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

Genome-wide Association Study and Genome Prediction of Verticillium Wilt Resistance in Spinach - Kenani Chiwina
Spinach Seed for Grain Consumption: Feasibility and Potential for Genetic Improvement - Carlos Avila
Progress and Insights Into Downy Mildew Resistance Mapping Efforts in Spinach - Gehendra Bhattarai
Screening Baby Leaf Salad Greens for Downy Mildew Resistance - Shunping Ding
Detection of Novel Lettuce Fusarium Wilt Pathogenic Variants in California - Santosh Nayak
Unraveling Gene Regulation on the Interaction of Lettuce (Lactuca sativa L.) and Xanthomonas hortorum pv. vitians Causal Agent of Bacterial Leaf Spot. - Byron Manzanero
Exploring Physiological Traits as Predictors of Heat Content in Chile Peppers (Capsicum annuum L.) - Muhammad Ibrar Khan

Verticillium wilt, caused by Verticillium dahliae Kleb., poses a significant threat to spinach (Spinacia oleracea L.) production, necessitating genetic resistance as the primary defense against this disease. This study conducted a comprehensive genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to Verticillium wilt resistance in spinach and to evaluate genomic prediction for disease resistance. GWAS utilized a panel of 98 spinach germplasm accessions and 20,742 SNPs obtained from whole-genome resequencing. Various statistical models, including GLM, MLM, FarmCPU, and BLINK, were employed using the GAPIT 3 tool for analysis. Two quantitative trait loci (QTL) regions on chromosome 6 were found to be significantly associated with Verticillium wilt resistance. Specifically, SNP SOVchr6_29382746 at 29,382,746 bp and three SNPs (SOVchr6_86904401, SOVchr6_86906249, and SOVchr6_86906255) at 86,904,401 bp and 86,906,249 bp, respectively, demonstrated notable associations with disease resistance. Genomic prediction exhibited high accuracy, with a prediction ability (GA) represented by an r value of 0.95 for the panel. The identified SNP markers, along with the high prediction ability, offer valuable tools for breeders to select Verticillium wilt-resistant spinach plants and lines through molecular breeding, incorporating marker-assisted selection (MAS) and genomic selection (GS) strategies.

Spinach production is constantly challenged by endemic diseases that significantly reduce producers’ income. Even when resistant cultivars and cultural practices are used, mild disease damage can happen, negatively affecting quality and therefore reducing its commercial value. In contrast, under those conditions, spinach could still produce seed for grain with valuable nutritional content that can fetch premium prices for the gluten-free niche markets. This project evaluated grain production as an additional source of income by assessing yield potential, nutritional quality, and economic feasibility and potential for improvement. A total of ~200 USDA-NPGS accessions were evaluated for GWAS. For all nineteen amino acids evaluated, a wide range in content was observed. E.g. aspartic acid population mean was 106.5 nmol/g with a minimum of 36.2 nmol/g and a maximum of 353.9 nmol/g. Similar results were observed for all eight minerals evaluated. E.g. K population mean was 9,998.1 mg/kg with a minimum of 3,227 mg/kg and a maximum of 24,770 mg/Kg. High diversity can be used to improve nutritional content in spinach seed. Several SNP markers associated with amino acid and mineral content were identified in more than one nutrient, indicating pleiotropic genetic control. Furthermore, protein digestibility tests indicate that spinach provides ~50% of all amino acids required in the diet as compared with Amaranth and Quinoa protein in grain that provided ~20% of all amino acid required. Therefore, indicating spinach grain has a higher nutritional content as compared with highly demanded Amaranth and Quinoa grains. Finally, a partial budgeting approach was used to assess the economic feasibility of producing spinach seeds for grain. The added costs totaled US$ 218.71/ac, including custom harvesting (US$ 24/ac), an additional application of fertilizers (US$ 17.36/ac) and fungicide (US$ 62.54/ac), extra irrigation costs (US$ 60.63), and US$ 54.18/ac in associated interest on production expenses. The break-even price of seeds was estimated to be equal to US$ 0.20/lb when the average experimental yield was considered (i.e., 1,089lbs/ac). Producing seed for grain could expand the farmer portfolio, increase farmed acreage, and fringe products.

Spinach (Spinacia oleracea) is a popular leafy vegetable crop in the US, particularly for the fresh market baby leaf spinach. However, downy mildew (DM), caused by the obligate oomycete Peronospora effusa, poses a significant challenge to spinach cultivation in California and Arizona as it reduces the quality and yield of spinach. This is particularly concerning given that the two production areas contribute over 85% of the total fresh market spinach in the US. The emergence of new races of P. effusa, with nineteen races reported and fourteen identified in the last two decades, presents a persistent threat as new races and variant isolates can overcome the existing resistance in commercially deployed cultivars. Furthermore, over 50% of the spinach market is organic production, so utilizing host genetic resistance is a crucial disease management strategy. To combat this challenge, we conducted screenings of germplasm, cultivars, and multi-parent progeny populations in greenhouse conditions to identify resistant sources and genomic regions associated with resistance to multiple races of P. effusa (specifically race 5, 13, and 16). The spinach population panel was sequenced utilizing genotyping by sequencing (GBS), low coverage resequencing, and 10x coverage whole genome resequencing (WGR) to generate single nucleotide polymorphisms (SNP) markers. Subsequently, genetic analysis was performed using disease phenotype response data obtained and SNP markers for the identification of resistance-associated SNP markers and candidate resistance genes. The molecular analysis and mapping efforts have yielded valuable insights into the basis of downy mildew resistance in spinach, providing essential molecular tools to facilitate breeding for disease resistance. This work will summarize the updated findings from these efforts. This work will enhance our understanding of resistance mechanisms, which will contribute to developing more effective breeding strategies, increasing selection gains and breeding efficiency in spinach.

