability of genomic information or required genetic linkage maps. In addition, most kernel traits have polygenic inheritance, and many genes and genomic regions affect genetic variations. In crop research, genomic selection would provide promising approach to accelerate the genetic gains and reduce the length of breeding cycle. Yet, application of genomic selection in almond breeding and research is limited. We present results demonstrating the predictive ability of whole-genome and pedigree-based models to identify elite candidate parents for almond kernel weight. In this work, we used ancestral pedigree and phenotypic data from 13,000 progeny that were derived from 57 parents and 291 families. Ancestral pedigrees were recorded from the available literature from the almond breeding programs in USA, Spain, Italy, France, and Australia. Average kernel weight was obtained for each progeny tree from 30 nuts. All parents were resequenced using whole-genome sequencing at a depth of 15x. Over 80k high quality, independent single-nucleotide polymorphisms were used to construct realised genomic relationship matrix and linkage disequilibrium (LD) regions were used to compute LD weights. Genomic best linear unbiased prediction (GBULP) using Asreml-R was used to predict genomic estimated breeding values (GEBV). Pedigree model derived from linear mixed model was used to predict individual tree effects (PEBV) to validate the predicted GEBVs. EBVs were compared using Pearson correlation coefficient (r) and elite candidate parents were selected based on the selection index. For kernel weight, both pedigree and genomic models resulted similar EBVs, and r was 0.97. A high level of correlation in EBVs obtained from two methods indicates the suitability of these models in estimating BVs for future predictions. Predicted elite candidate parents from this study can reduce the conventional breeding cycle of almond by 6 years. The constructed models mainly represent Australian context and multi-environmental trials are required to identify the broader applicability of these models.
Speakers
SG

Shashi Goonetilleke

The University of Queensland
Co-authors
CH

Craig Hardner

The University of Queensland
NA
MW

Michelle Wirthensohn

The University of Adelaide
NA
Friday September 27, 2024 10:15am - 10:30am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

10:30am HST

GG 3 - Alternative RNA Splicing Associated with Pecan Dichogamy
Friday September 27, 2024 10:30am - 10:45am HST
Coral 1
Pecan (Carya illinoinensis), a North American native nut crop, exhibits two distinct flowering habits where male and female flowering occur at separate times. Trees that shed pollen before their pistillate flowers become receptive are classified as protandrous or type 1 (recessive homozygous, pp), while those with pistillate flowers receptive before pollen shed are protogynous or type 2 (dominant heterozygous, PP/Pp). Establishing commercial pecan orchards requires planting both types of pecan cultivars to ensure optimal pollination for maximum production. To investigate critical genes associated with pecan heterodichogamous flowering, we collected tissues from four stages (dormant buds, swollen buds, immature catkins, and immature pistils) of three genotypes (PP, Pp, and pp). Paired-end RNA sequencing at 125/150 bp read lengths was conducted on an Illumina platform. Clean and unique reads were mapped to an annotated 'Pawnee’ reference genome. Out of 32,267 annotated genes, over 5,000 (~15%) were identified to have alternative splicing events associated with pecan flowering dichogamy. We illustrate by three genes that present significant alternative splicing patterns associated with dichogamy genotypes, distinguishing the pp genotype from PP and Pp genotypes. These genes exhibited 6-18 nucleotide differences in RNA sequence between the pp genotype and PP/Pp genotypes, potentially resulting in an altered protein product with 2-6 amino acid differences between type 1 and type 2 genotypes. This study provides evidence for the prevalence of alternative RNA splicing in the transcription regulation of pecan dichogamy.
Speakers
avatar for Xinwang Wang

Xinwang Wang

Plant Geneticist, USDA ARS
Co-authors
JR

Jennifer Randall

New Mexico State University
NA
JS

Joe Song

New Mexico State University
NA
WC

Warren Chatwin

USDA ARS Southern Plains Agricultural Research Center
NA
YL

Yiyi Li

New Mexico State University
NA
Friday September 27, 2024 10:30am - 10:45am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

