ASHS 2025 Conference

Tomato fruit quality is directly related to marketability and consumer appeal. Unfortunately, consumers are increasingly discontent with the flavor and quality of the product they are purchasing and requesting tomatoes with improved flavor, aroma, texture, and appearance making it a high priority for breeding programs. Traditionally, the selection for fruit quality traits in breeding programs has been done using conventional phenotyping approaches, in which large populations need to be screened. Although this approach has resulted in the release of high quality-high yielding cultivars, it is very time-consuming, delaying cultivar release. An alternative approach to improve breeding efficiency involves the use of modern molecular breeding techniques. In this study, a diverse panel of 305 tomato genotypes, including 284 tomato breeding lines developed by Texas A

Septoria Leaf Spot (SLS), caused by the fungal pathogen Septoria lycopersici, is a highly destructive foliar disease affecting tomatoes. SLS is most severe in the Northeast USA and North Carolina during periods of high humidity and elevated temperatures, which can lead to catastrophic yield loss. No quantitative trait loci (QTL) associated with SLS resistance have been reported. Therefore, the objective of this study was to map the QTL related to SLS resistance in tomatoes. An F2:4 mapping population consisting of 189 individuals derived from NC123S (susceptible) x Wisconsin 55 (moderately resistant) was assessed under both field and greenhouse conditions through artificial inoculation with a spore concentration of 15.3 x 10^4/mL at the Mountain Horticultural Crops Research and Extension Center, Mills River, NC, and Mountain Research Station, Waynesville, NC. The population was genotyped using the SPET (single primer enrichment technology) Allegro targeted genotyping method. SPET-derived SNP (single nucleotide polymorphism) molecular markers were used to construct a linkage map spanning 3810.2 cM. QTL analysis identified 12 QTLs associated with SLS resistance, including two major effects and ten minor effects, typical for at least two environments identified across the genome, explaining phenotypic variation (R² value) ranging from 3.7% to 13.5%. These results demonstrate that the genetic control of SLS resistance is polygenic. This study may provide a foundation for understanding the genetics of SLS resistance and marker-assisted selection (MAS) for transferring SLS resistance genes into elite tomato breeding lines.

Drought is a major abiotic stressor that significantly reduces the growth and yield of tomato (Solanum lycopersicum L.). To mitigate its adverse effects, the development and utilization of drought-tolerant cultivars, combined with advanced breeding strategies, offer sustainable solutions. In this study, a total of 157 USDA tomato accessions were evaluated under controlled greenhouse conditions using a randomized complete block design with four replications, incorporating both a water-deficit treatment and a well-watered control group. The results identified ten accessions, including PI 487624, PI 127828, PI 379018, PI 365903, PI 390515, PI 390663, PI 128657, PI 266376, PI 126444, and PI 298933, as drought tolerant, with leaf wilting and leaf rolling scores of less than four. Broad-sense heritability estimates ranged from 50 percent to approximately 58 percent, indicating a moderate genetic influence on drought tolerance. Correlation analysis revealed strong positive associations ranging from 0.50 to 0.99 among leaf wilting, leaf rolling, plant freshness, leaf thickness, and SPAD chlorophyll content, while negative correlations ranging from -0.40 to -0.81 were observed for plant fresh weight, leaf thickness, Quantum yield of Photosystem II (Phi2), and SPAD chlorophyll content traits. These findings provide valuable insights into tomato breeding programs focused on improving drought resilience in elite cultivars. We plan to expand the evaluation to a broader set of accessions and employ genome-wide association studies and genomic prediction to identify single nucleotide polymorphism markers and candidate genes associated with drought tolerance. The integration of genome-wide association studies and genomic prediction will facilitate marker-assisted selection and genomic selection, improving the efficiency of breeding programs aimed at developing drought-resilient tomato cultivars.

Blossom-end rot (BER) is a physiological disorder in tomatoes that renders the fruit to be unmarketable. In tomato, BER initiates around 7-10 days post anthesis (DPA) at the distal end of the fruit as a water-soaked symptom that can progress into a necrotic lesion covering the entire fruit during development. Calcium deficiency in the distal end of the fruit is thought to trigger BER initiation. In this study, we have used near isogenic lines (NILs) that segregate for BER and harbors quantitative trait loci (QTLs) BER11.1 and BER11.2. Physiological characterization indicated lower calcium concentration and reduced number of vascular bundles in the distal inner and distal pericarp tissue in the susceptible fruit in comparison to the with resistant fruit. To further delineate the molecular mechanisms underlying BER development and to identify the potential candidate gene(s) underlying QTL BER11.1

