ASHS 2024 Conference

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
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
Characterization of A Novel Locus for Fruit Flavor Aroma in Tomato - Qian Feng

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

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

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.

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 PIGs 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.