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.

Assessments of genes associated with plant host defense responses can be challenging as the defensive mechanisms that enable the host-mediated defense can be the very compounds that make gene expression assays particularly challenging. RNA extraction from woody plant tissues presents significant challenges due to endogenous phenolics, secondary metabolites, and stem polysaccharides. We have established an improved extraction protocol for Fraxinus species, yielding superior results to commercial kits. Our optimized approach, validated across diverse tissue types from over 10 Fraxinus species, consistently produces high-purity RNA with exceptional concentrations (>3000 ng/μL) and integrity (RIN scores 8.0-10.0). The RNA quality we have achieved allows us to detect and analyze rare transcripts that may play crucial roles in emerald ash borer resistance mechanisms. Our approach enables us to quantify copy numbers of defense genes triggered during insect attacks, shedding new light on the molecular basis of resistance pathways in ash trees. By employing digital droplet PCR and RNA-seq calibrated, we can determine the key defense genes' exact transcript copy numbers, including those encoding protease inhibitors, phenolic compounds, and terpenoid synthases central to anti-herbivory responses. We have validated a stable reference gene suite with reliable quality control and consistent expression benchmarks. These references serve as crucial yardsticks when measuring expression patterns across ash trees with varying levels of EAB vulnerability. By determining actual transcript numbers, we can make more meaningful comparisons between ash species and genotypes, helping us identify the critical expression thresholds needed for effective resistance. This work strengthens our partnership with the Chicago Region Tree Initiative, supporting efforts to build more resilient urban forests and protect endangered ash species. Through our detailed analysis of gene expression profiles across diverse ash populations, we are working to pinpoint the genetic signatures that confer EAB resistance. These findings will enable the development of efficient molecular screening tools (e.g., SNP marker panels, transcriptomic signature profiles, or RNA expression ratio tests) for large-scale population assessment and accelerate efforts for this important genus. (Co-authored by Dr. Nathan Maren, Woody Plant Breeder and Genomics Specialist at The Morton Arboretum).

Stomatal function is a critical determinant of overall plant vigor, health, and yield. Higher stomatal conductance is associated with higher yields, and therefore is a trait of interest for plant improvement. Although stomatal conductance is governed by a complex balance between many factors, stomatal size and density are two traits that set the foundation for a genotype’s response to the external/internal factors. Understanding the genetic architecture of these traits is a key first step in the process of genetic selection; unfortunately, phenotyping stomatal traits on the scale required for mapping studies can be logistically challenging. In this experiment, we microscopically imaged stomata in apple leaves and used two computer vision methods to rapidly phenotype stomatal traits- a convolutional neural network (CNN) and the web-based computer vision platform BioDock. Two apple populations with existing molecular marker information were phenotyped: a biparental mapping population of approximately 400 individuals and the USDA’s Malus germplasm collection. Genetic mapping was carried out using the ‘r/qtl’ and ‘GWASpoly’ packages in R for the mapping population and germplasm collection, respectively. Both computer vision models yielded accuracies >90% for phenotyping stomatal density in the training and validation datasets, demonstrating that these models are effective methods for quickly phenotyping large stomatal image datasets. Preliminary results indicated peaks associated with stomatal density on chromosome 1 and chromosome 7. Furthermore, stomatal density was negatively correlated with stomatal size- resulting in less variation in total stomatal area than either the distributions of distribution or size would indicate. Future work in this project will focus on identifying the genes involved in regulating stomatal density in apples, as well as generalizing the computer vision models to function on multiple plant species.

Pea (Pisum sativum) is a valuable legume crop recognized for its rich nutritional profile, offering plant-based protein, fiber, vitamins, and essential minerals. It holds a significant place in the growing plant-based protein industry, which is projected to reach $313.5 million by 2025. However, global pea production is declining due to soilborne diseases, notably root rots caused by Fusarium solani f. sp. pisi (Fsp). In our earlier study, we performed time-course transcriptome analysis on four Fsp-tolerant and four Fsp-susceptible pea genotypes during pathogen infection, identifying several Fsp-responsive genes. Interestingly, the dataset also contained Fusarium-derived genes, many of which encode ubiquitin, ubiquitin-like proteins, and the ubiquitin-40S ribosomal protein S31 fusion protein. EffectorP analysis revealed that these proteins are secretory in nature. We hypothesize that Fusarium secretes these proteins into host cells to manipulate the host’s ubiquitin-proteasome system, leading to the degradation of plant defense proteins. To explore this further, we investigated RING-type E3 ligase proteins in Pisum sativum, which play key roles in protein ubiquitination. A total of 663 genes encoding RING-type E3 ligases were identified, each containing at least one RING domain as predicted by the SMART database. Domain analysis revealed additional conserved motifs within these proteins. An Un-rooted Neighbor-Joining phylogenetic tree grouped the RING proteins based on shared domain architecture. Transcriptomic data indicates that these genes are differentially expressed during Fsp infection. The E3 Ligase genes are upregulated in Fsp-susceptible cultivars and downregulated in Fsp-tolerant cultivars. These genes can be used to generate future knock-out mutants and perform functional studies to enhance pea resistance to Fsp-induced root rot.