10:45am HST

GG 3 - Alaska Can Grow More Than Giant Vegetables: The Potential of Rhubarb for Specialty Crop Producers
Friday September 27, 2024 10:45am - 11:00am HST
Coral 1
Specialty crop producers in Alaska need consistent, suitable crop and varietal options for successful commercial production, as food security is a major concern in this state that imports 95% of its food. The climate in much of Alaska is ideal for cool season, perennial corps that are winter hardy, such as Rhubarb (Rheum sp.). Rhubarb was brought to Alaska through several waves of immigration from regions extending from Russia through England and is now established throughout the state. Once a site for the National Plant Germplasm System (NPGS) Arctic and Subarctic Plant Gene Bank, the University of Alaska Fairbanks Matanuska Experiment Farm and Extension Center still maintains a collection of 41 accessions of Rheum sp. in the field. In addition, a new collection of heirloom rhubarb plants has been assembled by a local grower and maintained in large pots. In this project, we collected leaf samples from the heirloom collection plants for genotyping and phenotyping, as well as benchmark samples from plants remaining in the former germplasm collection, to provide an understanding of relatedness and desirable characteristics. A 5 cm square sample of leaf tissue was harvest from each plant, dried, and sent to a commercial laboratory for genotyping. Size and color of leaves and petioles, dates of emergence, plant vigor, and juice quality were measured on plants from the heirloom collection. Finally, surveys carried out of the last 12 years targeted a diversity of stakeholders (commercial producers, business owners, and the general public) to identify rhubarb quality expectations, including flavor, juice content, petiole color, and plant vigor. Based on genotyping results, plants not genetically redundant to those in the NPGS rhubarb collection currently located in Pullman, Washington, will be added to the collection. We present recommendations for variety suitability for different climate regions of Alaska based on the traits measured, taking into account varieties of rhubarb currently available wholesale to Alaska. Recommendations are also presented for further research into commercial production and added-value characteristics.
Speakers
CM

Carol Miles

Washington State University
Co-authors
AC

Alex Cornwall

USDA ARS
NA
AK

Ann Kowenstrot

University of Alaska Fairbanks
MW
Friday September 27, 2024 10:45am - 11:00am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

11:00am HST

GG 3 - Utilization of Germplasm to Improve Illinois Horseradish
Friday September 27, 2024 11:00am - 11:15am HST
Coral 1
Horseradish (Armoracia rusticana, Brassicaceae) is an important specialty crop in Illinois, with most commercial production adjacent to St. Louis, Missouri in what is known as the Mississippi Bottoms. The continued development of new, improved horseradish cultivars is critical to sustain this important specialty crop industry, since horseradish clonal cultivars tend to "run out" and lose their productivity over a period of about 10 years. A small germplasm collection of clones from eastern Europe and Russia, as well as old cultivars no longer in wide use and other breeding materials that were saved from the breeding program has been maintained since the 1960s, first at University of Illinois until the early 2000s and now at Southern Illinois University-Carbondale. During the last 20 years, germplasm has been utilized from various sources to improve horseradish so this industry can sustain itself for the near future. The following examples are provided to illustrate the importance of new germplasm in new horseradish cultivar development. Accession 761A collected from Drążgów, Poland was instrumental in developing horseradish cultivars with tolerance to internal root discoloration which is caused by a soil-borne pathogen complex. The germplasm clone Czech has been very effective in transmitting its large root size trait to its resulting progeny and was used in many crosses made from 2005 to 2010. Many cultivars grown today have this germplasm source in their background. Another important clonal cultivar known as 9705 was widely grown during the 2000s and resulted from outcrossing accession 758A collected from Ribnica, Slovenia with an unknown male. Additionally, 315 is another very important cultivar that was the workhorse for the industry from 2005 to 2015 having lineage also from 758A. 15K was another industry workhorse in the late 1990s to early 2000s, and had its primary lineage traceable to 856A, an accession from the Czech Republic. These are a few examples of how germplasm sources have contributed to sustaining the Illinois horseradish industry and each will be discussed in further detail regarding their specific benefits. Moreover, most are still used in some capacity in the breeding program today.
Speakers
AW

Alan Walters

Southern Illinois University
Friday September 27, 2024 11:00am - 11:15am HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 3

12:44pm HST

Genetics and Germplasm 4 (GG 4)
Friday September 27, 2024 12:44pm - 2:15pm HST
Coral 1
Safeguarding Herbaceous Ornamental Plant Diversity: The Ornamental Plant Germplasm Center - Yu Ma
SNP-Enabled Genetic Diversity and Population Structure of Gladiolus (Gladiolus ×hybridus) Cultivars - Marie Abbey
Development of Genetic Fingerprinting of Azalea Cultivars Using SSR Markers - Seth Wannemuehler
A Chromosome-Scale Haplotype-Resolved Reference Genome of Lantana camara and Insights into Unreduced Female Gamete Production - Brooks Parrish
Identification of Flowering Dogwood QTLs for Bract Color using a Pseudo-F2 Population - Trinity Hamm
Evaluation of Hibiscus cannabinus as an Alternative Fiber Crop for Florida: Identification of Valuable Traits and Germplasm for Cultivar Improvement - James Webb

Moderator
TH

Trinity Hamm

University of Tennessee, Knoxville
Friday September 27, 2024 12:44pm - 2:15pm HST
Coral 1
  Oral Sessions, Genetics and Germplasm 4

