ASHS 2025 Conference

There is an urgent need to diversify high-value fruit crops in low-chill areas, especially as climate change decreases the number of chill hours in cropping areas. Apple is largely considered a temperate crop, yet a subset of germplasm exhibits strong flowering responses even after minimal chill. These genotypes originate from Israeli breeding programs, as well as heritage commercial varieties and backyard discoveries. Future breeding efforts will benefit from characterization of the genetic mechanisms that govern flowering in response to limited chill. In this study we hypothesized that examination of sequence polymorphisms and flowering associated gene sequence differences may permit grouping of low chill materials based on common mechanisms. Relatedness was examined using a series of simple sequence repeat markers (SSRs). In addition, genomic sequence from a number of low chill accessions, including Dorsett Golden, Shell of Alabama, and an early-flowering accession from Mississippi, was compared to publicly available reads from ‘Anna’ (low chill), moderate chill (‘Fuji’, ‘Gala’) and high chill (‘Honeycrisp’; ‘Antonovka’) varieties. Genomes were aligned to Golden delicious reference genome, and shared and unique variants were identified. The data show that all low and moderately low chill cultivars share common sequence polymorphisms not found in high-chill germplasm. Examination of flowering and dormancy-related genes shows common sequence polymorphisms shared within low chill materials that contrast against high chill genotypes. These include members of MADS-boxes family, Frigida family, Early bud break (AP2/ERF) family, auxin responsive factors, transcription factors DELLA family, FRIGIDA INTERACTING PROTEIN, and others. This study illuminates potential mechanisms of low-chill responses, opening opportunities for marker-assisted breeding and increased genetic diversity in development of low chill apple cultivars.

Prior to the formal breeding programsof the 19th century, farmers contributed to apple (Malus× domestica Borkh.) breeding by selecting trees based on the desirable characteristics. The transcontinental seed spread was common, and modern breeding programs identified elite commercial trees and high quality fruits. There is a rekindling interest in low-chill apples, both as a high value crop in the USA Southeast, as well as development of new varieties to confront climate change. But the genetic record is poor. Dorsett Golden (DG) is low chill apple cultivar believed to have been discovered in The Bahamas by a Mrs. Dorsett in 1950. As legend has it, she was a jet-setting traveler that loved apples, and planted a set of trees when she relocated to the Bahamas. This allegedly led to the identification of ‘Dorsett Golden’. While this quickly became the accepted story, some questioned the claim. Observations of phenological data in DG trees next to other Israeli germplasm (e.g. ‘Anna’, ‘Ein Shemer’) led Dr. Wayne Sherman to posit in 1980 that DG’s origin was likely from the Israeli breeding program. To test this hypothesis, whole genome sequence from DG was compared to ‘Anna’ and other reference sequences in public databases. Consistent with Dr. Sherman’s 45 year old predictions, DG shares it’s most significant sequence similarity to ‘Anna’, and less with other low-chill varieties. The majority (~92%) of the total variants are in intergenic, upstream, downstream, or intronic regions suggesting recent divergence of ‘Anna’ and DG. The results are consistent with Dr. Sherman’s phenological data that suggest that DG possessed genetics more similar to Israeli genotypes than a chance seedling from Golden Delicious as legend describes. Most importantly, the study illustrates the power of genomic sequencing in selection of parents for low-chill apple crosses as well as debunking horticulutral methology.

Salinity is a major constraint on tomato crop production and is increasingly intensified by changing climate conditions. This study aimed to develop superior salt-tolerant tomato cultivars by evaluating genetic variation in salt tolerance, identifying associated single-nucleotide polymorphism (SNP) markers through genome-wide association studies (GWAS), and performing genomic prediction (GP). A total of 265 tomato accessions from the USDA germplasm collection were evaluated at the seedling stage under controlled greenhouse conditions with saline stress (200 mM NaCl). Nineteen accessions were identified as salt-tolerant, exhibiting leaf injury scores ≤3.0 (on a 1–5 scale) and chlorophyll reduction of

Lettuce (Lactuca sativa L.) is one of the most important leafy vegetable crops worldwide. Soil salinity adversely affects lettuce production leading to considerable yield losses. Identification of genetic loci controlling salt tolerance will facilitate molecular marker development and thereby assist breeders in developing lettuce cultivars with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) to identify marker-trait association for salt tolerance at the seedling stage using 409 diverse lettuce accessions and 56,820 high-quality single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology. Several statistical models, including GLM, MLM, FarmCPU, and BLINK were employed using the GAPIT version 3 software tool for GWAS. Based on three important seedling stage traits affected by salinity, i.e., shoot fresh weight (FW), shoot dry weight (DW) and chlorophyl index (SPAD), 13 significant salt tolerance related SNPs representing 10 QTLs were identified on lettuce chromosomes 1, 3, 4, 6, 7, 8 and 9. Notably, a major QTL on chromosome 4, encompassing four significant SNPs within a 116 bp region of the lettuce reference genome (v8), explained 49% of the phenotypic variation for FW. The identified salt tolerance-related QTLs provide a valuable resource for developing assays for marker-assisted selection to breed lettuce cultivars with improved salt tolerance.