Fresh market tomato (Solanum lycopersicum) is one of the most important vegetable crops in the US, but this labor-intensive industry faces severe labor shortages and rising production costs amid heavy competition from lower-cost imports. With labor accounting for over 30% of total production expenses, much of which is due to harvesting, the industry's long-term sustainability depends on developing more labor-efficient systems. Mechanical harvesting presents a promising solution, but tomato fruit are highly susceptible to bruising, a challenge that could be amplified by mechanized handling. Fruit firmness plays a crucial role in resistance to internal bruising, making it a key breeding target for improving harvest efficiency and post-harvest quality. The UF/IFAS tomato breeding program has developed tomato lines with traits beneficial for mechanical harvesting, including compact growth habit (CGH) and increased fruit firmness. To investigate the genetic basis of fruit firmness in CGH lines, bi-parental populations were developed from firm and soft inbred parents. Genome-wide association analysis identified multiple minor-effect QTLs, confirming the quantitative nature of this trait in the population. Variance component analysis revealed that fruit firmness is primarily controlled by additive genetic variance, suggesting a strong potential for improvement through selection with appropriate strategies such as genomic selection (GS), which has been successfully used to improve quantitative traits in many crop species. GS models were successfully trained to predict fruit firmness, demonstrating the feasibility of integrating GS into the UF/IFAS tomato breeding program. Model optimization, including adjustments to training population size, marker density, and the incorporation of significant QTLs as fixed effects, improved prediction accuracy and computational efficiency. This study confirms the presence of significant fruit firmness variability in UF/IFAS germplasm, supporting its use in breeding firmer CGH tomatoes suited for mechanical harvest. Future research will refine GS models by incorporating multi-trait and multi-environment analyses, leveraging variance-covariance relationships to enhance prediction accuracy and accelerate genetic gains.

Speed breeding is a technique that utilizes controlled environments and optimal lighting (photoperiod) conditions to accelerate germination, development, and maturity of plants. One of the major constraints for its adoption and implementation in vegetable breeding programs is the high cost associated with growth chambers. The objective of this study is to develop a Speed Breeding protocol for chile peppers using an improvised, low-cost growth chamber constructed using polyvinyl chloride (PVC) plastic, greenhouse film, mylar reflective film, full-spectrum and far-red light-emitting diode (LED) growth lights. Four C. annuum L. genotypes, namely, NuMex Lotalutein (a serrano type), NuMex Odyssey (New Mexican), NuMex Las Cruces (cayenne), and Early Jalapeno (jalapeno) were planted in two randomized flat trays, using SunGro propagation soil, and watered twice daily. After reaching the 2-3 leaf stage, the treatments (control and Speed Breeding, SB) were transplanted into 8” pots, incorporating sterilized and LM-AP soil mixtures. The control group was cultivated in standard greenhouse conditions for growing chile peppers, exposed to normal daylight intensity and duration, and an average temperature of 21°C and humidity of 40%. The chamber was also constructed in the same greenhouse. From weeks 1 to 5 after planting, the SB-treatment was subjected to 20h/4h light/dark conditions daily, and 9h/15h light/dark after week 5. Light intensity was increased by ~100 photosynthetic active radiation (PAR) weekly after week 5, from ~150 PAR to ~800 PAR. Data was recorded weekly to examine the effects of treatment on germination rate, plant size, leaf number and color, number of flowers, buds, and fruits, and days to flower and fruit. There were significant differences (Tukey HSD, P < 0.05) between treatments for germination rates, number of buds, fruits, leaves, and days to flowering. The SB-treated pepper plants exhibited faster and higher germination, darker green leaves, and a higher number of buds and fruits compared to the control. For instance, SB plants started flowering, on average, about 20 ± 5 days earlier, germinated 5 ± 1 days earlier, and had, on average, 15 ± 2 more buds than the control. Notably, all genotypes under the SB-treatment had at least one fully mature fruit ~106 days after sowing. These results suggest that, at minimal costs, there is a potential to achieve increased generation times to accelerate cultivar development and genetic improvement in chile peppers.

Watermelon is a preferred fruit in the Caribbean and all over the world and is the second most consumed cucurbit by harvest weight in the Virgin Islands after cucumber. While quality of water of watermelon is commonly judged by sweetness, the ratios of types of sugars are hardly considered. Watermelon is classified as one of the fruits with very high glycemic index, GI – the measure by which a dietary intake increases the blood sugar compared to pure glucose whose GI is 100. Watermelon is normally promoted as a highly nutritious as it is one of the best sources of potassium, but can be both a blessing and curse, especially for consumers with high blood sugar-related ailments. Here we report on preliminary efforts we are making to produce watermelons that have reduced GI. We are using hybridization as well as exploiting genotype-by-environment interactions to influence sugar composition in fleshy fruit tissues. We have obtained three hybrids that have at least 22% reduced glucose and at per brix compared to the parents. We are also testing a series of shadehouse systems, two of which show the potential to lower glucose ratio in the fruits. We hope to refine these methods and evaluate the watermelon lines for yield and sugar trait stability before recommending plant materials and production systems to interested farmers. Key words: Hybrids, sugar, glycemic index, genotype by environment, production system, sucrose, watermelon.

The need to improve crops has never been critical with the rising population and climate change resulting in high abiotic stress and disease pressures in production areas. In recent years, artificial intelligence (AI)-based approaches have been implemented in the context of plant breeding and crop improvement. Modern AI tools hold the promise of accelerating the development of resilient, higher-yielding, and more sustainable horticultural crops, by rendering a deeper understanding of complex genetic systems and phenotypes, and how these interact with their environment to express desirable traits. As an approach, AI is an important component of the plant breeding toolbox which may now currently be an indispensable addition to modern vegetable breeding programs. For example, AI allows for the prediction of phenotypic values through genetic markers, and this allows plant breeders to perform selection even before the trials are conducted in the field. The ASHS Vegetable Breeding and Interest Group seeks to provide research updates from experts who have worked on the applications of AI in crop breeding and genetic improvement. The workshop will provide a summary of various AI methodologies, recent advances, and render opportunities for future collaboration and research directions in the implementation of AI in vegetable breeding programs. Objectives 1. Summarize the different AI approaches used in breeding and genetic improvement of various traits in vegetables 2. Provide the attendees with recent advances in AI for plant breeding 3. Discuss future research directions and applications of AI in plant breeding programs The workshop will be conducted during the annual ASHS meeting (July 28- August 1, 2025) in New Orleans, Louisiana. The workshop will be in-person. Audience: The workshop will be open to all ASHS attendees (both public and private sectors) and will be interactive.