12:45pm HST

GG 4 - Safeguarding Herbaceous Ornamental Plant Diversity: The Ornamental Plant Germplasm Center
Friday September 27, 2024 12:45pm - 1:00pm HST
Coral 1
Ornamental crops play an indispensable role in enriching our daily lives, offering not just visual delight but also therapeutic benefits. Moreover, the floriculture industry stands as a pivotal pillar within the nation’s agriculture sector, experiencing a substantial 16% increase in sales from 2019-2022, marking it as one of the fastest-growing industries. Safeguarding ornamental plant diversity has become more crucial than ever to sustain this industry and ensure its continued growth and resilience in the face of climate changes and evolving consumer preferences. Located in Columbus, OH, the Ornamental Plant Germplasm Center (OPGC) is one of 20 gene banks in the U.S. National Plant Germplasm System. Established through a cooperative effort between the USDA-ARS and The Ohio State University, it began operations in 2001. The center’s main goals are to acquire, document, maintain, characterize, and distribute herbaceous ornamental genetic resources and associated information for conservation, and to enhance scientific research as well as the floriculture and nursery industry. Current priority genera include Begonia, Coreopsis, Lilium, Phlox, Rudbeckia, and Viola. Since the OPGC began operation, 7350 accessions have been acquired, representing significant diversity within the 432 genera and over 2000 species of herbaceous ornamentals conserved. More than 13,000 germplasm items have been delivered free of charge to researchers, breeders and educators around the world. This presentation will outline the core functions of OPGC, including its germplasm collection, conservation techniques, and collaborative research initiatives.
Speakers
YM

Yu Ma

Ohio State University
Co-authors
SS

Susan Stieve

The Ohio State University
NA
Friday September 27, 2024 12:45pm - 1:00pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

1:00pm HST

GG 4 - SNP-Enabled Genetic Diversity and Population Structure of Gladiolus (Gladiolus ×hybridus) Cultivars
Friday September 27, 2024 1:00pm - 1:15pm HST
Coral 1
Studies on genetic diversity and population structure provide important insights for determining ancestry and target trait enhancement in breeding programs. Gladiolus(-i), Gladiolus ×hybridus (Iridaceae), is a tetraploid, asexually-propagated, herbaceous perennial floricultural crop. Gladioli have tall flower stalks which make them ideally suited for cut flowers (floral design) and annual garden plants. Gladiolus is an important cut flower crop (in the top 5) for floral design. The purpose of this study was to analyze the genetic diversity of cultivated gladiolus germplasm to determine ancestry and relatedness. In this study we examine 549 unique gladiolus cultivars using DNA marker-based analysis. Samples were collected from the public (University of Minnesota) and private (Meyer, Otto) sector breeding programs in Minnesota and Europe. Population genetic diversity was analyzed using 17,556 single nucleotide polymorphism (SNP) markers developed by low-density DArTseq technology. Despite phenotypic differences, primarily in flower color or type (ruffled, etc.), the genetic diversity of gladiolus cultivars is low. The heterozygosity value was Ho=0.09 and the Fischers (FHOM) inbreeding coefficient was FHOM=0.40. SplitsTrees showed no differentiation, the average minor allele frequency (MAF) and polymorphism information content (PIC) was MAF=0.12 and PIC=0.15. The lack of significant genetic diversity among cultivars as well as breeding programs demonstrates a narrow germplasm base for this important cut flower crop. We discuss our findings and recommend ways to use these conclusions to improve future genome-wide association studies (GWAS) as well as increase efficiency and diversity in breeding goals.
Speakers
MA

Marie Abbey

University of Minnesota
Marie Abbey is a researcher at the University of Minnesota Horticultural Science department. She has studied perceptions of biotechnology, invasive plant species, and aquaponics. Her current research is in flower breeding and molecular genetics.
Co-authors
NO

Neil O Anderson

University of Minnesota
NA
RE

Rajmund Eperjesi

University of Minnesota
NA
Friday September 27, 2024 1:00pm - 1:15pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

1:15pm HST

GG 4 - Development of Genetic Fingerprinting of Azalea Cultivars Using SSR Markers
Friday September 27, 2024 1:15pm - 1:30pm HST
Coral 1
Azaleas (Rhododendron spp.) are economically important ornamental flowering shrubs in landscapes around the world with thousands of cultivars representing many species of Rhododendron. Because azalea is an asexually propagated crop, potential discrepancies in plant identity may occur throughout the propagation pipeline, which can lead to mislabeling during propagation and commercialization processes. For example, the University of Minnesota (UMN) cultivar ‘Electric Lights Double Red’ is currently being propagated but flower morphology of the propagules differed from the original plant leading to uncertainty of propagule identity. Previous studies have identified DNA markers, specifically simple sequence repeats (SSRs), capable of differentiating azalea hybrid offspring from different species of the section Pentanthera. This study aims to leverage these previously developed SSR markers to authenticate the identity of breeding germplasm at the UMN and uniquely fingerprint other cultivars on the market. The evaluated azaleas pedigrees include up to 15 different species of deciduous azalea. Therefore, a total of 15 SSR markers that amplified fragments from several species of section Pentanthera were selected for this study. DNA was extracted from lyophilized leaf samples of 139 azalea cultivars using a Qiagen DNeasy Plant Pro Kit. Preliminary analysis of the azalea DNA using the selected SSR markers has identified the presence of 16 expected unique cultivars and 3 pairs of previously known duplicates. The outcome of this research will demonstrate the feasibility of providing azalea breeders, growers, and producers a marker-based system for assuring cultivar trueness-to-type and protection of intellectual property.
Speakers
SW