Downy mildew presents major challenges to baby leaf salad greens production in California. Baby kale (Brassica oleracea) particularly holds substantial economic value in the region with a crop value of over $12 million in 2022. Downy mildew, caused by the oomycete pathogen Hyaloperonospora brassicae, infects baby kale resulting in leaf chlorosis, necrosis, and sporulation, rendering affected leaves unmarketable. Resistant varieties offer an effective solution, reducing the need for pesticides and promoting sustainable disease management in baby kale production. This research aims to screen baby kale plant materials (accessions) for resistance to downy mildew isolates from across California. Initially, 212 baby kale accessions were evaluated for resistance using a downy mildew isolate from Gilroy, CA. Plants were inoculated with downy mildew spores and incubated in high-humidity conditions before being evaluated for disease symptoms. The initial screening indicated an average disease severity of 31%. From this screening, 50 accessions showing the lowest disease severity were further screened against seven additional downy mildew isolates. Among the subset of 50 accessions, disease severities ranged from 0.1% to 7.6%. Notably, nine accessions consistently exhibited a disease severity of 0%, and 17 accessions maintained disease severities of 0.1% or 0.2% across all seven isolates, making an elite secondary subset of accessions. Ongoing research includes replication trials with a secondary subset of accessions and the two most virulent and weak downy mildew isolates. This research will identify resistant baby kale varieties, providing valuable insights for breeders and improving downy mildew management practices in kale production systems.

Fusarium wilt (FW), caused by the soilborne fungus Fusarium oxysporum f.sp. lactucae (FOL), is an economically important disease of lettuce (Lactuca sativa L.). Four pathogenic races of FOL have been reported, though only race 1 is known to exist in the United States. Recently, California coastal lettuce growers have experienced changes in the severity and incidence of FW. Some race 1-resistant cultivars have exhibited susceptibility, whereas some susceptible cultivars have displayed a reduction in disease severity. In order to determine whether such changes in disease patterns are responses to potentially novel variants, we collected FW symptomatic plant samples from commercial fields in Salinas Valley and Santa Maria, recovered the fungus, and conducted a series of pathogenicity tests in controlled conditions over two years (2022 and 2023) using a standard set of FOL race differentials. Pathogenicity tests revealed two new FOL variants, Fol621s and 916, that elicited novel disease reaction patterns on the standard differentials which have never been reported in the United States or other parts of the world. Isolate 916 incited severe FW on race 1-resistant ‘Costa Rica No. 4’, whereas Fol621s was less virulent on race 1-suceptible ‘Banchu Red Fire’. This study provides valuable information critical for the development of FW management strategies, including broad-spectrum resistance breeding efforts against multiple FOL races and novel variants.

Bacterial leaf spot (BLS) of lettuce is a sporadic and destructive foliar disease that poses an economic threat to farmers, particularly those within Florida due to the subtropical environmental conditions. The disease is caused by the bacteria Xanthomonas hortorum pv. vitians (Xhv), which has three races. There are no chemical interventions that can effectively control this pathogen, creating a significant challenge for farmers to manage BLS. Additionally, most commercial lettuce cultivars are susceptible to BLS, emphasizing the need to improve host resistance. Resistance to Xhv race-1 has been identified in heirloom lettuce PI 358001-1 and ‘La Brillante’, and PI 667690. To facilitate and accelerate modern plant breeding techniques and the introgression of resistance into new cultivars, the identification of resistance genes is crucial. However, a detailed description on how these genes is regulated in the lettuce genome remains unknown. To aid in the understanding of the interaction between lettuce and Xhv, a gene expression study was conducted. A total of 180 plants each of La Brillante (R), PI 358001-1 (R), PI 667690 (R), and Okeechobee (S) were grown in laboratory conditions for 21 days. Half of the plants were mock inoculated with buffer, and the remaining plants were inoculated with Xhv race-1 isolate L7. Leaf samples were collected at 24-, 72-, and 144-hours post-inoculation, and RNA was extracted for sequencing using the Illumina NovaSeq 6000 platform. The analysis of differentially expressed genes and their associated pathways revealed distinct reactions upon interaction with Xhv. Additionally, similar reactions were observed in other crops and their respective Xanthomonas pathovars, such as the upregulation of peroxidases, chitinases, and proteases, were observed between inoculated and mock-inoculated plants, such response was time point dependent. Primers will be designed and validated for these candidate genes using qPCR with additional time points to confirm their expression across key plant development stages. These findings provide valuable insights into the molecular resistance of lettuce to BLS, unlocking new opportunities for molecular breeding techniques, identification of chemical compounds within the plant that control BLS, and the development of new resistant cultivars. This knowledge will benefit not only the UF/IFAS lettuce breeding program, but also be disseminated to other research groups working to breed BLS-resistant lettuce cultivars.

Chile peppers (C. annuum L.) are valued for their capsaicinoid content, which contributes to their pungency (heat) and has various health benefits, including anti-inflammatory and anti-cancer properties. Assessing photosynthetic efficiency through the LICOR-600 porometer/fluorometer (https://www.licor.com/env/products/LI-600/) provides insights into the physiological vigor of the plants. This study employs a comprehensive suite of machine learning models to investigate the correlation between photosynthetic efficiency (stomatal conductance and chlorophyll a fluorescence) and Scoville Heat Units (SHU) to predict the capsaicinoid content within 20 chile pepper varieties. Photosynthetic data were collected at two sites, Fabian Garcia Science Center and Leyendecker Plant Science Research Center, Las Cruces, NM, with readings taken from three different leaves of each of five plants per genotype. Capsaicinoid levels were quantified using High-Performance Liquid Chromatography (HPLC) for each variety. Correlation and principal component analyses (PCA) were implemented to discern the primary influencers on capsaicinoid production. Five predictive models were explored: Decision trees, Random forests, Ridge regression, LASSO Regression, and Support Vector Regression. Each model was applied to predict both total SHU values and categorical SHU labels (mild, hot, very hot). Among these, the decision tree model was the most superior, achieving an R² of 0.77. Initial findings indicate notable variability in photosynthetic activity and capsaicinoid concentrations across the varieties, suggesting a significant but complex relationship that may guide future genetic improvements. The challenges in modeling can be attributed to data collection constraints. Additionally, uniform growing conditions across all test plants might have limited the variability necessary for more definitive model differentiation. This analysis not only advances our understanding of the physiological and genetic factors affecting capsaicinoid content but also underscores the complexities of modeling agricultural traits under consistent environmental conditions. Future research should consider more frequent data collection and the introduction of environmental stressors to better capture the dynamics influencing capsaicinoid production in chile peppers. Key word: High-Performance Liquid Chromatography, Scoville heat unit, photosynthetic efficiency

Improved postharvest storage is a major target for vegetable-crop production. Nutritional contents and flavor are traits highly affected from harvesting to final consumption. Several reports have demonstrated that these traits are strong driving factors impacting consumers’ decisions and preferences when purchasing food. Therefore, these are economically important traits related to strong commercialization potential and improved market value. Assessing the potential variation in post-harvest shelf life among vegetable crops will be critical to identify parental lines that can be used in breeding programs to improve these traits and their effect on the quality of produce. Additionally, investigating the genetic mechanisms underlying post-harvest shelf life in horticultural crops is critical. This will result in the development of molecular breeding tools associated with improving shelf life, which will accelerate breeding. This interest group seeks to provide case studies from experts worldwide who have worked on breeding for nutritional contents, flavor, and post-harvest shelf life in vegetables.