Moderators: Dennis Lozada, New Mexico State University
Devi Kandel, Langston University

Speakers:
The following speakers were invited and those indicated with (*) have agreed to the invitation.

• Dr. Zhihang Song* (University of Georgia; Accelerating Plant Breeding with Plant Phenotyping Technologies and AI)
• Dr. Mahdi Haghshenas-Jaryani* (New Mexico State University; Autonomous “AI-enabled” Robots for Chile Pepper Precision Farming)
• Dr. Allen Van Deynze (University of California- Davis; TBA)
• Dr. Lirong Xiang (North Carolina State University; TBA)

Carrots are one of the most popular vegetables, valued for both their culinary uses and health benefits. While carrot breeders have primarily focused on enhancing appearance to meet consumer expectations, flavor is also an important factor. Sugars, which are key to carrot flavor, are the focus of this project. Carrots accumulate two main types of free sugar-reducing sugars (glucose and fructose) and non-reducing sugars (sucrose). Carrots with high percentage of reducing sugar tend to have sweeter, less harsh and more preferred flavor. The balance between sucrose and reducing sugars is controlled by a dominant gene called Rs, where heterozygous plants have a higher proportion of reducing sugars. In this study, we conducted a genome-wide association study (GWAS) using a diverse set of carrot accessions grown over five years to identify SNP markers linked to sugar composition in carrots. The enzyme acid-soluble invertase isozyme II, which breaks down sucrose into glucose and fructose, was identified as the most significant candidate gene. To further validate this gene’s involvement in the Rs locus, we are using genome editing techniques. Details of this genome editing work will be presented.

Purple carrots (Daucus carota L.) are becoming increasingly popular as a fresh market novelty food and as sources of natural pigments in foods and beverages. Anthocyanins are associated with many health benefits, such as reduced cardiovascular disease risk, fewer types of cancers, and reduced inflammation. Increasing anthocyanin content in purple carrots is therefore worthwhile for plant breeders and consumers. An interesting trait in carrots is heavy pubescence in the highest anthocyanin-producing breeding lines. Pubescence has been shown to be linked to anthocyanin content and abiotic stress resistance in other plant species. An F2 mapping population was created between two purple breeding lines developed from two separate Turkish accessions. The population contrasted in the level of pubescence and anthocyanin content in petioles and roots. Anthocyanin content was determined in the taproots and the level of pubescence was scored visually and through image analysis. Pubescence mapped to two loci that may be related with transcriptional regulation of trichome density and length. Anthocyanin content appears to be inhibited by a single locus that is unlinked with pubescence in this population. Epigenetic silencing was also observed in the purple carrot population and has implications on the development of high anthocyanin content varieties. Information from this study will provide genetic markers for increasing anthocyanin content in purple carrot breeding populations and developing pubescent varieties with abiotic stress resistances.

Chile peppers (Capsicum annuum L.) hold a vital position in global agriculture and diets, valued for their unique flavor, diverse uses, and nutritional benefits. Among their bioactive compounds, carotenoids play a significant role, acting as antioxidants and precursors to vitamin A, with immense implications for human health. This study aims to identify carotenoid diversity and determine the genetic control of carotenoid production in a diverse population of 127 chile pepper genotypes. Fruits grown in Las Cruces, NM, were harvested in the 2024 growing season. High-performance liquid chromatography (HPLC) will be employed to profile individual carotenoids such as β-carotene, lutein, capsanthin, capsorubin, zeaxanthin, and violaxanthin. To optimize carotenoid extraction and minimize degradation, three different saponification methods were tested, varying in incubation time and temperature: 30 minutes at 50°C, 30 minutes at room temperature, and 60 minutes at room temperature. The best results were obtained with 30 minutes of incubation at room temperature. After getting HPLC results for the whole pannel this data will be integrated with genome-wide association studies (GWAS) to identify key genetic loci and candidate genes associated with carotenoid content. The study aims to provide a foundation for marker-assisted selection to improve the nutritional quality of chile peppers. The findings have direct implications for breeding programs, enabling the development of biofortified chile pepper varieties.

Fruit morphology has a significant impact on the agronomic performance of chile peppers, influencing both yield potential and mechanical harvest efficiency. Through the integration of genome-wide association studies (GWAS) with Tomato Analyzer, an image-based phenomics tool, we aim to identify single nucleotide polymorphism (SNP) markers associated with fruit architecture and morphology. A Capsicum association mapping panel (CAMP) consisting of 128 genotypes with three checks evaluated in Las Cruces, NM under an augmented design for the 2024 growing season. The design consisted of ten blocks, each with a different number of test genotypes whereas checks were replicated in each block. Ten green and ten red fruits (N=20) for each genotype were scanned using a flatbed scanner and images were processed using Tomato Analyzer software to record fruit architecture. Best linear unbiased predictions (BLUPs) were calculated for maximum fruit height (MAXH; cm), maximum fruit width (MAXW; cm), curved fruit height (CURH; cm), width mid-height (WMH; cm), area (ARA; cm2), and perimeter (PER; cm). High narrow sense heritability (h2) ranging between 0.80 and 0.98 was observed. A medium to high Pearson correlation (r=0.56–1.00) was observed for all traits except WHM. After filtration and imputation, 40,709 genotyping-by-sequencing (GBS) SNP markers were used to perform multi-locus GWAS. A total of 129 SNP markers associated with seven basic fruit measurements across 10 chromosomes were identified. The SNP marker SCM002812.1_10016804 on chromosome 1 at 10.02 Mb was found to be associated with the potential candidate gene YABBY4, which can regulate fruit developmental processes. Other candidate genes identified included Gibberellin receptor GID1B, Cyclin-L1-1, and U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase), regulating plant growth hormones, cell division, and methylation, respectively. The findings of this study will be relevant for the development of molecular markers for marker-assisted selection and studying expression levels of genes regulating fruit development in a comparative analysis using chile pepper genotypes with contrasting fruit morphology.