Seth Wannemuehler

University of Minnesota
Co-authors
DL

Diana Lopez Arias

University of Minnesota
NA
SH

Stan Hokanson

University of Minnesota
NA
SM

Steve McNamara

University of Minnesota
NA
Friday September 27, 2024 1:15pm - 1:30pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

1:30pm HST

GG 4 - A Chromosome-Scale Haplotype-Resolved Reference Genome of Lantana camara and Insights into Unreduced Female Gamete Production
Friday September 27, 2024 1:30pm - 1:45pm HST
Coral 1
This comprehensive study unveils the first annotated, haplotype-resolved, chromosome-scale reference genome of Lantana camara, alongside insights into candidate genes for unreduced female gamete production through ovary transcriptome sequencing. L. camara, a native of the Caribbean, plays a dual role as a valued ornamental plant and a challenging invasive species. The absence of a high-quality genomic resource has previously limited the exploration of its ornamental and invasive characteristics. This work closes this gap by delivering a critical genomic resource for L. camara, essential for ornamental breeding programs and invasive species management. The genome of a diploid L. camara breeding line UF-T48 was assembled de novo, utilizing HiFi and Hi-C reads, achieving phased genome assemblies with a BUSCO score of 97.7% and LAI score of 19.37, indicating high quality. This assembly resolved all 22 chromosomes into pseudochromosomes, with an average length of 117 Mb, and annotated 83,775 protein-coding genes, laying a foundational step for Verbenaceae family genomic research. Simultaneously, this research delves into the plant’s reproductive biology, specifically targeting the mechanism of unreduced female gamete production, a trait that has played an important role in the evolution and spread of lantana, contributed to the plant’s invasiveness, and and complicated the development of sterile triploids. By aligning RNA-seq data to the reference genome, we identified differentially expressed genes associated with cell division and meiosis, crucial for understanding the genetic underpinnings of unreduced gamete production. These findings not only enhance the genetic comprehension of L. camara but also provide invaluable genomic resources for future genetic studies, conservation efforts, and breeding strategies aimed at producing non-invasive sterile cultivars. This pioneering genomic and transcriptomic analysis marks a significant leap forward in researchers’ ability to manipulate L. camara for both horticultural innovation and environmental management.
Speakers
BP

Brooks Parrish

University of Florida
Co-authors
ZD

Zhanao Deng

University of Florida
Friday September 27, 2024 1:30pm - 1:45pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

1:45pm HST

GG 4 - Identification of Flowering Dogwood QTLs for Bract Color using a Pseudo-F2 Population
Friday September 27, 2024 1:45pm - 2:00pm HST
Coral 1
Flowering dogwoods (Cornus florida L.), known for their showy spring display and year-round appeal, are extensively planted as ornamental trees. In 2019, dogwoods ranked third in value for deciduous flowering trees in the U.S., generating more than $31 million in wholesale and retail sales. Tennessee is vital to this industry. The state leads the country in the number of dogwood plants sold, with almost double the number of trees sold as the next top producing state in the country. The showy bracts of dogwoods are modified leaves with a spectrum of color ranging from white to red, with many intermediate colors and patterns. Cornus florida ‘Cherokee Brave’ with deep pink bracts and ‘Appalachian Spring’ with creamy white bracts are two popular cultivars. Partially phased reference genomes have recently been assembled and annotated for these cultivars, ranging from 1,253 to 1,266 Mbp in length with 28,558 to 28,768 annotated protein coding genes. With these newly annotated genomes providing greater context, a QTL analysis was conducted using a pseudo-F2 population of ‘Cherokee Brave’ × ‘Appalachian Spring’ which segregates for bract color. Genotyping was completed using double-digest restriction-site associated DNA sequencing (ddRADseq) with PstI and MspI. With increasing demand for high-throughput phenotyping, six different phenotypic methods were utilized to determine which method was optimal for QTL detection. The phenotyping methods included: 1) manual characterization into binary classes (white or pink); 2) manual characterization into five classes (white, light blush, medium blush, pink, red); 3) colorimeter readings; 4) image analysis using full inflorescence; 5) image analysis using bracts detached from inflorescence; and 6) one bract per inflorescence. QTLs were identified using all phenotyping methods. The QTLs identified here will be used as the foundation for developing a marker assisted selection system for bract color in flowering dogwoods.
Speakers
TH