Coordinator(s)

• Carlos Avila, Texas A&M AgriLife Research, Weslaco, TX, United States

Moderator(s)

• Dennis Nicuh Lozada, New Mexico State University, Plant and Environmental Sciences, Las Cruces, NM, United States
• Devi Kandel, Langston University, United States

Speaker/Participant(s)

• Carmit Ziv, Institute of Postharvest and Food Science, ARO, Volcani Institute, Israel
  Breeding for improved postharvest quality of peppers during cold storage (15 mins)
  Summary: Dr. Ziv's research program studies postharvest disease control of fruity vegetables by developing environment-friendly treatments to control postharvest fungal rot, understanding resistance mechanisms of phytopathogenic fungi to cold storage, uncovering the role of lipids in determining the interactions between fruits and pathogenic fungi during storage.
• Carlos Avila, Texas A&M AgriLife Research, Weslaco, TX, United States
  Lack of locule gel increases post-harvest shelf-life and quality in tomato (15 mins)
  Summary: Dr. Avila's research program is focused on the development of tomato and spinach cultivars adapted to Texas conditions. Research work includes the characterization of plant a/biotic stress and vegetable quality trait regulation using molecular, physiological, and biochemical approaches to develop applied strategies to improve breeding efficiency and ultimately crop resistance and quality. Current efforts include the development of firm long shelf-life tomato cultivars with improved flavor and nutritional content.
• Bhimu Patil, Texas A&M University, Vegetable and Fruit Improvement Center, College Station, Texas, United States
  Post-harvest shelf life and nutritional quality in horticultural crops (15 mins)
  Summary: Dr. Patil has been actively involved in both research and educational activities related to global level ‘Foods for Health’. His research, in collaboration with trans-disciplinary scientists, related to bioactive-derived assays led to isolation and characterization of certain bioactive compounds in citrus and turmeric and other vegetables. His research is also focused on pre and postharvest effects on bioactive compounds in citrus, onion and recently his work is focused on other vegetables and fruits.
• Alexander Goldshmidt, Institute of Plant Sciences, ARO, Volcani Institute, Israel
  Exploring the Role of CLASS-II KNOX mediated Ripening Pathways for the Discovery of Novel Genetic Approaches to Extend Fruit Shelf Life (15 mins)
  Summary: Dr. Goldshmidt research is focused on investigation of the genetic factors and networks controlling development of the pericarp tissues in fruits of Solanaceae crops tomato and pepper. His lab seek to use their research to develop novel genetic solutions and tools to extend fruit's shelf life and improve its consumer attractiveness and nutritional values.
• Barbara Blanco Ulate, UC Davis, United States
  Control of fruit ripening, improvement of fruit quality, and fruit-pathogen interactions. (15 mins)
  Summary: Dr. Blanco-Ulate's research program integrate systems biology approaches with biochemical and physiological analyses to study fruit development and quality traits, and to establish a novel framework for the early detection and efficient management of fruit diseases.

Genome-wide Association Study and Genome Prediction of Bolting Trait in Spinach - Hanan Mohammedsaeed Alkabkabi
Towards the Improvement of Lettuce for Heat Tolerance Adapted to Controlled Environment Agriculture - German Sandoya Miranda
Root Phenotyping in Chile Pepper: Key Steps and Challenges with the RhizoVision Explorer - Ehtisham Khokhar
Towards Mechanical Harvest: Leveraging Genomic Selection to Increase Fruit Firmness in Fresh Market Tomato - Jessica Chitwood-Brown
Genome-wide Association Study and Genome Prediction of Tallness Trait in Spinach - Ibtisam Alatawi
Capitalizing on the Global Capsicum Core Collection to Advance Pepper Breeding - Derek Barchenger
Private-public Partnership for Sustainable Cucurbit Breeding and Production in Asia - Narinder Dhillon

Spinach (Spinacia oleracea L.) stands as a globally significant vegetable celebrated for its rich array of nutritional and health-promoting compounds. Bolting, a crucial trait in spinach cultivation across diverse seasons and regions, is heavily influenced by photoperiod sensitivity. The premature induction of bolting in spinach due to extended daylight exposure can render the plant unsuitable for market. This study aimed to conduct a comprehensive genome-wide association study (GWAS) to pinpoint single nucleotide polymorphism (SNP) markers associated with late bolting in spinach and to perform genomic prediction for this trait. GWAS was executed on a panel of 295 USDA spinach germplasm accessions, utilizing 16,563 SNPs derived from whole-genome resequencing. Various statistical models, including GLM, MLM, FarmCPU, and BLINK, were deployed in the analysis using the GAPIT 3 tool. A significant quantitative trait locus (QTL) region on chromosome 6 was identified, with three SNP markers — SOVchr6_13545609, SOVchr6_13545882, and SOVchr6_13545887 — located between 13,545,609 bp and 13,545,887 bp, demonstrating robust associations with late bolting. Additionally, the gene SOV6g004620, encoding a TTF-type domain-containing protein and situated at 13,566,721 bp to 13,567,164 bp on chromosome 6, emerged as a potential candidate for regulating bolting. Genomic prediction exhibited a high prediction ability (GA) with an r value of 0.85. The identified SNP markers and GA metrics present valuable tools for breeders to selectively cultivate late-bolting spinach plants and lines through marker-assisted selection (MAS) and genomic selection (GS), thereby facilitating enhanced spinach breeding endeavors.