Marker-assisted selection is important to facilitate the process of genetic improvement in vegetable breeding programs. A set of 192 trait-associated single nucleotide polymorphism (SNP) markers identified from previous genome-wide mapping studies has been developed at the New Mexico State University (NMSU) Chile Pepper Breeding and Genetics Program (NMSU-192) through the PlexSeq Genotyping Technology of AgriPlex Genomics (https://www.agriplexgenomics.com/plexseq-technology). The NMSU-192 SNP array consists of SNPs associated with easy destemming (14 SNPs), plant architecture and morphology (76), yield and yield components (78), and Phytophthora capsici resistance (24). Genetic diversity analysis using the NMSU-192 demonstrated the feasibility of the SNP array to characterize 188 Capsicum spp. genotypes based on fruit architecture and morphology. Together with parental and reference genotypes, F2:3, F3:4, and F4:5 segregating families of chile pepper breeding lines will be genotyped using the NMSU-192 for marker-assisted breeding and selection at the NMSU Chile Pepper Breeding and Genetics Program. The NMSU-192 will be a valuable component of the breeding toolbox for the genetic improvement of traits relevant to the chile pepper industry in New Mexico and in the pepper genetics community.

Establishing a successful breeding program requires careful planning across multiple dimensions, including crop prioritization, stakeholder engagement, infrastructure development, germplasm acquisition, and definition of breeding goals. With these priorities in mind, we are developing a comprehensive vegetable breeding program focused on pepper (Capsicum spp.), anchored by both statewide and national stakeholder surveys and concept mapping exercises. These efforts have informed infrastructure development, germplasm sourcing, and trait prioritization aligned with end-user needs. As a foundational step, we assembled the UGA-CAPSI-CORE collection, a curated panel of over 450 diverse pepper accessions, including breeding lines, improved landraces, and ex-PVPs. This collection is currently being evaluated for key horticultural traits through conventional field-based assessment and high-throughput phenotyping. In parallel, a preliminary experimental subset is undergoing targeted screening for major biotic stresses, including Phytophthora capsici (Phytophthora blight), Colletotrichum spp. (Anthracnose), Meloidogyne incognita (Root-knot nematode), and insect pests such as pepper weevil (Anthonomus eugenii), green peach aphid (Myzus persicae), and whitefly (Bemisia argentifolii). Fruit quality parameters, including firmness, color, total soluble solids, and vitamin A and C content, are also being evaluated in the same subset. To complement phenotypic evaluation, we have screened the UGA-CAPSI-CORE collection for Phytophthora resistance using publicly available SSR markers, with allele binning conducted via TANDEM software. Whole genome resequencing (WGRS) of the full collection is currently underway to provide a high-resolution view of genetic diversity and trait architecture. Looking ahead, we are expanding the program to include transcriptomics and metabolomics analyses in response to P. capsici infection, enabling a systems-level understanding of host-pathogen interaction. The integration of phenotypic, genotypic, transcriptomic, and metabolic data will accelerate discovery of candidate genes and molecular markers for use in genomics-assisted breeding. This multipronged strategy positions the UGA vegetable breeding program to deliver pest- and disease-resistant, and nutritionally enhanced pepper cultivars for Georgia and beyond.

Modern sweetpotato breeding programs evaluate hundreds of genotypes across successive generations to identify lines with superior storage root quality traits. However, traditional phenotyping methods rely on manual storage root evaluation, limiting both the scale and speed of selection. Small Unmanned Aircraft System (sUAS)-based high-throughput phenotyping offers scalable, image-based alternatives that enable breeders to collect highly detailed data with reduced bias, facilitating genomic selection. By linking image-derived phenotypes to genotypic data, these approaches could shorten the breeding cycle by supporting earlier or more optimal selection decisions. In this study, we developed an image-based yield estimation pipeline for early generation and advanced sweetpotato breeding lines using sUAS-based RGB (0.17 cm pixel⁻¹) and multispectral imagery. The pipeline leveraged a previously developed Mask R-CNN segmentation model for sweetpotato storage root detection that was pre-trained using mobile RGB images and fine-tuned using annotated aerial images to optimize performance for sUAS applications. Imagery was acquired in 2024 from two research fields immediately after harvest. Ground truth plot-level root yield was collected using mechanical singulation in an optical sorter (Exeter Engineering). The Mask R-CNN model generated instance masks of individual storage roots directly from plot-level RGB imagery, with root metrics such as length, diameter, and volume estimated using multiple geometrical methods. The model demonstrated strong predictive performance across both locations. Combined-location analysis yielded a correlation coefficient of 0.94 for storage root weight estimation (0.88 and 0.97 for individual locations) with a root mean squared error (RMSE) of 1.24 kg plot⁻¹. Root count estimation achieved a correlation coefficient of 0.78 (0.73 and 0.92 independently) with an RMSE of 11 roots plot⁻¹. These results indicate robust yield estimation across diverse genotypes and field conditions. Furthermore, these findings highlight the potential of combining aerial imagery and deep learning to streamline yield assessment in sweetpotato breeding programs. Future work will focus on enhancing model accuracy by incorporating root feature analysis, quality classifications, and expanded datasets to further support breeding decisions and accelerate selection pipelines.