Trinity Hamm

University of Tennessee, Knoxville
Co-authors
DH

Denita Hadziabdic

University of Tennessee, Knoxville
NA
DS

DeWayne Shoemaker

University of Tennessee - Knoxville
NA
MN

Marcin Nowicki

University of Tennessee, Knoxville
NA
MS

Margaret Staton

University of Tennessee, Knoxville
NA
RT

Robert Trigiano

University of Tennessee, Knoxville
NA
SB

Sarah Boggess

University of Tennessee, Knoxville
NA
WK

William Klingeman

University of Tennessee, Knoxville
NA
Friday September 27, 2024 1:45pm - 2:00pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

2:00pm HST

GG 4 - Evaluation of Hibiscus cannabinus as an Alternative Fiber Crop for Florida: Identification of Valuable Traits and Germplasm for Cultivar Improvement
Friday September 27, 2024 2:00pm - 2:15pm HST
Coral 1
Hibiscus cannabinus, commonly referred to as Kenaf, is an annual warm-season plant that can thrive in the Southeastern United States. It serves as a vital source of natural fiber with diverse applications, such as biocomposites, paper pulp, textiles, industrial absorbents, animal bedding, and potting medium. A set of 86 accessions of Hibiscus cannabinus, acquired from USDA-GRIN, underwent evaluation in Central Florida for various parameters, including plant height, basal width, stem width 50 cm above the plant base, stalk fresh weight, stem fresh weight, stalk dry weight, leaf dry weight, bast weight, and core weight. Significant variations were observed among accessions for all the measured variables. Notably, stalk dry weight emerged as the key trait of interest, representing the plant portion with desirable fibers for various applications. The top Duncan grouping for stalk dry weight comprised eight accessions: PI 329191 (18-85), PI 639889 (18-157) known as "Whitten," PI 270111 (18-55) known as "G-32," PI 603071 (18-152) known as "Dowling," PI 638930 (18-154) known as "74200 I4," PI 638932 (18-156) known as "Yue 74-3," PI 270106 (18-50) known as "G-14," and PI 468077 (18-137). Out of the 86 USDA-GRIN accessions examined, these eight have been identified as the top-performing choices for field production in Central Florida. Furthermore, these selected accessions are deemed desirable parents for future cultivar improvement endeavors, aiming to develop enhanced cultivars of Hibiscus cannabinus specifically tailored for production in Central Florida.
Speakers
JW

James Webb

University of Florida
Co-authors
CA

Conner Austin

University of Florida
Friday September 27, 2024 2:00pm - 2:15pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 4

2:29pm HST

Genetics and Germplasm 5 (GG 5)
Friday September 27, 2024 2:29pm - 4:15pm HST
Coral 1
Breeding for Photoperiod Insensitive and Indeterminate Flowering Habit in Pigeonpea - Diego Viteri
Breeding for Improved Tomato Flavor - Denise Tieman
Genome-Wide Association Study Identifies Key SNPs Associated with Mineral Element Accumulation in Spinach (Spinacia oleracea) - haizheng xiong
Comparative Analyses of Tissue-Specific Transcriptome Responses to Salt Stress in Lettuce Roots and Leaves - Modan Das
QTL Mapping Of Horticulturally Important Plant Architectural Traits In Cucumber (Cucumis sativus L.) - Thi Nguyen
Screening Sweetpotato Germplasm for Resistance to Meloidogyne incognita - Phillip Wadl
Variation for Non-Acclimated and Acclimated Heat Tolerance Among Potato Germplasm: Indication of Separate Genetic Control - Jiwan Palta

Moderator
PW

Phillip Wadl

USDA, ARS, U.S. Vegetable Laboratory
Friday September 27, 2024 2:29pm - 4:15pm HST
Coral 1
  Oral Sessions, Genetics and Germplasm 5