Lettuce (Lactuca sativa L.) is one of the top ten most consumed vegetables in the United States. In Controlled Environment Agriculture (CEA), lettuce is one of the most cultivated vegetables. The crop yield is severely affected by heatwaves during production. As a result of severe warmer temperatures, lettuce develops physiological disorders such as bolting and tipburn and consequently less marketability and yield. In order to reduce cooling costs and extend the growing season of lettuce crops, breeding heat-tolerant germplasm is imperative. In this research our aim was to confirm heat tolerance in lettuce identified in fields when grown in hydroponics. Initial screenings were conducted at the North Florida Research and Education Center- Suwannee Valley. One hundred and four lettuce accessions from four morphological types (Boston, Latin, leaf, and romaine) were planted in a Nutrient Film Technique (NFT) hydroponic system in a passively vented greenhouse in two experiments. Germplasm included commercial cultivars, plant introductions, legacy cultivars, and breeding lines from the University of Florida /Institute for Food and Agricultural Sciences (UF/IFAS) Lettuce Breeding Program. Data was collected on head weight and related characteristics including marketability, head height, density and width, and core length. Presence of disorders such as bolting, chlorosis and tipburn were also registered as indicators on the negative effects of warmer temperatures. Germplasm with tolerance to warmer temperatures were identified within each of the lettuce types used on this research. This germplasm had an acceptable head weight with less plants that bolted and insignificant presence of tipburn. Several of the germplasm considered heat tolerant are commercial cultivars currently used by the industry in CEA. Similarly, breeding lines from the UF/IFAS Lettuce Breeding Program showed better tolerance than commercial germplasm and are candidates for breeding and genetics studies to decipher mechanisms of heat tolerance in lettuce for this specific environment. Mapping and breeding populations will soon be developed to first study the genetics of tolerance to warmer temperatures and to select germplasm in this specific environment. While tolerant germplasm will aid to decrease cost production for CEA, additional management strategies should be optimized to decrease even further cost of production for growers.

Genetic studies of root architecture provide valuable insight into the overall yield potential of chile pepper (Capsicum annuum L.) under various biotic and abiotic conditions. Phytophthora root rot , caused by soil born pathogen Phytophthora capsici, is one of the most destructive diseases of chile pepper that incur huge losses under severe infection. Rotting of the roots and crown are the primary symptoms with lesions on stem, wilting, and necrosis leading to the plant death. RhizoVision Explorer is a high throughput phenotyping tool that facilitates precise and in-depth phenotyping of root architecture. In this study, four chile pepper cultivars were planted in three replications under greenhouse conditions. A virulent isolate ‘6347’ was used to inoculate the cultivars. At maturity, shoots were removed, and roots were thoroughly washed to prepare them for scanning. A flatbed scanner was used where a transparent plastic flat allowing roots to be submerged in the water was set up to proceed with scanning and analysis using the RhizoVision Explorer. Analysis of variance (ANOVA) demonstrated significant differences between the treated and control groups coupled with strong positive correlation (r > 0.90; P < 0.001) for maximum number of roots (MNR), number of root tips (NRT), total root length (TRL), depth (DPT), maximum width (MAXW), and width-to-depth ratio (WDR). Preliminary results provided insights into root architecture under P. capsici infection and the optimization of key procedures such as root washing and scanning. Overall, the efficiency of root phenotyping using the RhizoVision Explorer under pathogen infection could be improved by modifying specific steps related to the washing and processing of chile pepper samples. Keywords: High throughput phenotyping, Phytophthora blight, root architecture

Mechanical harvesting could help address the challenges related to the cost and availability of labor experienced by Florida’s fresh market tomato industry. However, tomato fruit are very susceptible to bruising, which is likely to be exacerbated by mechanical harvest. Previous studies have found that fruit firmness plays an important role in cultivar resistance against internal bruising. The UF/IFAS tomato breeding program has worked to develop tomato lines with traits important for mechanical harvest, including a compact growth habit (CGH) and increased fruit firmness. To investigate the inheritance and genetic architecture of fruit firmness among CGH lines in the program, bi-parental populations were developed from firm and soft inbred parents. Genome wide association analysis identified multiple significant fruit firmness quantitative trait loci (QTLs) with minor effects, underscoring the quantitative nature of the fruit firmness trait among the population studied. The dissection of fruit firmness variance components revealed mostly additive variance components. Genomic selection (GS) models were successfully trained to predict fruit firmness, demonstrating the viability of GS integration into the UF Tomato Breeding program. Significant gains in prediction accuracy and computational efficiency were achieved through model parameters fine-tuning such as training population size and marker density optimization, and modeling of significant QTLs as fixed effects. This work demonstrates that significant fruit firmness variability exists in the UF/IFAS tomato breeding program germplasm and can be selected for to develop firm-fruited CGH tomatoes intended for mechanical harvest. Furthermore, the successful training of fruit firmness GS models will aid in the efficient development of CGH fresh market tomato cultivars intended for mechanical harvest. The training of multi-trait and multi-environment genomic selection models to leverage the variance-covariance information between traits and between testing environments may result in increased prediction accuracies and needs to be explored.

Spinach (Spinacia oleracea L.) is a highly nutritious leafy green known for its abundance of health-promoting components. Plant height (tallness), particularly relevant for efficient machine harvesting, is a critical trait of interest in spinach cultivation. This study aimed to conduct a genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers associated with tallness in spinach and to perform genomic prediction for this trait. GWAS was conducted on a panel of 307 USDA spinach germplasm accessions, utilizing 15,058 SNPs derived from whole-genome resequencing. Various statistical models, including GLM, MLM, FarmCPU, and BLINK, were employed in the analysis using the GAPIT 3 tool. Significant quantitative trait loci (QTL) were identified on chromosome 2, along with two QTL on chromosome 6. Specifically, the SNP marker SOVchr4_38323167 at 38,323,167 bp on chromosome 4, and two SNPs, SSOVchr6_8139833 and SOVchr6_91175684 at 8,139,833 bp and 91,175,684 bp respectively on chromosome 6, exhibited robust associations with tallness. Genomic prediction demonstrated high accuracy, with a prediction ability (GA) represented by an r value of 0.71 in the panel. The identified SNP markers and genomic prediction metrics provide valuable tools for breeders to select spinach plants and lines with desired tallness traits through marker-assisted selection (MAS) and genomic selection (GS), thereby enhancing spinach breeding efforts.

