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

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.

Advances in Phytophthora, Pythium, and Phytopythium Species Detection, Isolation, Culture, Diagnostics, and Virulence Rejuvenation - Timothy Waller
Effect of Planting Date on Strawberry Yield - Samantha Simard
Evaluation of Irrigation Strategies in Watermelons - Juan Enciso

The Lower Rio Grande Valley farmers traditionally irrigate vegetable crops with furrow irrigation systems. To conserve water and mitigate the effects of droughts, there is a need to adopt more efficient irrigation and fertilization methods and practices in vegetable crops to increase crop production quality and profitability. Farmers that use furrow irrigation systems apply from 4 to 6 inches per irrigation depending on their furrow length and apply more than five irrigations during the vegetable growing season, and using between 20 inches (1.7 ac-ft) and 40 inches (3.3 ac-ft) of irrigation water in their fields. Vegetables have a shallow root system, so farmers must irrigate frequently to maintain good moisture levels during the growing season for optimum growth, possibly wasting water. We use image analysis derived from Unmanned Aerial Systems (UAS) and irrigation soil water sensors to provide management recommendations to schedule drip and surface irrigation to conserve additional amounts of water. We established replicated research experiments using subsurface drip irrigation and soil water sensors (watermark sensors) to irrigate watermelons and other vegetable crops. We grew plants under three different water levels to trigger irrigation (50, 75, and 100 cb). A drip irrigation system with plastic mulch was placed in the field, as well as soil-water sensors, to measure and monitor the soil moisture. After calculating the water used in the three water level treatments, the 50 cb treatment used 0.27 ac-ft, the 75 cb treatment used 0.24 cb and 0.22 ac-ft was used by the 100 cb treatment. According to our results, we could conserve up to 3.0 ac-ft with our recommendations. We concluded that watermelons could be managed when the soil-water sensor readings range between 50 and 75 CB and approximately 0.3 ac-ft of water using subsurface drip irrigation. We obtained an average yield of 53,536 lb/ac, when irrigated under the 50 cb treatment, 42,059 lb/ac at 75 cb, and 36,719 lb/ac at 100 cb.

Not only are Phytophthora, Pythium, and interesting Phytopythium species potentially devastating horticultural pathogens, they regularly present challenges in vitro. In this study, multiple established and novel methodologies were built upon to bolster researchers’ ability to quickly isolate, differentiate, and promote virulence of multiple oomycetes principally collected from symptomatic conifers and nearby water sources. These methods allow greater flexibility in generating clean mycelial cultures for genetic characterization, varying pathogen structures for use in novel bioassays (such as synchronized production of sporangia or zoospores), and ultimately inoculations to evaluate oomycide efficacy or make headway towards completion of Koch’s postulates for previously uncharacterized host: pathogen pairings. Phytopythium vexans (Pp. vexans) (n=8 isolates), three Phytophthora species / species complexes including P. cinnamomi (n=10), P. cryptogea / drechsleri complex (n=4) and P. humicola (n=2), as well as 5 tentative species of Pythium, were evaluated. Isolations took two forms, standard root sampling onto Phytophthora selective media (PARPH), or water-based sampling through a modified ‘baiting/trapping’ technique that utilized on-site collected water samples in the laboratory. The ‘baits’ were Cannabis sativa seed, Vigna radiata beans, and Rhododendron maximum leaves suspended in aerated water samples or slurry of silt/soil. Samples were evaluated on V8-agar (V8A), pea agar (PA), pea broth (PB), potato dextrose agar (PDA), cornmeal agar (CMA), and water agar (WA), each of which provided distinct morphological indicators and structures useful in diagnostic guides and in bioassays or inoculations. As is typical with all plant pathogens, the longer they remain in culture, the less virulent they may become. With oomycetes, this is compounded as the pathogen will often go into chlamydospore or oospore formation (long lived survival structures) which are not ideal for experimentation. Inclusion of germinated then surface sterilized (70% ethanol for 30s) Vigna radiata and Lupinus perennis sprouts into recently poured (still liquid) 1/8 clarified V8 juice agar (1/8 clV8A) provided a media capable of rejuvenating the pathogen due to presence of living roots and dynamic plant nutrients. This allows for more predictability of zoospore formation, especially if they are intended to be used with a time sensitive trials. In numerous incidences multiple species of Phytophthora and Phytopythium vexans isolates went into zoospore release simultaneously by utilizing these approaches in combination with resource starvation and culture washing with sterile distilled water. Taken together these approaches will greatly aid any researcher working with root disease oomycetes in culture.