2:30pm HST

GG 5 - Breeding for Photoperiod Insensitive and Indeterminate Flowering Habit in Pigeonpea
Friday September 27, 2024 2:30pm - 2:45pm HST
Coral 1
Pigeonpea [Cajanus cajan (L.) Mill.] is an important legume consumed in the Caribbean basin. Cultivars with indeterminate flowering habit have sensitivity to the photoperiod in Puerto Rico. The objectives of this research were to: (1) develop two breeding lines with indeterminate flowering habit that can be planted year-round, and (2) evaluate their agronomic performance. IIPG-7 and IIPG-11 breeding lines, derived from the bi-parental cross ‘ICPL 86012’/‘Guerrero’, were developed by pedigree and bulk breeding methods. Both breeding lines, their parents, and cultivars checks were tested in field trials in Isabela and Lajas, Puerto Rico in 2022 and 2023. IIPG-7 and IIPG-11 were early genotypes that initiated flowering between 73-84 days after planting (dap), and reached harvesting maturity at 121-127 dap compared with indeterminate cultivars ‘Ariel’, ‘Blanco Yauco’, ‘Kaki’, ‘Pinto Berrocales’, and ‘Super Pinto’ that initiated flowering between 91 to 102 dap and reached maturity at 138-148 dap. These cultivars had seed yield values over 1,000 kg/ha while IIPG-7 and IIPG-11 produced between 721 to 1,010 kg/ha under short day conditions in both locations. In contrast, IIPG-7 and IIPG-11 were the only indeterminate genotypes that initiated flowering between 42-88 dap, reached maturity between 88-172 dap, and seed yields varied from 626 to 2,449 kg/ha under long day conditions in Isabela and Lajas. These new breeding lines can be used to develop pigeonpea cultivars with insensitivity to the photoperiod.
Speakers
DV

Diego Viteri

University of Puerto Rico at Mayagüez
Co-authors
AL

Angela Linares Ramirez

University of Puerto Rico
Friday September 27, 2024 2:30pm - 2:45pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

2:45pm HST

GG 5 - Breeding for Improved Tomato Flavor
Friday September 27, 2024 2:45pm - 3:00pm HST
Coral 1
Consumers are dissatisfied with the flavor of modern commercial tomatoes; however, modern tomato varieties have many desirable agronomic traits such as shelf life, disease resistance and yield. The flavor deficiency in modern tomatoes is due to a cumulative loss of superior alleles affecting flavor volatiles while breeding for other traits. The lack of breeder focus on the consumer is largely due to the genetic complexity of the tomato flavor phenotype as well as a lack of a simple assay that can define consumer preferences. Tomato flavor is a result of interactions between sugars, acids and aroma volatiles, with volatile compounds giving the tomato fruit its characteristic aroma and flavor. We have quantified 68 flavor biochemicals in over 700 tomato varieties, including modern, heirloom and ancestral tomato accessions. Over 160 of these varieties were evaluated by a large consumer panel for fruit flavor quality traits including overall liking. Genome Wide Association Studies (GWAS) identified genetic loci associated with altered levels of acids, sugars and aroma volatiles. We have used marker-assisted breeding to introgress loci associated with flavor biochemical levels from heirloom varieties into modern tomato varieties. Introduction of seven flavor loci affecting a variety of flavor volatiles into a modern tomato variety has resulted in altered flavor volatile profiles and improved flavor as assessed by a consumer panel.
Speakers
DT

Denise Tieman

University of Florida
Co-authors
HK

Harry Klee

University of Florida
NA
MA

Modesta Abugu

North Carolina State University
NA
Friday September 27, 2024 2:45pm - 3:00pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

3:00pm HST

GG 5 - Genome-Wide Association Study Identifies Key SNPs Associated with Mineral Element Accumulation in Spinach (Spinacia oler
Friday September 27, 2024 3:00pm - 3:15pm HST
Coral 1
Understanding the genetic basis of mineral element contents in crops is crucial for improving their nutritional value. This study conducted a comprehensive Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with the accumulation of 14 essential mineral elements in spinach (Spinacia oleracea). Utilizing a diverse collection of 281 spinach accessions, we assessed the content of Boron (B), Calcium (Ca), Cobalt (Co), Copper (Cu), Iron (Fe), Potassium (K), Magnesium (Mg), Manganese (Mn), Molybdenum (Mo), Sodium (Na), Nickel (Ni), Phosphorus (P), Sulfur (S), and Zinc (Zn), expressed in micrograms or milligrams per gram of dry weight (µg/gDW or mg/gDW). Genotyping revealed 83,952 SNPs across the spinach genome, analyzed using GAPIT3 and TASSEL5 software platforms. Statistical models employed included General Linear Model (GLM), Mixed Linear Model (MLM), FarmCPU, and BLINK within GAPIT, alongside SMR and GLM in TASSEL. Our analysis uncovered 33 significant SNP-trait associations distributed among the minerals: one for B, Cu, P, and K; two for Ca, Ni, Fe, Zn, and S; three for Mo and Mg; four for Na and Co; five for Mn. These findings highlight the genetic diversity influencing mineral nutrient accumulation in spinach and offer valuable markers for breeding nutritionally enhanced spinach varieties.
Speakers
HX

haizheng xiong

University of Arkansas
Co-authors
avatar for Ainong Shi

Ainong Shi

Associate Professor, University of Arkasnas
Dr. Ainong Shi is a faculty member in the Department of Horticulture at the University of Arkansas. His research laboratory specializes in plant breeding and genetics, particularly focusing on vegetable crops such as arugula, cowpea, and spinach for cultivar and germplasm development... Read More →
HA