Detecting Phytophthora capsici (P. capsici) based solely on visual symptoms is challenging and often leads to misdiagnosis. Farmers frequently harvest seemingly healthy fruits, only for fruit rot to develop after shipping. Furthermore, other pathogens can mimic P. capsici symptoms on cucurbits and peppers, and plants may even suffer simultaneous attacks by multiple pathogens, complicating identification. Without timely and accurate diagnosis, P. capsici can spread rapidly, causing significant crop losses. Current diagnostic methods, including traditional microscopy-based culture techniques and polymerase chain reaction (PCR), are time-intensive and lack sensitivity for early-stage infections. This study introduces an optimized Oxford Nanopore Technology (ONT) genomic approach for rapid and precise detection of P. capsici in plant samples, both in laboratory and field settings. Designed for portability and capable of sequencing reads up to 100 kb, the ONT MinION device—smaller than a smartphone—provides a promising solution for in-field diagnostics. Plant tissue samples, symptomatic and non-symptomatic, were collected from cucurbit and pepper fields through collaborators during late summer and early fall. Total DNA was extracted using a magnetic bead-based kit (Primerdesign, Southampton, UK). Sequencing libraries were prepared using ONT’s 1D-cDNA sequencing kit, loaded onto a MinION 107 v9.5 Flow Cell, and analyzed using the Mk1B MinION device. Raw sequence reads in fast5 format were converted to fastq or fasta, with high-quality reads subjected to BLAST searches against the NCBI database for P. capsici identification. The deployment of ONT enables the generation of actionable genomic data in real-time, enhancing our understanding of P. capsici and its role in Phytophthora blight disease development in cucurbits. This technology represents a breakthrough in the rapid, field-based diagnosis of P. capsici, providing farmers with an efficient tool to mitigate crop losses. Keywords: Oxford Nanopore Sequencing Technology (ONT), Phytophthora capsici, Raw sequence reads, Phytophthora blight.

Ashy stem blight and white mold caused by Macrophomina phaseolina (Tassi) Goidanich and Sclerotinia sclerotiorum L. de Bary, respectively are important fungi pathogens affecting common bean (Phaseolus vulgaris L.) worldwide. Genetic resistance is the most environmental friendly approach to control both diseases. Our objective was to evaluate the response of Phaseolus spp. germplasm to three fungal isolates. Two runner bean accessions (P. coccineus L.), and 23 common bean genotypes including 10 UPR-Mp breeding lines derived from multiple-parent crosses were inoculated with the NY133 S. sclerotiorum isolate and PRI21 and PRI24M M. phaseolina isolates by the cut-stem method in the greenhouse. The disease severity was evaluated at 35 days post-inoculation. Middle American common beans ‘Othello’, TARS-MST1, and ‘Verano’ were susceptible (mean scores > 6.5) to all fungal isolates whereas the runner beans PI 183412 (Sel-1 and Sel-2) and breeding line UPR-Mp-57 were susceptible to NY133. Andean common beans A 195, ‘PC 50’, PRA154, PRA155, and VA 19 were intermediate (scores 4-6) to NY133, PRI21, and PRI24M. In contrast, Middle American beans 92BG-7 and BAT 477 were intermediate to NY133 and PRI21, and susceptible to PRI24M. The runner beans PI 183412-Sel-1 and PI 183412-Sel-2, and common bean breeding lines UPR-Mp-22, UPR-Mp-48, UPR-Mp-54, and UPR-Mp-57 were resistant (scores < 3.5) to PRI21 and intermediate to PRI24M. Conversely, UPR-Mp-34 and UPR-Mp-54 were resistant to NY133. This information should help to select parents with higher levels of resistance that may be used in breeding programs for both diseases.

In light of the increasing demand for resilient crops amid global food security concerns, recent advances in omics technologies have accelerated plant breeding efforts. Nonetheless, their effectiveness is often undermined by limited phenotypic resolution, particularly under field conditions. Traditional approaches based on single daily measurements are insufficient to capture the full spectrum of genotypic responses, especially when environmental stress is present. This study explores the potential of thermal imaging using unmanned aerial vehicles (UAVs) to monitor canopy temperature (CT) in wheat, providing a non-invasive proxy for assessing plant water status. A collection of 184 genetically distinct wheat genotypes was examined under both irrigated and rainfed conditions within a Mediterranean agroecosystem. Thermal data were recorded across multiple phenological phases (from anthesis to grain filling) and at various times throughout the day. The analysis revealed that both developmental stage and time of observation substantially influenced CT patterns, thereby impacting the detection of genotype-specific responses to drought. The most pronounced thermal contrasts between irrigation regimes were observed during the milk-dough and dough stages, particularly in the mid-afternoon when vapor pressure deficit (VPD) reached its peak. These insights support the integration of diurnal thermal phenotyping into breeding pipelines as a means to enhance the identification of drought-adaptive traits in cereal crops.