A forum for discussion of potential collaborations with regards to fruit, vegetable, and edible crops – i.e. citrus, breeding, production systems, postharvest, pomology, crop management, viticulture, etc.

Watermelon, Citrullus lanatus, is an important vegetable crop in the United States of which the annual watermelon crop value exceeded $534 million in 2021. In recent years, production has been disrupted by the rapid spread of a serious plant pathogen, Phytophthora capsici. The closest ancestors of today’s domesticated watermelon are thought to be Citrullus mucosospermus and Citrullus amarus, several accessions of which have known resistance to Phytophthora capsici fruit rot, but are untested in regards to stem and root rot. Popular commercially available cultivars, such as ‘All Sweet’, ‘Laelanau’, ‘Penghu’, and ‘Sunshade’, as well as Texas A

Fusarium wilt, caused by the fungal pathogen Fusarium oxysporum f.sp. lycopersici (Fol), threatens tomato crops globally. Fol causes substantial yield losses in susceptible plants and is persistent once established in fields, making gene-based resistance a high-priority for growers. Historically, Fol strains isolated in the Midwest United States have been predominantly race 1, and I-based resistance has been widely deployed and effective. However, there have been increasing numbers of samples sent to diagnostic clinics in the Midwest with Fusarium wilt symptoms, suggesting a potential shift in Fol race prevalence and the need to deploy additional resistances. The aim of our project is to introgress the I3 resistance gene, effective against race 3 Fol, into Midwest-suited processing tomato lines. I3 was originally identified in Solanum pennellii, a wild relative of cultivated tomato (Solanum lycopersicum), and a minimal introgression which reduced linkage drag was developed and introduced into Fresh-Market tomatoes by the University of Florida. We developed backcross families with the I3 gene using the Florida minimal introgression and recurrent parents from the Ohio processing tomato breeding program. Lines were selected for advancement based on I3 genotyping, background genome selection using unlinked single nucleotide polymorphisms (SNPs), and phenotyping of relevant yield and quality characteristics. Our analysis found no significant differences in yield and quality traits between the backcross selections and their recurrent parents, indicating the rapid conversion of parents through this strategy. We are currently combining the I3 and I2 resistance genes through further crossing and will ultimately develop high-performing processing tomato lines suited to Midwest growing conditions that are resistant to all three Fol races.

Understanding germplasm diversity is essential in pepper (Capsicum annuum L.) breeding to enhance disease resistance and fruit quality. This study evaluated morpho-phenological characteristics of UGA-CAPSI-CORE, a collection of 352 globally sourced germplasm classified into six varietal groups (VGs): banana, bell, Italian frier, mini bell, mini sweet, and specialty peppers evaluated in two replications during summer 2024. A total of 12 traits, including eight quantitative (e.g., germination, plant vigor, plant height) and four qualitative traits (e.g., growth habit, fruit position, fruit color), were assessed. Significant phenotypic variation was observed across varietal groups. Germination rates averaged 64%, with mini sweet peppers exhibiting highest germination (71.63%) and least in banana peppers (57.30%). Flowering time slightly varied (87–103 days), with banana peppers flowered late (89.3 days) than Italian frier (88.5 days). Specialty peppers were longer (41.49 cm) while bell types shorter (34.22 cm). Banana peppers and bell types exhibited taller (17.55 cm) and shorter (14.98 cm) stems, respectively. Lodging susceptibility was highest in Italian frier (29.12%) and lowest in mini bell (19.78%). Days to maturity was consistent, with mini sweet accessions requiring slightly longer time (142.51 days) than Banana peppers (141.34 days). Fruit morphology varied significantly, with bell peppers producing the highest lobe count (3.38) and banana peppers having single-lobed fruits. ANOVA confirmed significant variation (p < 0.001) in key traits, and cluster analysis identified six distinct clusters. This study elucidates the genetic diversity within the evaluated germplasm, providing valuable insights for breeding program to focus on enhancing productivity, adaptability, and fruit quality.

Phytophthora capsici is a devastating pathogen in peppers (Capsicum annuum L.), responsible for root, stem, and fruit rot, often leading to yield losses of 40% to 60% in outbreak conditions. Marker-assisted selection (MAS) offers a precise strategy for accelerating resistance breeding. While high-throughput genotyping approaches such as genome-wide resequencing (WGRS) are increasingly adopted, SSR markers remain a practical and informative tool for initial diversity assessment, especially in large and diverse germplasm collections. In this study, 485 globally sourced pepper accessions including 473 accessions from C. annuum and 12 accessions from seven wild Capsicum species were evaluated using 31 SSR markers previously reported to be linked with Phytophthora resistance. Eighteen markers showing robust and reproducible amplification were selected for full-panel genotyping. To ensure consistent and accurate allele calling, SSR allele binning was performed using TANDEM software. The resulting dataset revealed substantial allelic richness, reflecting the broad genetic diversity of the collection. Gradient PCR was also performed to optimize amplification of the 13 initially non-amplifying markers, resulting in six additional markers now suitable for further screening. Downstream diversity analyses, including PCA, STRUCTURE, and phylogenetic clustering, are currently in progress. Additionally, WGRS is planned for this germplasm panel, and integration of SSR and SNP datasets will allow for a comprehensive assessment of genetic relationships, population structure, and resistance allele distribution. Together, these efforts will support the identification of novel resistance sources and inform strategic breeding for improved Phytophthora resistance in pepper.