Hanan Alkabkabi

University of Arkansas
NA
IA

Ibtisam Alatawi

University of Arkansas
NA
KC

Kenani Chiwina

University of Arkansas
NA
Friday September 27, 2024 3:00pm - 3:15pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

3:15pm HST

GG 5 - Comparative Analyses of Tissue-Specific Transcriptome Responses to Salt Stress in Lettuce Roots and Leaves
Friday September 27, 2024 3:15pm - 3:30pm HST
Coral 1
Lettuce is one of the most important leafy vegetable crops world-wide. Salt stress adversely affects lettuce production, leading to considerable yield losses. Understanding the molecular mechanisms underlying the salt stress response is essential for breeding and development of lettuce cultivars with improved salt tolerance. Thus, the objective of this research was to identify differentially expressed genes (DEGs) in lettuce root and leaf tissues under salt stress and non-salt stress conditions. We have compared two salt-stress tolerant and two salt-sensitive accessions from crisphead and leaf horticultural types. Differential gene expression was compared between salt-tolerant and salt-sensitive accessions from the same horticultural type to minimize the effect of horticultural types on the comparison. In the root samples of the salt-tolerant accessions, we identified 3,789 and 4,022 DEGs, while for the salt-sensitive accessions 9,030 and 9,945 DEGs were identified, for the crisphead and leaf types, respectively. In leaf tissues, we observed 5,683 and 9,445 DEGs in the salt-tolerant accessions and 5,836 and 10,172 DEGs in the sensitive accessions, respectively, for the crisphead and leaf types. Thus, the number of DEGs was higher in sensitive accessions of both root and leaf tissues, with a notably greater disparity in root tissues. Functional annotations of the DEGs indicated stress response as a common biological process in both root and leaf tissues. Protein phosphatase inhibitor and peroxidase were the most significantly enriched molecular function terms in roots, while chaperone and glycosyltranferase molecular function terms were most significantly enriched in leaves. Gene Ontology (GO) enrichment analysis determined that genes related to the organic substance biosynthetic process were most significantly enriched in roots, while genes related to photosynthesis, response to light stimulus, chlorophyll binding and regulation of the jasmonic acid-mediated signaling pathway were significantly enriched in leaves. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that plant hormone signal transduction, biosynthesis of secondary metabolites, and the MAPK signaling pathway were significantly enriched terms in both root and leaf tissues, while cysteine and methionine metabolism terms were most significantly enriched in roots and photosynthesis was most significantly enriched in leaves. Identification of the salt-stress responsive genes and the results on their expression patterns in salt-tolerant vs salt-sensitive cultivars obtained in the present study open the door for further functional analysis of these genes and their utilization in improving salt-stress tolerance in lettuce.
Speakers
MD

Modan Das

USDA-ARS
Co-authors
BM

Beiquan Mou

USDA-ARS
NA
IS

Ivan Simko

USDA-ARS
NA
Friday September 27, 2024 3:15pm - 3:30pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

3:30pm HST

GG 5 - QTL Mapping Of Horticulturally Important Plant Architectural Traits In Cucumber (Cucumis sativus L.)
Friday September 27, 2024 3:30pm - 3:45pm HST
Coral 1
Cucumber (Cucumis sativus L.) is an economically important vegetable crop cultivated worldwide. Plant architectural traits, such as lateral branch number (LBN), vine length (VL), number of nodes (NN) and internode length (IL), may directly influence production practices, plant performances, fruit yield and quality. Despite their importance, investigation on the genetic basis of these traits in cucumber is limited. In this study, we conducted QTL mapping for VL, NN, IL and LBN using bi-parental F2, F2-derived F3 and recombinant inbred line (RIL) populations. There are significant positive correlations between LBN, VL and NN. Estimated board-sense heritability using entry-mean basis of the RIL population was high, ranging from 0.66 to 0.84. Two linkage maps were developed through genotyping-by-sequencing of 140 F2 individuals and Diversity Arrays Technology (DArTag) SNP genotyping of 135 RIL, containing 1912 and 334 SNP loci in seven linkage groups and spanning 1077 and 948 cM, respectively. QTL mapping analysis detected a total of 79 QTLs associated with the four traits in six environments or populations. Based on their physical locations, 66 QTLs were distributed in ten QTL clusters harboring four major-effect and six minor-effect QTLs. Each of the major- and minor-effect QTLs was supported by consistent and reproducible detection from at least three environments. Notably, major-effect QTLs for VL, NN and LBN were co-localized in two genomic regions on Chr1 (3.73 Mbp) and Chr6 (3.78 Mbp), and the major-effect QTL for IL was mapped in a 3.98-Mbp region on Chr5. These findings provide a framework for dissecting the genetic architecture of these complex traits, and valuable genetic information for cucumber breeders to employ molecular-assisted breeding approaches and develop improved varieties with enhanced productivity.
Speakers
TN