Unlike other crops, access to genetic and genomic tools enabling more efficient breeding is limited in pepper. The majority of the research in pepper is based on analyzing traits in biparental populations, and in addition, limited access to pathogen strains or races reduces the wide-scale applicability of the developed molecular markers across populations and breeding programs. In contrast to research in bi-parental populations, genome-wide association studies utilizes the broad range of genetic diversity present in natural populations, including historical recombination events, which allows for the identification of more alleles potentially associated with the trait. A well-designed core collection captures the diversity that is present in an entire germplasm collection, which is crucial for preserving unique alleles and traits and facilitates more efficient phenotyping and GWAS. A core collection of 423 accessions was assembled representing the genetic diversity present in the G2P-SOL global collection of 10,038 wild and cultivated Capsicum accessions from 10 major genebanks .The G2P-SOL Capsicum core collection has been phenotyped for resistance to anthracnose, bacterial wilt, phytophthora blight, and Chili leaf curl virus, as well as for heat stress component traits in several locations in Asia. Genome wide association studies have revealed multiple significant loci associated with the individual traits. These loci are being utilized in the breeding program to more efficiently develop and release cultivars.

The global cucurbit breeding program of the World Vegetable Center (WorldVeg) focuses on tropical pumpkin (Cucurbita moschata) and four gourds: bitter gourd (Momordica charantia), ridge gourd (Luffa acutangula), sponge gourd (Luffa aegyptica = cylindrica) and bottle gourd (Lagenaria siceraria). This breeding program uses the diversity of hitherto unexploited landrace collections to develop high yielding and disease resistant lines and F1 hybrids with a range of fruit types suitable for various market segments. The program supports breeding research of partners from national agricultural research and extension systems organizations and the private seed industry to develop better cucurbit cultivars for the benefit of stakeholders along the vegetable value chain. To facilitate these partnerships, the WorldVeg cucurbit team displays improved cucurbit lines and F1 hybrids during the cucurbits open field days at the WorldVeg East and Southeast Asia Research and Training Station, located on the campus of the Kasetsart University in Kamphaeng Saen, Thailand. This annual event attracts breeders, pathologists, product development managers, marketing and sales managers, R

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.

The Power of Breeding and Genetics in Controlled Environment Horticulture - Krishna Bhattarai
Novel Summer Squash: Breeding Tromboncino Types for U.S. Markets - James Myers
Mapping QTL for Bacterial wilt resistance and plant height in Tomatoes - Dilip Panthee
Effects of Prolonged Photoperiod on Chile Pepper Plant Architecture and Growth Habit - Shahab Nourbakhsh
Seasonal Lettuce Germplasm Trials in Northeast Florida Hydroponics - Evelyn Fletcher
Marker Development for Cadmium Accumulation in Spinach - Danyelle Forte

Controlled environment (CE) horticulture production has shown its potential to cope with the impact of climate change such as rising temperatures and declining water availability. Drives like “locally grown”, and “food miles reduction” favor CE-based food production which represents a $50 billion market for fresh, local, and sustainable food. CE production systems use advanced technology for climate control and mechanized growing practices for which infrastructure and software development have taken a good start. Contrastingly, the breeding and development of plants designed to best perform in CEs to reduce energy usage, allow automation, and increase profits are just beginning. The US CE producers can benefit from the breeding and development of new cultivars with modified stature that offer high-density planting and shortened crop cycles, ease in maintaining and harvesting, and allow automation. Utilization of plant genetics to breed for plant statures will increase crop diversity in CEs. Additionally, discovering new genetics in plant germplasms to enhance crop quality for nutrition, flavor, taste, color, and texture through breeding can meet consumer needs for fresh, high-quality, nutritious, and sustainably produced food. Several other opportunities exist where leveraging genetics to breed new crops that produce nutraceuticals, biofuel, macro and micronutrients, and bioactive compounds can sustain the CE horticulture industry, feed the increasing population, improve health, and cope with climate change.

Cucurbitaceae family squash and pumpkins are all New World domesticates from different parts of the Americas. While many types are eaten as winter squash at full maturity, others – termed summer squash – are used as vegetable where the immature fruit is eaten. The summer squash we are most familiar with belong to the species Cucurbita pepo. The immature fruit of C. maxima and C. moschata are sometimes used as summer squash and a few land race types have been developed mainly for summer squash use. ‘Tromboncino’ (also called Trombetta or Zucchetta Rampicante), is one such C. moschata summer squash from the Ligura region of Italy. It is most closely related to the butternut winter squashes. Originally domesticated in the tropical lowlands of Middle America, it is more tolerant of high temperatures, humidity and pest and diseases. Tromboncino is essentially a butternut squash with an extended neck that has been adapted to use as an immature vegetable but can also be used as a winter squash. The heritage varieties of Tromboncino are long-vined with prolific fruit production and produce few seeds. The seeds are found in a bulb at the end of the fruit, leaving a long seedless neck for culinary preparation. It has a firmer, meatier texture and a flavor profile that is more similar to a mature butternut squash. Tromboncinos are at their highest quality when used at 6-12" long, but they can be eaten at later stages until fully mature. The main breeding objective of the OSU vegetable breeding program was to develop a tromboncino type with better adaptation to the cool summers of Western Oregon, shift plant architecture to a bush plant habit while retaining prolificacy, and shorten fruit length for fresh market production. Another objective was to combine the tromboncino type with skin colors other than the traditional tan color of the heritage variety. We have been able to accomplish most objectives although the plant architecture is not yet comparable to the bush habit of C. pepo summer squash. Some types have dark green as well as yellow skin colors (conditioned by the precocious yellow gene). Two advanced lines are in the process of being released.

Bacterial wilt (BW) of tomatoes, caused by Ralstonia solanacearum, is a devastating dis-ease that results in large annual yield losses worldwide. Management of BW of toma-toes is difficult due to the soil-borne nature of the pathogen. One of the best ways to mitigate the losses is through breeding for disease resistance. Moreover, plant height (PH) is a crucial element related to plant architecture which determines nutrient management and mechanical harvesting in tomatoes. An intra-specific F2 segregating population (NC 11212) of tomatoes was developed by crossing NC 84173 (tall, BW susceptible) x CLN1466EA (short, BW resistant). We performed quantitative trait loci (QTL) mapping using single nucleotide polymorphic (SNP) markers and the NC 11212 F2 segregating population. The QTL analysis for BW resistance revealed a total of three QTLs on chromosomes 1, 2, and 3, explaining phenotypic variation (R2) ranging from 3.6% to 14.9%. Whereas, QTL analysis for PH also detected three QTLs on chromo-somes 1, 8, and 11 explaining R2 ranging from 7.1% to 11%. This work thus provides information to improve BW resistance and plant architecture-related traits in toma-toes.