Chile pepper (Capsicum annuum) is widely produced and consumed, but farmers face significant challenges associated with high temperature stress. Tolerance to high temperatures is a phenotype comprised of numerous component traits each of which contribute to the overall performance of the plant. Our aim was to identify the key mechanisms associated with heat stress response in the leaves and in the floral organs of chile pepper. One-month-old plants of heat-sensitive (AVPP1609-038) and -tolerant (AVPP1609-015) recombinant inbred line (RIL) of chile pepper were subjected to heat stress (38 and 28°C day and night temperatures) and control conditions (32 and 24°C day and night temperatures) in growth chambers with a 14-hour photoperiod. Leaf and floral bud samples were collected for RNA extraction at 11 and 18 days after treatment, respectively, with four biological replicates per tissue. Differentially expressed genes (DEGs) were identified by comparing tolerant and sensitive RILs across treatments and tissues. For the heat-tolerant AVPP1609-015 under heat stress, 1,118 DEGs were identified, with 649 specific to floral buds, 381 in leaves, and 88 shared between the two tissues. Biological processes such as RNA splicing and heat acclimation were predominantly upregulated in floral buds, while lipid catabolism was enhanced in leaves. Developmental processes were consistently suppressed in both tissues for the RILs under heat stress conditions. For the heat-tolerant AVPP1609-015 nuclease activity was strongly suppressed, likely to preserve nucleic acid integrity under heat stress. Hormonal regulation showed tissue specificity, with salicylic acid playing a pivotal role in leaves and ethylene in floral buds, potentially associated with flower abscission. Additionally, key transcription factors associated with heat tolerance were identified. While some mechanisms of heat tolerance were shared between tissues, distinct responses were observed as well, suggesting the need for different breeding approaches to enhance heat tolerance in vegetative and reproductive tissues of chile pepper. These findings provide valuable insights for developing heat-resilient chile pepper and a foundation for future research.

Herbicide tolerance in plants is an increasingly valuable trait due to the high labor and costs associated with weed control in agriculture. Herbicide application remains the most effective and widely used weed management strategy, making the development of tolerant plants essential. First discovered in the 1970s and commercially grown since 1984, herbicide resistant crops have become a key tool in agriculture, with increasing demand for new tolerant varieties. Chemical mutagenesis and CRISPR-mediated gene editing have been used to induce mutations and develop herbicide tolerant plants. Chemical mutagenesis involves treating plant tissue with mutagens such as ethyl methanesulfonate (EMS) to induce random mutations, followed by screening to identify tolerant mutants. This conventional approach has played a significant role in breeding programs and remains widely used for developing herbicide tolerant crops. EMS mutagenesis has successfully generated ALS-resistant varieties in several agronomic crops, including Clearfield® maize, rice, and wheat, which are resistant to imidazolinone (IMI) herbicides without being classified as genetically modified (GM). It is particularly effective for developing crops resistant to ALS- and ACCase-inhibiting herbicides, as these mutations typically require only minor changes in the target genes. CRISPR-mediated gene editing, using tools such as CRISPR-Cas9, base editing (CBE, ABE), and prime editing, enables precise modifications in plant genomes to confer herbicide tolerance. These advancements have revolutionized crop development through their efficiency, precision, and cost-effectiveness. By targeting herbicide receptor genes such as ALS, ACCase, and EPSPS, CRISPR-based systems have produced herbicide tolerant varieties in several agronomic crops. CRISPR is particularly valuable for engineering tolerance to non-selective herbicides, such as glyphosate, due to the complex genomic architecture of the EPSPS gene. Chemical mutagenesis facilitates the discovery of novel mutations and is particularly useful in understudied species lacking the genomic information required for CRISPR-based modification. In contrast, CRISPR-based genome editing provides a highly precise and efficient method for developing herbicide tolerant crops, especially when targeting complex genes. Integrating chemical mutagenesis with CRISPR-mediated gene editing expands the range of available herbicide tolerance traits and offers new opportunities for sustainable weed management. These advances in agronomic crops provide a strong foundation for extending herbicide tolerance studies to horticultural and specialty crops, where research has been more limited despite similar weed management issues.