Seed increase is an essential step in germplasm management, enabling the effective use of genetic resources in breeding, evaluation, and conservation. This study focused on multiplying seed stocks and assessing phenotypic diversity in a globally sourced collection of 485 Capsicum accessions. The collection comprises accessions belonging different species of Capsicum including C. annuum (473), C. chinense (4), C. baccatum (3), C. chacoense (1), C. flexuosum (1), C. frutescens (1), C. galapagoense (1), and C. rhomboideum (1). Evaluated accessions were obtained from diverse genebanks (domestic and international), and collaborative breeding programs that comprises landraces, heirlooms, breeding lines, and exPVPs. To ensure sufficient seed availability, 352 accessions were grown in a greenhouse during summer 2024 and an additional 133 accessions were grown during winter 2024. Simultaneously, twelve agronomic and morphological traits, six pre-harvest (e.g., germination rate, plant vigor, internode number and length) and six post-harvest (e.g., fruit size, pericarp thickness, yield) were recorded. Significant phenotypic variation was observed across varietal groups. Bell and mini bell peppers showed high germination rates (>65%) and marketable yields, with bell types producing the heaviest fruits (79.8 g) and thickest pericarps (5.2 mm). Banana peppers exhibited the longest fruits (13.8 cm) and high plant vigor, while mini bells were completely resistant to lodging. These findings highlight both successful seed multiplication and the phenotypic richness of the collection, offering a valuable resource for pre-breeding, core collection development, and trait-specific selection.

Spinach (Spinacia oleracea L.) produces two types of seeds: spiny and spineless. Seed spine is one of the most important agronomic traits that affect seed treatment, mechanized harvesting and planting, and sowing. This study aimed to identify single nucleotide polymorphism (SNP) markers associated with seed spines in spinach through a genome-wide association study (GWAS), with the goal of developing SNP markers for marker-assisted selection (MAS). GWAS was conducted for the seed spine trait in a panel of 307 diverse spinach accessions using 147,977 SNPs generated from whole genome resequencing. Using MLM, FarmCPU, and BLINK models in GAPIT 3 and TASSEL 5, two significant SNPs associated with seed spines: SOVchr3_141167900, and SOVchr3_141168649 were identified on the chromosome 3. (LOD) values of t-test analysis identified homozygous alleles associated with the spiny and spineless traits in each of the two SNP markers, with LOD values greater than 80.00, and 80.00, respectively. The gene SOV3g042220, located between 141,172,904 bp and 141,183,504 bp on chromosome 3, is proposed as a potential candidate gene associated with the seed spine trait. This research provides valuable insights for MAS in spinach breeding, facilitating the development of spinach lines with desirable seed characteristics.

Vitamin C (VC), also known as ascorbic acid and ascorbate, is a water-soluble antioxidant in plants that promotes skin health and immune function in humans. Spinach (Spinacia oleracea L.), a leafy green vegetable widely valued for its health benefits, has been identified as a target for nutritional enhancement, including increased VC content. However, the complex inheritance of VC necessitates advanced selection methods to accelerate cultivar development. In this study, VC- associated single nucleotide polymorphism (SNP) markers identified through genome-wide association (GWAS) were employed for genomic prediction (GP) to estimate prediction accuracy (PA) for VC content in spinach. A dataset of 147,977 SNPs generated from whole genome resequencing was analyzed in a panel of 347 spinach genotypes using six GWAS models. Sixty-two SNP markers, distributed across six spinach chromosomes, were significantly associated with VC content. PA was assessed using randomly selected SNP sets and GWAS-derived SNP marker sets across various GP models. Results demonstrated that PA exceeded 40% when using 1,000 or more SNPs. Furthermore, incorporating GWAS-derived SNP markers improved PA, achieving a r-value greater 0.70 through Bayes ridge regression (BRR) model. This study highlights the potential of GWAS-derived SNP markers for marker-assisted selection (MAS) and genomic selection (GS) in spinach breeding programs aimed at enhancing VC content. Keywords: Genomic Selection, Genome-Wide Association Study, Spinach, SNP, Prediction Accuracy