Evaluation of Vegetable Soybean Breeding Lines for Yield and Related Traits - GuoLiang Jiang
Could Broccoli's Ancestral Lineage Hold the Key to Increased Fatty Acid Content? - Alaina Kleine
Characterization of A Novel Locus for Fruit Flavor Aroma in Tomato - Qian Feng
Identification and Validation of Novel Resistance Loci to Fusarium oxysporum f.sp. lycopersici Race 3 in Tomatoes - Samuel Ipinyomi
Enhancing Fusarium Wilt Race 2-Resistance and Brix Content in Watermelon through Genomic Selection - Anju Biswas
Introgressing QTL from a Wild Relative to Improve Gummy Stem Blight Resistance in Watermelon - Cecilia McGregor
Genome-wide association study reveals potential loci for powdery mildew resistance in the USDA core collection of Cucurbita pepo - Prerna Sabharwal
BreedwithBIMS (Breeding Information Management System) for Crop Breeders - Ksenija Gasic

This experiment sought to examine the effects of prolonged photoperiod and modified temperature and humidity in chile peppers, aiming to develop a protocol to accelerate their growth and enhance breeding efficiency. Four genotypes from three Capsicum species (C. annuum - Chimayo, Early Jalapeno; C. chinense - Orange Habanero; Chiltepin - C. annuum var. glabriusculum) were planted in two randomized flat trays per entry using SunGro propagation soil. After reaching the 2-3 leaf stage, they were transplanted into 8” pots, incorporating sterilized and LM-AP soil mixtures. The experimental population was grown in an improvised growth chamber with an average temperature of 25°C and humidity of 60% and exposed to a 20-hour daily cycle of 450 nm full spectrum LED grow lights and 730 nm Far Red LED grow lights and 4 hours of darkness. The control group grew in normal greenhouse conditions, exposed to normal daylight intensity and duration and an average temperature of 21°C and humidity of 40%. Weekly data recordings included plant growth measurements of plant height and leaf count. Basal branches were counted approximately 12 weeks after planting, and leaf widths were recorded 14 weeks after transplanting. Number of flowers and fruits were also recorded at 14 weeks after transplanting. Data were analyzed using RStudio, and Tukey HSD was used to detect differences between treatments and among genotypes. In terms of plant height, all experimental plants demonstrated a significant increase compared to the control group, both in absolute amounts and in rates, especially later in the growth stage. The leaf numbers in experimental plants were significantly lower than the control group, except for Orange Habanero, which showed no significant difference. Early Jalapeno, in both treatments, exhibited no significant difference in basal branches. In contrast, the remaining experimental plants displayed fewer or no basal branches compared to the control group. All experimental plants exhibited significantly wider leaves in comparison with the control group. While most experimental plants started flowering earlier, no significant differences were observed between numbers of flowers and fruits. The faster growth rates observed hold the promise of accelerated progress and improved efficiency in breeding initiatives, offering a fundamental shift in the way we approach crop development. Additionally, fewer number of basal branches may have implications for machine harvestability, as fewer basal branches is considered a desirable trait for machine harvesting.

Vegetable soybean (Glycine max), also known as edamame, is a specialty soybean that is harvested at R6 growth stage. Vegetable soybean has steadily increased in acreage and market demand although it is relatively new to North America. It is of significance to develop new cultivars that are more adapted to local environment and crop management system to promote specialty crop production and meet the market requirements. In this study, 14 genotypes of vegetable soybean, including 10 breeding lines and 4 check cultivars, were evaluated during 2020-2023 for potential uses as edamame. There were significant differences among genotypes in both fresh pod and mature seed yields, agronomic and seed composition traits investigated. The year effects and genotype x year interactions were also significant in most cases. Fresh pod yield averaged 11,227.5 kg ha-1, ranging 9,800.1 – 13,154.3 kg ha-1, and mature seed yield averaged 2,814.7 kg ha-1, ranging 2,029.2 – 3,175.2 kg ha-1. The average 100-seed weight of 14 genotypes was 26.9 g, ranging 23.1 – 30.1 g. Maturity averaged 153.3 days after planting, ranging 147.1 – 159.5 days. On a dry weight basis, seed protein, oil and sucrose contents averaged 43.5%, 18.7% and 5.0%, respectively. The estimates of broad-sense heritability were medium to high (66.82 – 94.90%) for most of the traits, while the heritability estimates for fresh pod yield and duration from flowering to maturity were relatively low (23.44% and 42.29%). Several breeding lines exhibited good yield, larger seed size, higher contents of protein, oil, oleic acid and sulfur-containing amino acids, suggesting the potential of release and commercial production.

The Hastings Agricultural Extension Center adopted the lettuce variety trials in 2018 for the demonstration of alternative row crops. Within the Tri-County Agricultural Area (TCAA), the term "alternative" refers to any crops outside of the traditional rotations - potatoes and cabbage. While these crops are the staple of the community, the acreage has been reduced due to tight profit margins and competitiveness for chipping contracts. Lettuce, along with artichokes and pumpkins, have been one of the newly adopted commodities for North Florida. What initially began as field trials expanded into the controlled systems of protected agricultural and hydroponics. Three seasons of germplasm trials with 14 newly developed lines in the hydroponic towers were conducted in Hastings to evaluate their soilless potential. Under 20% shade, lettuce was grown in the Verti-Gro system with 40% perlite, 30% coconut coir and 30% peat moss. These trials were also home to many field tours for the community, and opportunities for local growers to witness and observe their growth habits. Data evaluations included marketability, timing (if observed) of bolting, tip burn, and head weights. Weights ranged from 0.10 - 0.85 kg, with Botrytis and Sclerotinia being the most common disease pest identified. Since the trials began, our lettuce acreage has increased from 15 to 100 in the county, including two organic growers and one conventional, and with opportunities for more research to benefit these diversified growers.

