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

Tropical crops have a tremendous impact on global food systems and are well represented in Hawaii. There are many different diseases (bacterial/viral/fungal) that can impact yields. In this session, we invite an audience from a broad pool of research interests and backgrounds to attend and learn about a range of food and forestry crops that are important in Hawaii, including papaya, sweetpotato, the native koa tree and banana and the production systems unique to these crops. The wide range of crops from tuber, to fruit, to forestry has led to a variety of challenges that have attracted less attention compared to pathology problems associated with temperate crops. Short topic presentations in these areas will begiven by and from the perspective of university, non-profit institution, and USDA ARS researchers and a local commercial grower followed by discussions between speakers and individual break out groups consisting of workshop attendees. Attendees will have the opportunity to sample a few varieties of tropic fruit crops and view items made from koa. Through these talks and interactive discussions, we aim to convey the scope of tropical diseases that occur, successful strategies to overcome them given different crop-specific constraints and highlight their relevance to research on emerging problems impacting agriculture in temperate and other regions due to climate and environmental changes.
Coordinator(s)

Dr. Jon Suzuki, USDA ARS DKI U.S. PBARC, Hilo, HI, United States
Dr. Michael Kantar, Associate Professor, Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa,, Honolulu, United States

Participants:

Dr. Nathan Fumia (HARC - Hawaii Agricultural Research Center) – Understanding the role of selection on fungal disease tolerance in Acacia koa, an endemic Hawaiian hardwood (8 minutes).
A common occurrence during neo-domestication is the interplay of traits such as seedling vigor and disease resistance. The focus of this study is the effect of crossing on a wild species being selected for a domesticated form, including decisions such as number of parents, number of crosses, and number of progeny. Our aim is to begin breeding scheme development for wild species (neo-domestication) using Acacia koa as a novel study system. Breeding population size was changed in the koa orchard through thinning of individuals, a form of pollen control in the population, with the major criterion being a low durability of resistance where trees succumb to disease over time, caused by Fusarium oxysporum. This is an opportunity for insight during the development of expectations in population improvement through augmented crossing parameters, informing situational changes through breeding cycles in neo-domestication programs.
Dr. Anna McCormick (University of Hawaii at Manoa) – Examining viral presence in collections of Hawaiian heirloom sweetpotato varieties (8 minutes).
Sweetpotato has been a staple crop in the Hawaiian Islands since Polynesians settled the islands ~1,200 years ago. Previous work has established that Hawaiian Heirloom sweet potato varieties represent unique germplasm that are more closely related to each other than varieties from other parts of the world. While much work has been done characterizing Hawaiian heirloom plant genetics, much less work has been done characterizing viral genetic presence and diversity. In this study we explored viral presence across an extant collection of 70 Hawaiian heirloom varieties sourced from five different botanical collections over three Islands (O’ahu, Maui and Big Island Hawai’i). Samples were examined for the presence of four viruses from the family Potyviridae namely; Sweet potato virus G (SPVG), Sweet potato virus C (SPVC), Sweet potato virus 2 (SPV2), Sweet potato feathery mottle virus (SPFMV), and one from the family Geminiviridae; Sweet potato leaf curl virus (SPLCV). We found high levels of virus across all collections, including many instances of double and triple infections. These findings have large implications for conservation and local fresh markets.
Dr. Lorin Harvey (Mississippi State University) – Research and discovery of best practices for U.S. sweetpotato clean foundation seed (CFS) programs. (8 minutes)
Sweetpotato is an important crop for the U.S. and worldwide. Infection by viruses which accumulate over time in this and numerous other major perennial crops cause major yield losses annually. The problems in sweet potato are being addressed through Sweetpotato CleanSEED, a multi-state, transdisciplinary funded research project funded by a USDA-NIFA-SCRI grant to develop strategies that improve sweetpotato crop health and yield through developing quality control standards for producing clean foundation seed, improved detection methods, identification of undiscovered viral diseases, and development of cultural practices for efficient clean foundation seed production in both the laboratory and greenhouse to reduce disease transmission in this clonally propagated crop.
Ryan Domingo (USDA ARS U.S Pacific Basin Agricultural Research Center) - Identifying Carica papaya cultivars demonstrating increased partial resistance towards Phytophthora palmivora utilizing a novel rapid phenotyping assay. (8 minutes)
Extensive production loss and mortality of Carica papaya is associated with Phytophthora palmivora in Hawaii and other papaya growing regions of the world. Currently there is no commercial papaya cultivar fully resistant against P. palmivora, however it is important to identify those that contain partial resistance reducing pathogen proliferation. This talk will explore a novel rapid phenotyping assay quantifying P. palmivora growth along papaya seedling stems comparing several genotypes within the USDA germplasm collection. Implications resulting from this study provides farmers, breeders and other stakeholders insight towards cultivars displaying increased partial tolerance towards P. palmivora.
Gabriel Sachter-Smith (Hawaii Banana Source) - Maintaining commercial vitality of the banana industry through germplasm resources and strategies to mitigate disease (8 minutes).
Bananas have been grown in Hawaii since the first waves of Pacific Islander migrations starting over 1000 years ago. Today, bananas represent one of the most widely consumed fresh produce items in Hawaii, despite a steady downward trend in local production since the introduction of Banana bunchy top virus (BBTV) in 1989. To date, no commercially viable cultivar with strong resistance to BBTV has been identified or created, and various ways to combat the virus used in other parts of the world have proved challenging to apply in Hawaii. However, the pressure of the virus and overall impact on a farm can be mitigated using a combination of cultural practices and semi-tolerant cultivars. Through the use of frequent crop rotations, on-farm generated clean plant systems, and working with buyers to adapt alternative varieties to new markets, banana production can be maintained and improved in Hawaii.