Leaf base color in spinach (Spinacia oleracea L.) exhibits substantial phenotypic variation, potentially influencing consumer preference and nutritional content. To elucidate the genetic basis of this variation, we conducted a genome-wide association study (GWAS) utilizing a diverse panel of 313 USDA-GRIN accessions of spinach. This population, characterized by a predominance of white (65%) and red (35%) leaf base colors, was genotyped using whole-genome resequencing (WGR) resulting in the identification of 83,261 high-quality single nucleotide polymorphisms (SNPs) after rigorous filtering. Genetic diversity analyses and association mapping were performed using multiple statistical models, including mixed linear model (MLM), generalized linear model (GLM), BLINK, and FarmCPU, implemented in GAPIT 3, TASSEL 5, and rMVP software. The GWAS identified three significantly associated SNPs (SOVchr3_140405053, SOVchr3_140405474, SOVchr3_140412359) located on chromosome 03, which collectively contribute to leaf base color variation. Within a 50kb flanking region of these SNPs, we identified three candidate genes: SOV3g042000 (membrane protein), SOV3g041980 (mariner transposase), SOV3g041990 (pentatricopeptide repeat). These genetic loci explained 30.55% of the phenotypic variation observed in leaf base color. These findings provide critical insights into genetic architecture governing leaf base color in spinach. The identified SNPs and candidate genes represent valuable targets for marker-assisted selection and gene editing, facilitating the development of improved spinach cultivars with desired leaf base color. Overall, this study contributes to a comprehensive understanding of the genetic control of leaf pigmentation, ultimately supporting targeted breeding strategies for spinach varieties.

Spinach (Spinacia oleracea L.) is a globally valued vegetable, renowned for its rich nutritional content and health-enhancing benefits. Leaf texture, ranging from smooth to savoy, is an important trait influencing consumer preference, taste, and nutritional compositions. This study aimed to conduct a comprehensive genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers associated with leaf texture in spinach, along with genomic prediction (GP) to facilitate trait screening in breeding programs. GWAS was performed on a panel of 103 USDA spinach germplasm accessions using 12,744 high-quality filtered SNPs obtained from whole-genome resequencing. Several statistical models, including MLMM, MLM, FarmCPU, and BLINK, were applied using the GAPIT 3 tool. Two significant quantitative trait locus (QTL) regions were identified on chromosome 1, spanning from 13,798,232 bp to 51,588,552 bp. Within this region, three SNP markers—SOVchr1_13798232 (LOD 5.84), SOVchr1_51500008 (LOD 9.73), and SOVchr1_51588552 (LOD 5.77) and—showed strong associations with leaf texture. Additionally, another SNP marker, SOVchr2_8225269, on chromosome 2, also exhibited a strong association with this trait. Furthermore, the gene SOV1g002810, located between 13,795,625 bp and 13,803,405 bp on chromosome 1, encodes a ULP_PROTEASE domain-containing protein and is proposed as a potential candidate associated with the trait. GP revealed strong predictive accuracy (PA), with an r value of 0.43. The identified SNP markers and PA metrics provide valuable tools for breeders to spinach breeding programs through marker-assisted selection (MAS) and genomic selection (GS), thereby accelerating the development of spinach lines with desired leaf textures.

Soil salinity is a critical abiotic stress that severely limits spinach (Spinacia oleracea L.) growth and productivity, particularly in salt-affected agricultural regions. Developing salt-tolerant cultivars and identifying genetically diverse germplasm are essential strategies to improve spinach resilience under saline conditions. In this study, 150 spinach accessions from the United States Department of Agriculture (USDA) germplasm collection are evaluated under control and salt stress (300 mM NaCl) conditions in a controlled greenhouse environment. The experiment was conducted using a randomized complete block design with three replications. Seedlings were assessed for chlorophyll content (SPAD value), leaf injury score (1–7 scale; 1 representing no visible injury and 7 representing completely necrotic leaves), and seedling height (cm). Substantial genetic variation was observed among the accessions. Five accessions were identified as salt-tolerant based on trait performance, including higher chlorophyll content, lower leaf injury scores, and greater seedling height under salt stress. These included CPPSIH 3 04, PI 171860, PI 177082, PI 171859, and PI 174387. Broad-sense heritability was high for chlorophyll content, leaf injury score, and seedling height, indicating that these traits are largely controlled by genetic factors under salinity stress. A negative correlation was detected between chlorophyll content and leaf injury score, suggesting that accessions maintaining higher chlorophyll content tended to exhibit less foliar damage under salt stress. These findings highlight valuable genetic resources for spinach breeding programs focused on improving salinity tolerance. Future studies will expand the evaluation to a broader collection of spinach accessions and implement genome-wide association studies (GWAS) to identify single nucleotide polymorphism (SNP) markers that can facilitate molecular breeding for salt tolerance.

Sweet potato (SP) is a staple in many countries, primarily used for human consumption, but also showing potential for animal feed, ethanol production, ornamental use, and industrial applications. SP is mistakenly considered tolerant to drought, but water shortage can significantly compromise the yield and quality of this crop. It is frequently cropped in drought-prone environments, characterized by sandy soil and high temperatures. Identifying drought-tolerant genotypes is essential for the development of future-ready cultivars. This study aimed to evaluate physiological, biochemical, and morphological responses of sweet potato genotypes to water deficit conditions. A completely randomized experimental design was adopted in a 2 x 20 factorial scheme with four replicates. The first factor consisted of two water regimes, 20 and 100% of pot capacity. The second factor included 20 genotypes. Plants were grown in 12L-pots filled with a 2:1 soil-to-sand mixture. All plants were irrigated at full pot capacity for five weeks to ensure establishment. Subsequently, water regimes were imposed employing time-domain reflectometry (TDR) sensors, and evaluations were conducted four weeks later. Parameters assessed included chlorophyll fluorescence, biomass, water potential, gas exchange, biochemical parameters, and secondary metabolites. Genotypes responded differently to water regimes, revealing considerable genetic variability for drought tolerance. Water deficit negatively affected the performance of several genotypes, particularly in relation to the variation of minimum fluorescence (Fv/F0), leaf water potential, and electron transport rate. Correlation analysis showed strong associations among traits of stressed plants. There was a high positive correlation between leaf water potential and fresh mass of the aerial part, as well as the photosynthetic rate with the chlorophyll fluorescence parameters Fm and Fv/F0. Genotypes ‘Luiza’, ‘Canadense’, ‘CIP-420717', ‘Maria Isabel’, and ‘CIP-440186' exhibited superior performance under drought conditions and are promising candidates for breeding programs targeting drought tolerance.