In the pursuit of agricultural productivity, generations of breeding have often prioritized yield-related traits, inadvertently leading to the loss of desirable genetic traits linked to nutritional content. This phenomenon, known as the genetic lag effect, has implications for human health, particularly concerning the availability of essential nutrients such as omega-3 fatty acids. As omega-3 fatty acids are crucial for various aspects of human health, including heart health, cognitive function, and hormone regulation, it is imperative to explore alternative sources beyond traditional fish-derived options. The demand for plant-based alternatives is rising due to dietary preferences and concerns over fish oil production, emphasizing the need to investigate alternative sources of omega-3 fatty acids. Broccoli, with its rising consumption and rich nutritional profile, presents a promising avenue for addressing this need. For humans, the ideal ratio of omega 6 to omega 3, is 1:1. Yet, the American diet offers an astonishing 30:1 ratio! Broccoli has a ratio of 1:3 ratio. This is comparable to fish ranging from 1:1 to 1:7. Despite its potential, most broccoli breeding programs have focused primarily on grower-oriented traits rather than those beneficial to human health. Thus, there is an opportunity to enhance the nutritional content of broccoli, particularly its omega-3 fatty acid profile, to offer greater health benefits to consumers. This study investigates the omega-3 fatty acid profiles of 35 lines, 9 elite and 26 landrace broccoli cultivars, to address the pressing need for nutrient-rich foods. Our research employs lipid extraction from various tissues of broccoli plants, including bouquets, stems, and leaves. The lipid sample is screened using Gas Chromatography-Mass Spectrometry (GC-MS) for precise quantification and identification of fatty acids. Preliminary results reveal significant variation in omega-3 fatty acid content, specifically levels of alpha-linolenic acid (ALA) among the broccoli lines studied, highlighting the potential for breeding programs to select and develop varieties with enhanced nutritional profiles. By prioritizing consumer-oriented traits in crop breeding, such as omega-3 fatty acid content, we aim to contribute to developing biofortified broccoli varieties that offer sustainable and health-promoting dietary options. This research underscores the importance of diversifying food sources and prioritizing human health outcomes in agricultural practices to address evolving dietary needs and promote overall well-being.

California is the largest spinach producing state in the USA, accounting for 75% of hectares planted. The major production area is the Salinas Valley, which is known to have geogenic cadmium soils. Spinach is a hyperaccumulator and its affinity for divalent cations, like zinc and iron, likely contributes to the accumulation of Cd. Cadmium has known adverse health effects in humans, so California’s Office of Environmental Health Hazard Assessment’s (OEHHA) set a limit of 4.1 ug Cd per day by consumption. Consequently, growers do not produce spinach on high cadmium soils, limiting their ability to rotate crops throughout the valley. Even so, a few fresh leaf market spinach samples with foliar concentrations of Cd above the limit have been reported.

Our long-range objective is to develop improved fresh market spinach germplasm that restricts Cd uptake while maintaining nutritional quality. We have observed phenotypic variation for foliar cadmium concentration in a wide diversity of spinach germplasm with over 500 accessions originating from 42 countries, showed that greenhouse evaluations in high Cd soil largely reflected phenotypic performance in the field, and developed populations segregating for Cd uptake. We have also developed a hydroponic system that reflects field and greenhouse Cd uptake, but that is more controlled and scalable. Our current objectives are to identify quantitative trait loci (QTL) in the spinach genome associated with Cd accumulation. We have developed a biparental mapping population for genetic mapping by crossing high and low individuals which was evaluated in hydroponics earlier this year and will be evaluated in field conditions this fall. Markers tagging major QTL loci will be developed into high-throughput KASP markers for routine use in breeding.

Tomato flavor has become an important trait for targeted crop improvement. Because of the historical emphasis on yield and other agronomically important traits, many modern tomato varieties have lost their rich flavor, leading to consumer dissatisfaction. While volatile compounds play an important role in defining the distinct tomato flavor, little is known about their biochemical pathways, making it difficult to build a desirable volatile profile. Identifying the genes involved in volatile production can help us better understand the biochemistry as well as accelerate the breeding process. This study focuses on two consumer-desired volatiles, 1-nitro-2-phenylethane and phenylacetaldehyde, and has mapped a novel QTL on chromosome 8 by combining results from linkage mapping and GWAS (genome-wide association study). A cluster of Amino Acid Decarboxylases (AADCs) were identified as the candidate genes underlying this QTL and a total of four SV haplotypes of the AADC cluster were found in the Varitome collection. Among these haplotypes, Type III was lost during domestication and is a likely beneficial allele to increase the concentrations of phenylacetaldehyde and 1-nitro-2-phenylethane in tomato fruits. Preliminary data of transgenic plants created by CRISPR/Cas9 suggested a positive involvement of this AADC locus in volatile production. Enzymatic analysis of the AADC proteins and incorporation of the beneficial allele into modern tomato varieties is in progress. The outcome of this study will provide breeders valuable tools to facilitate the selection process for better tomato flavor. Characterization of volatile pathways will also give us insights on plant secondary metabolite biosynthesis and the evolution history during adaption and domestication. This research is funded by NSF IOS 2151032.

Fusarium wilt disease caused by the soil-borne pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is a major threat in tomato-producing regions that can lead to acute yield losses. Host resistance as compared to other control strategies provides an effective and reliable means to contain the spread of the pathogen. Given that genes that confer resistance to all the three known Fol races are single dominant genes, there is a risk of resistance breakdown by the mutating pathogen. Furthermore, in the face of imminent race 4 emergence, building a quantitative and durable resistance shield by pyramiding novel resistant genes in commercial cultivars becomes pertinent. S. pennellii has been previously identified as a repository for resistant genes to Fol3 and recently, two novel loci mapped at chromosomes 3 and 10 were identified from two accessions- LA 1522 and LA 750 respectively using bulk segregant analysis QTL seq. Preliminary analysis was conducted to develop molecular markers for both chromosomes and validate their co-segregation with the region of introgression associated with resistance. We found co-segregating markers for resistance harbored by chromosome 3 and designated the locus as I8. This marker therefore constitutes additional genomic resources for marker-assisted selection of this trait. Although we found markers that co-segregate with resistance on chromosome 10, we provide initial evidence that this resistance is the same with the I6 locus previously identified on chromosome 10 and derived from LA 716 while complementary phenotypic screens showed partial penetrance of this locus. Together, these resistance loci (I6 and I8) could constitute a qualitative shield against the pathogen in commercial cultivars. Efforts are underway to fine map these loci and characterize them under field conditions and against other previously known races.

