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

Sponsoring Professional Interest Groups
Technology: Coordinator Milt McGiffen - milt.mcgiffen@ucr.edu
Teaching Methods: Coordinator, Kathryn Orvis – orvis@purdue.edu
Controlled Environment: Coordinator, Kent Kobayashi - kentko@hawaii.edu

Supporting Professional Interest Groups
Federal Partners: Matthew Mattia - Matthew.Mattia@usda.gov
Plant Biotech: Kedong Da - kda@ncsu.edu
Ornamentals/Landscape and Turf; Youping Sun - youping.sun@usu.edu
Local Food Systems: Charles H. Parrish II - chip.parrish@pm.me

Artificial intelligence and related topics, e.g., robotics, have been a long time coming in agriculture. For decades there have been predictions of intelligent robots replacing humans, and large farms run by a few humans with many autonomous tractors and other devices. But with the now widespread use of artificial intelligence in everyday life,
the moment has arrived. We developed this colloquium by casting a wide net out to all the Professional Interest Group Chairs, and have assembled talks and demonstrations from general topics to specific applications.

Two online meetings were held, where Professional Interest Groups officers and those interested suggested speakers and discussed topics. Further discussions over email helped fill in the details to create this colloquium.

We will have a block of speakers for the diverse topics we present below, as well as panel discussions on how AI is and can be incorporated into various aspects of Horticulture, so that there is ample time for questions and discussion.

Title: Overview of the Colloquium

Speaker: Milt McGiffen, Cooperative Extension Specialist, Department of Botany and Plant Sciences,
University of California, Riverside, CA.

AI in Ornamentals

Title: FloraCount: An App for Rapid Assessment of Pollinator Attractiveness to Annuals and Perennial Plants.

Description: Customers are interested in buying annuals and perennials that support pollinators. Protocols for rapid assessment in flower trail evaluations are not available. We have developed a mobile app that can be used to analyze in real time the users’ observational data and quantitatively rank the relative utility of observed cultivars to pollinator communities. This app takes into account pollinator groups, relevant floral characteristics and landscape.

Presenter: Harland Patch
Assistant Research Professor
Department of Entomology
Penn State University
549 Ag Sciences & Industries Building
University Park, PA 16802

Title: Approach to Biodiversity Protection: Employing AI and IoT Systems for the
Containment of Box Tree Moth Proliferation.

Description: The box tree moth (BTM, Cydalima perspectalis) is an invasive pest first confirmed in Niagara County, New York in 2021. This invasive pest can significantly damage and potentially kill boxwood (Buxus species) plants if left unchecked. This presentation describes our advances in combining deep learning algorithms for enhanced computer vision with IoT-enabled smart traps, to facilitate the early detection and continuous monitoring of BTM populations and to protect the prevalent ornamental boxwood in U.S. landscapes.

Presenter: Yanqiu Yang (she/her)
Ph.D. Graduate Research Assistant
Department of Agricultural and Biological Engineering
Pennsylvania State University
3 Agricultural Engineering Building
University Park, PA 16802

Title: Landscapes from Words: The Future of Landscape Design with AI.

Description: The ongoing text-to-graphic artificial intelligence (AI) revolution has the potential to change the field of Landscape Architecture dramatically. The ability to produce original high-quality graphics, manipulate the viewer's perspective of images, and amend the rendering style through text inputs are significant advancements that will
inform new design process models. These changes can lead to expanded design exploration, improved accessibility for non-designers to contribute to creating visual concepts, enhanced ability to integrate data analysis and visualizations, and streamlined collaboration between clients and project stakeholders using a shared visual language. This talk focuses on two dimensions of change that may result from the rapid evolution of text-to-graphic AI, including (1) faster iterations and exploration of design options and (2) the advancement of methods that result in more inclusive and responsive design. In the classroom, students are just beginning to acknowledge the existence of text-to-graphic AI, which allows them to experiment with text-based design options that allow them to quickly visualize and explore a wide range of site program alternatives. Nevertheless, how do we manage the ethical and creative boundaries within an academic setting? In a research context, methods supporting rapid manipulation of both generated images and existing landscape photography represent advances that allow for greater collaboration surrounding landscape design decisions (Incorporating resilience strategies, protecting vernacular landscape elements that support a sense of place, or representing new design proposals that modify the landscape). These approaches allow stakeholders to gain remarkable advances in influencing the design process through shared visualization development. However, as with any emerging technology, practitioners, educators, and researchers need to respond to the challenges presented by text-to-graphic AI by developing and testing new design process models and public engagement techniques that can improve landscape decision-making and streamline collaboration.

Presenter: Aaron Thompson
Assistant Professor
Department of Horticulture and Landscape Architecture
Purdue University
625 Ag Mall Drive
West Lafayette, IN 47906

Title: Developing Guidelines for Extension’s Use of ChatGPT and Other Generative AI
Tools.

Description: A new technological era marked by the advent of Artificial Intelligence (AI), particularly generative AI and Large Language Models (LLMs) like ChatGPT has necessitated the need to navigate this domain with a compass of ethicality, safety, and effectiveness. Penn State’s experience developing guidelines for Extension’s use of
generative AI tools which will be shared and discussed.

Presenter: Michael Masiuk
Assistant Director – Horticulture Programs
Penn State Extension
342 Agricultural Administration Building
University Park, PA 16802

Panel: 30 minute panel with the above speakers, to allow time for Q&A and discussion.

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.