In Florida, lettuce is cultivated in the southern region in wintertime, a period marked by environmental fluctuations. The dominant Histosols in this area are prone to subsidence and exhibit an increased pH due to the incorporation of calcium carbonate, leading to a reduction in phosphorus (P) availability. In the northern part of Florida, lettuce has the potential to be cultivated in sandy soil to supply the high demand of lettuce, however this type of soils naturally exhibits low P availability. To sustainably produce lettuce in these soils, P efficient cultivars should be bred. Prior, lettuce genotypes were identified as P-efficient and P-inefficient across types. The objective of this study was to determine the influence of Genotype × Environment (G×E) interaction on lettuce cultivated under low P inputs. A multi-environment trial was conducted using 22 P-efficient or P-inefficient genotypes in eight experiments distributed across the lettuce season (Fall, Winter, and Spring) at two locations and distributed in a randomized complete block design with four replicates. Five experiments were conducted in histosol soils, and three in sandy soils. Each experiment was cultivated under a standard and a reduced P fertilizer rate . Data collected included head weight, and marketability. The analysis of the G×E for these traits under low P conditions utilized three methodologies: the Finlay-Wilkinson approach, that determines the stability of each genotype across environments independently; the Genotype Genotype × Environment biplots, that discerns the 'which-won-where' patterns for mega-environments and identifies the most stable genotype(s) across environments; and the Bayesian AMMI, that aims to understand genotype stability across environmental factors. The results demonstrated that both crossover and non-crossover G×E interactions are statistically significant, accounting for 16% of the variance for season and for soil types in head weight. These interactions explained 27% of the variance for marketability for P fertilizer treatments, accounting 15% and 9% for season and soil types, respectively. The romaine breeding line 60183 and cultivar Tall Guzmaine were identified as P-efficient, exhibiting non-crossover interaction and stability across P rates, seasons, and soil types. Iceberg cultivars Honcho II, and Cibola, and the loose-leaf RSX743 were P-efficient and exhibited crossover interactions. The analysis revealed that winter planting in both soil types is the most stable and productive environment, with histosol soils achieving higher yields under low P input. Results of this study highlight the importance of G×E interactions to be considered when breeding lettuce cultivars for low P inputs.

Bacterial leaf spot (BLS) of lettuce, caused by Xanthomonas hortorum pv. vitians (Xhv), is a major disease limiting lettuce production worldwide, particularly in tropical environments such as the Everglades Agricultural Area (EAA) in Florida. The pathogen is highly aggressive, rapidly dispersing under favorable conditions, and its sporadic outbreaks make disease prediction and management challenging. While Xhv is primarily known to infect lettuce (Lactuca sativa L.), its potential to colonize alternative hosts, including crops and weeds in lettuce-growing regions, remains poorly understood. This study aimed to evaluate the host range and epiphytic capabilities of Xhv by inoculating two isolates (‘L7’ and ‘SC8B’) onto common leafy vegetable crops and weeds frequently found in or around lettuce fields. A total of 26 plant species were tested, including weeds from Malvaceae (n=1), Portulacaceae (n=1), Amaranthaceae (n=2), Asteraceae (n=3), Brassicaceae (n=1), and Poaceae (n=1), along with vegetable crops from Asteraceae (n=6), Brassicaceae (n=7), and Apiaceae (n=5). Disease severity was assessed 12 days post-inoculation (DPI) using a 0–5 rating scale based on symptomatic foliage area. Initial water-soaked lesions were observed on susceptible lettuce (‘Okeechobee’) at 2 DPI, progressing to necrotic lesions and severe infection with an average disease severity score of 4 at 12 DPI. Notably, symptomatic responses were also observed in endive (Cichorium endivia L.), escarole (C. endivia var. latifolium), and coriander (Coriandrum sativum L.), with median disease severity scores of 3, 3, and 2, respectively. Symptoms in these crops were consistent with BLS in lettuce, including water soaking, chlorosis, and necrosis. In contrast, Brassicaceae species and all tested weeds remained asymptomatic. Bacterial isolations from symptomatic and asymptomatic leaves revealed colonies morphologically consistent with Xhv, displaying yellow pigmentation on nutrient agar. To confirm pathogenicity, hypersensitivity and compatibility response assays were conducted by infiltrating recovered bacterial isolates into resistant (‘PI 358001-1') and susceptible (‘Okeechobee’) lettuce cultivars. Typical disease symptoms developed on susceptible lettuce, confirming Koch’s postulates. The asymptomatic nature of weed species suggests they may serve as reservoirs, potentially contributing to pathogen persistence and dissemination in lettuce fields. These findings provide new insights into Xhv epidemiology and highlight alternative host species that may play a role in disease outbreaks. Understanding the pathogen’s ecological interactions is critical for developing effective disease management strategies and mitigating economic losses in lettuce production systems.