Complex traits in plants are influenced by many genes, each having a small impact. Using marker-assisted selection (MAS) alone is not sufficient to improve these traits in elite cultivars. Genomic selection (GS) is a promising breeding approach for enhancing complex traits like resistance to Fusarium oxysporum f. sp. niveum (Fon) race 2 and increasing sugar levels (brix content) in watermelon. In our study, we wanted to see how well GS can predict disease resistance and sugar levels in an interspecific citron melon (Citrullus amarus) by cultivated watermelon (Citrullus lanatus) population. We created an F2:3 population by crossing USVL252-FR2 (resistant to Fon race 2, low brix; C. amarus) with ‘Sugar Baby’ (susceptible to Fon race 2, high brix; C. lanatus). We tested disease resistance in a growth chamber and measured sugar levels in a field trial using a randomized complete block design of the F3 families. We resequenced the DNA of 150 F2 plants to identify genetic differences. Disease response was assessed 28 days after inoculation, and sugar levels were measured with a brix meter to gauge sweetness. To predict disease resistance, we used two genomic models - Random Forest and GBLUP - which we found to be effective in previous studies. We compared the performance of univariate models (looking at disease and sugar levels separately) and bivariate models (looking at disease and sugar levels together) to identify the best approach for selecting superior cultivars based on these traits. We assessed model performance using ten-fold cross-validation. Our goal is to focus on these important polygenic traits and select superior genotypes early in breeding to develop watermelon cultivars with improved disease resistance and high sugar content.

Watermelon (Citrullus lanatus) is an economically important horticultural crop known for its sweet red flesh and is a popular summer snack. The southeastern US is an important production region for watermelon, but the hot and humid weather is conducive for the development of fungal diseases. Gummy stem blight (GSB), caused by three species of Stagonosporopsis; S. citrulli, S. caricae and S. cucurbitacearum, is an important disease that can cause severe yield losses worldwide under these favorable conditions. Currently, no resistant cultivars are available for this disease and management depends on preventative fungicide spay programs. Host resistance has been previously identified in C. amarus, an inedible crop wild relative of watermelon. However, different Stagonosporopsis spp. isolates elicit different responses in different resistant host genotypes which complicated resistance breeding. To address these issues, we (i) developed a point-of-care assay that can differentiate S. citrulli from the other two species and (ii) introgressed resistance QTL from wild C. amarus into cultivated watermelon. A dipstick-based DNA extraction method was coupled with an S. citrulli specific loop-mediated isothermal amplification (LAMP) assay to detect as little as 1 pg of DNA with real time fluorescence quantification and endpoint colorimetric detection formats. To address host resistance, we developed high throughput KASP markers spanning the QTL regions, and used marker assisted backcrossing to introgress QTL into the cultivar Crimson Sweet. Eight BC2F3 intogression lines were evaluated in the field for resistance to GSB. Two of the lines showed high levels of resistance to GSB under field conditions. KASP assays were also developed for background selection for known domestication alleles to accelerate selection for fruit quality traits. The developed detection assays, KASP markers and introgression lines can contribute to accelerated breeding for host resistance and general breeding efforts for GSB in watermelon.

Summer squash (Cucurbita pepo) is a significant vegetable crop in the United States with an annual value exceeding $216 million. The production of summer squash is significantly hindered by powdery mildew (PM), a fungal disease caused by Podosphaera xanthii. Management of PM relies on costly and routine application of fungicides. Moderate resistance to PM (designated PM0) in C. okechobeensis is widely deployed in commercial summer squash cultivars. However, it is important to expand the repertoire of alleles against PM in squash to complement and reduce the risk of PM0 resistance breakdown. In the current study, the USDA core collection of C. pepo (n= 207) was evaluated for PM resistance in Florida (greenhouse), New York (greenhouse), and Michigan (field) using a randomized complete block design across three reps, each with five plants. ‘Success PM’ (carrying PM0) and ‘Early Prolific’ Straightneck cultivars were used as resistant and susceptible checks, respectively. Pathogen inoculum was provided through naturally infected plants. At the 6th true-leaf stage, symptom severity data were collected on a scale of 0-100% based on visible pathogen sporulation on the surface of ‘top 4th leaf’, ‘bottom 4th leaf’, ‘stem above 4th leaf’, ‘stem below 4th leaf’, and ‘whole plant’. Across locations, ‘Success PM’ and ‘Early Prolific’ were consistently tolerant and susceptible, respectively. On the other hand, wide phenotypic variation was observed across the C. pepo core collection with accession 189 showing resistance across locations. The multi-location phenotype data was combined with genome-resequencing data (4 million SNPs) for the core collection to conduct a genome-wide association study using three statistical models (MLM, FarmCPU, and Blink). GWAS analysis for the FL dataset revealed significant genomic loci associated with PM resistance for ‘top 4th leaf’ (Chr 11 and 20), ‘stem above 4th leaf’ (Chr 4, 14 and 16), and ‘whole plant’ (Chr 13, 15, 18 and 20). Resistance loci for ‘top 4th leaf’ and ‘whole plant’ co-located on Chr 20, suggesting potential linkage/ pleiotropy for the two traits. For NY, significant hits for PM resistance were detected for the ‘top 4th leaf’ (FarmCPU: Chr 2, 4, 7, 13 and 19; Blink: Chr 3, 4, 5 and 19) and ‘bottom 4th leaf’ (Chr 6, 14 and 19). However, no significant GWAS hits were observed using MI data. The significant loci detected in this study will be validated and deployed in marker-assisted selection to improve PM resistance in squash.

With the continuous development of new scientific technology and methodology, breeding programs are both producing and utilizing a large amount of big data. This requires efficient management systems to keep track of various types of data such as performance, pedigree, geographical and image-based data as well as genotype data. Access to integrated breeding data in a database enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility by breeders. The Breeding Information Management System (BIMS) is a free, open-source, secure and online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data that has been available in several crop databases. But what about the crops that do not have a database? We report the utility of a new BIMS website (www.breedwithbims.org) that allows any crop breeders can use BIMS. One of the key features of BIMS is that users can import new trait data via an Android App called Field Book as well as historical data via templates. Field Book app allows breeders to collect phenotype data with less possibility of transcription errors. BIMS is also BrAPI compliant so that breeders can send and receive data from other BrAPI compliant resources including the Field Book App. Potential for streamlining data collection and management for vegetable crops will be presented.