Thi Nguyen

Research Assistant, University of Wisconsin- Madison
Co-authors
YY

Yassine Yahia

University of Wisconsin-Madison
NA
YW

Yiqun Weng

University of Wisconsin-Madison
NA
Friday September 27, 2024 3:30pm - 3:45pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

3:45pm HST

GG 5 - Screening Sweetpotato Germplasm for Resistance to Meloidogyne incognita
Friday September 27, 2024 3:45pm - 4:00pm HST
Coral 1
Meloidogyne incognita is the most common root-knot nematode found in agricultural regions worldwide. It can cause severe damage to many crops including sweetpotato storage roots, causing them to be unmarketable and resulting in significant yield losses. Identifying resistant crop varieties is one of the most effective ways to manage M. incognita. To identify germplasm with resistance to M. incognita, 47 sweetpotato accessions obtained from the USDA germplasm repository were screened in replicated greenhouse assays. ‘Beauregard’ was used as a susceptible control and ‘Regal’ as a resistant control. Sweetpotato slips containing 3 nodes each were planted in an autoclaved 1:1 mixture of sand and potting mix in Deepot D25L containers and arranged in a randomized block design, with 2-3 replicates per an accession. Two weeks after planting, each plant was inoculated with 10,000 M. incognita eggs. Eight weeks after inoculation, plants were harvested and rated for fibrosity, galling, number of egg masses, and eggs per gram of root. Resistance was defined as accessions with mean galling ≤ 10% and mean eggs per gram of root ≤ 500. Based on these criteria, 12 accessions were identified as having resistance to M. incognita.
Speakers
PW

Phillip Wadl

USDA, ARS, U.S. Vegetable Laboratory
Co-authors
CW

Catherine Wram

USDA, ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory
NA
HB

Hannah Baker

USDA, ARS, U.S. Vegetable Laboratory
NA
WR

William Rutter

USDA-ARS
NA
Friday September 27, 2024 3:45pm - 4:00pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5

4:00pm HST

GG 5 - Variation for Non-Acclimated and Acclimated Heat Tolerance Among Potato Germplasm: Indication of Separate Genetic Control
Friday September 27, 2024 4:00pm - 4:15pm HST
Coral 1
Several studies have documented variation in potato germplasm for heat tolerance of leaf tissue. Most researchers have relied on screening for heat stress by exposing excised leaf tissue (grown under non-stress condition) to a short-term (minutes-hours) of acute heat stress (37-55C). It is well known that plants vary in their ability to acclimate to heat stress know as priming. This priming can enable plant to survive subsequent temperatures that are lethal to plants grown under non-stress condition. Our recent studies show that potato plants under prolonged heat stress (35/25C, day/night, for 3-5 weeks) newly developed leaves (acclimated) can maintain health under heat stress by modifying anatomy and physiology. These results show that potato plants have the ability to acclimate to heat stress that results in increased heat tolerance. In the present study, we screened to potato germplasm for heat tolerance of leaf tissue before and after heat acclimation. Ion leakage after exposure of excised leaf tissue to 50C, was used as a screening assay and a reduction in this leakage was used to assess the heat acclimation ability. Wide variety of potato germplasm including commercial cultivars and accessions of various wild species were screened. Our result show significant genotypic variations in acclimated and non-acclimated heat tolerance. Furthermore, the heat acclimation ability appears to be independent of non- acclimated heat tolerance. For example, certain clones of the species Solanum commersonnii had similar non-acclimated heat tolerance but large variation in acclimated tolerance was found among various clones of this species. Similar results were obtained for different clones of Solanum microdontum and Solanum kurtzianum. As expected, the cultivars Zarewo, DTO and Papa Cacho were found to have higher non-acclimated heat tolerance than the others, but Papa Cacho had the highest heat acclimation ability. Our results suggest that non-acclimated heat tolerance and acclimated heat tolerance are under separate genetic control and that selection for both non-acclimated and acclimated heat tolerance may be useful for successful breeding for heat tolerance of potato leaf tissue.
Speakers
JP

Jiwan Palta

UW Madison
Co-authors
AD

Alfonso DelRio

University of Wisconsin Madison
NA
JB

John Bamberg

University of Wisconsin Madison
NA
JS

Justin Schabow

University of Florida
NA
Friday September 27, 2024 4:00pm - 4:15pm HST
Coral 1
  Oral presentation (Individual talk), Genetics and Germplasm 5
 
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