ASHS 2024 Conference

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

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

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 %.

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.

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.

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.

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.

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.

Schoenocaulon officinale or sabadilla (Melianthiaceae) is endemic to the Americas with Mexico as the Center of Origin and Diversity. Sabadilla is a subtropical geophytic perennial, producing tunicate bulbs. It reproduces by seed and asexually (daughter bulbs), producing apetalous floral inflorescences. Flowering occurs >1.5 years from seed with annual flowering occurring up to eight years. Sabadilla seeds contain two insecticidally active lipophilic alkaloid compounds: veratridine and cevadine, in concentrations of 0.5-6.0%. These compounds are used as “green pesticides” with a mode of action that is similar to pyrethrins; attachment to sodium channels in insects, causing continuous overactivation. Sabadilla has been used by Native American cultures for thousands of years for its insecticidal properties and medicinal uses. However, about sabadilla, little is known about this species as a crop plant. The purpose of this research was to examine population differences of extant, wild collections in Venezuela. In 2019, seeds (24 subsample seed lots from sympatric plants, bulked by site) were collected from seven locations in The Ávila National Park and the vicinity of Colonia Tovar across three different states (Vargas, Miranda, Aragua). Seed lots were germinated to determine % germination and genetic variation. Dried leaf samples (n=333 genotypes) were used for DNA extraction for genotype by sequencing (GBS) for low-density single nucleotide polymorphic (SNP) marker generation (DArT-seq). Genetic variation within and among populations was determined using principle component, Admixture, AMOVA, and IBS analyses (RStudio).

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.

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.