Optimizing planting date for strawberry in California production is a sustainable measure to maximize yield and maintain plant health. The goal of this project is to assess the optimal planting date for two predominant cultivars: 'Monterey' and 'Fronteras'. The trial was conducted in field 25 at Cal Poly, San Luis Obispo. The experimental area consisted of 3 beds, each 53.5 ft. long. Standard 64-inch beds with 4 rows of plants per bed and 3 lines of drip tape were used. Beds were planted at two-week intervals: 26 Oct, 9 Nov, 23 Nov 2022. Each bed was planted with four plots of ‘Monterey’ and four plots of ‘Fronteras’ (20 plants/plot). Plug plants were produced at North Carolina State University’s nursery and shipped overnight to Cal Poly and planted in the field the next day. First harvest was 13 Apr 2023 when the first fully red fruit were observed. Fruit were harvested, counted, and weighed twice weekly. The trial was completed 8 Aug 2023 and replicated in the 2024 growing season.

The aims of the federal initiative Sustainable Agriculture Research and Education (SARE) are multifaceted: 1) Foster responsible management of the nation's natural resources through the dissemination of location-specific, regional, and sustainable agricultural and ranching techniques, 2) Improve the livelihoods of farmers and ranchers, 3) Safeguard the well-being of individuals involved in food and agricultural systems by reducing reliance on harmful substances, 4) Encourage agricultural variety and resilience, and 5) Assess the local economic, social, and environmental impacts of adopting sustainable agricultural practices. To achieve these goals, SARE offers numerous grant opportunities for research projects, catering to farmers, ranchers, non-governmental organizations, and universities. SARE operates across four regions within the United States. New Mexico is in the Western region (WSARE) which is composed of individual state professional development programs in the area’s 13 states and 4 Pacific Island protectorates. In 2023, the NM WSARE Professional Development Program coordinated a Sustainable Agriculture Summit to better prioritize research and training needs in the state. The event was held in Santa Fe, NM, USA on 30 March, with a total of 58 participants in the full-day event. Among them were 32 agriculture professionals and 26 farmers and ranchers. The event consisted of two main sessions, a panel discussion, followed by an open forum. The panel was comprised of past Western SARE grant recipients and individuals who had submitted proposals, they provided overviews of their projects. Following the panel, summit participants engaged in a brainstorming session to identify critical sustainable agriculture project needs for producers in NM, focusing on research and training needs not previously emphasized in past funding. The priority areas identified by the participants were, in order of importance, 1) Irrigation/water use efficiency, 2) Farm economics, direct markets, and direct sales, 3) Non-traditional production, 4) Pest management, 5) Labor aids and technology adaptation, and 6) Generational transfer of farms and ranches. Each of these priorities was clearly outlined, and potential projects were identified accordingly. The outcomes of this summit were communicated to WSARE, the NM Department of Agriculture, and other funding agencies, offering valuable feedback to guide future proposals and funding initiatives in NM.

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.

Sponsored by National Issues Committee
Our work in horticulture is made possible to a great extent by Federal funding. That funding will only be available if Congress continues to value the work that we do with it. Therefore, all ASHS members should regularly let their representatives know how the funds are helping in your state or district. This session provides an understanding of how to confidently and effectively contact your Congressional district office about the value of programs that you know and use. This program is designed to be of particular value to members in the Western US, who are not likely to come to Washington DC for policy discussion.

This session will be a panel discussion to understand the perspective from the various offices involved and how they interact. The panel includes the actual people involved in this Congressional district.

• Kendra Oishi, District Chief, Office of U.S. Representative Jill Tokuda, Hawaii 2nd District.
• Anthony Ching, Director of Federal Relations for the University of Hawaiʻi System.
• Thomas Björkman, ASHS National Issues Committee and Cornell University
• Russell Galanti, Extension Educator, University of Hawaiʻi.