To fully evaluate jujube germplasm, we sampled sour jujubes both from Las Cruces, NM and western Texas to examine their fruit and seed metabolomic profiles to facilitate further employment of those jujube germplasm trees. Samples were taken from the NMSU campus and Tornillo/Fabens, TX which had both the wild type and middle types (cross between wild ones and cultivars). Jujube germplasm fruit metabolomic profile reveals that jujube cultivar samples were similar to germplasm samples from Texas. Sour jujube samples in NM were separated from sour jujube from TX. Sour jujube in TX were mingled together with Cross in TX. So-called Cross and sour jujube were arbitrary classifications. Without cultivars, germplasm was separated by location NM vs TX, not by sour jujube or Cross. For significant compounds, there were only 110 significant different compounds between TX sour jujube vs Cross, while Cross vs NM sour jujube, TX sour jujube vs NM sour jujube or TX vs NM, had over 700. TXS and Cross group overlaid and NM group was totally separated from the other two groups. TX samples had significantly higher contents of large numbers of amino acids and derivatives. More compounds were identified from seed samples and their grouping/PCA results were similar to fruit metabolomic results. Cross samples were mixed together with TX sour jujubes and NM sour jujubes were separated from TX samples. New Mexico samples in Las Crues near graduate student housing area were planted at similar time which could be from one nursery, closed related to each other. Texas germplasm was the result of human selection, not the original sour jujubes but cross between sour jujubes or sour jujube and cultivar-like germplasm. The dominant triterpenes were different between fruit and seeds. In fruit flesh, pomolic acid was the dominant one with Honeyjar as the highest, followed by rutundic acid, Cleanothic acid, 2,3,23-Trihydroxyurs-12-en-28-oic acid, 2,3,23-Trihydroxyolean-12-en-28-oic acid, madasiatic acid, which were higher for NM samples than TX samples. In seeds, the dominant triterpenes were oleanolic acid, mangiferotic acid, momordicoside I aglycone, 3,13,15-trihydroxyolenonane-12-one, jujubogenin, and pomolic acid. The contents of the first three metabolites were equivalent and much higher than the rest, ranging from 0.5X108 to 1.5x108 depending on germplasm. Pomolic acid was much lower in seeds than in fruit. The data contained over 1600 metabolites in fruit and over 2000 for seeds which would be good references for future utilization of those jujube germplasm for horticultural or pharmaceutical purposes.

The accumulated genetic, genomic, and breeding data for Prunus species is often underutilized in breeding applications. This study examines 25 years of curated Prunus data in the Genome Database for Rosaceae (GDR, rosaceae.org) to uncover the genetic architecture of key traits, and provide actionable insights for Prunus breeding. The curated dataset includes 177 genetic maps, primarily for almond, apricot, peach, and sweet cherry, and 28,971 trait-associated loci. Most of the trait associations (72.4%) were from genome-wide association studies (GWAS), 18.7% from quantitative trait loci (QTL), and 8.9% from Mendelian trait loci. We identified 17 potential QTL hotspots for fruit morphology, fruit quality, and disease resistance, as well as 17 syntenic regions among peach, sweet cherry, and almond. These findings provide valuable resources for tool development for Prunus breeding, particularly for complex polyploid genomes and less-studied species.

Pears (genus Pyrus) are one of the most widely cultivated temperate fruit. Both abiotic and biotic stress, however, can be harsh constraints on pear cultivation; in America pear production has nearly ceased in the Eastern half of the nation, and in Europe extreme weather has become a growing threat to production, especially in Southern growing regions. Currently, high-quality reference genomes exist for the most widely cultivated Pyrus species, but little genomic information is available on ornamental, less cultivated, and wild Pyrus species. These species inhabit a wide range of climates across Eurasia, exhibiting diverse physiological adaptations to disease, high temperature, and water stress, while also showing variation in fruiting physiology and tree architecture. Discovery of genomic features responsible for this wide functional diversity could be applied to accelerating the genetic improvement of commercially cultivated Pyrus species. In order to characterize the genetic diversity within Pyrus, Nanopore whole genome DNA sequencing has been completed on 24 Pyrus accessions collected from the National Clonal Germplasm Repository, enabling highly contiguous (median N50 ~30Mb) and complete (median ~99% BUSCO assessed completeness), telomere-to-telomere assemblies with Hifiasm. Ab initio gene prediction via the BRAKER pipeline followed by comparative analysis with OrthoFinder has been used to find biome specific genes, while synteny analysis via MCScanX allows for the exploration of structural alterations in the evolution of Pyrus. These newly characterized Pyrus accessions represent an expansion of genomic resources to aid in the development of more resilient pears for the future.

Peach (Prunus persica (L.) Batsch) is a member of the genus Prunus within the Rosaceae family and represents one of the most extensively cultivated temperate deciduous fruit crops, ranking after apples and pears in global production. Due to its diploid genome (2n = 16) and relatively small genome size (~230 Mb), peach serves as a model species for fruit tree genome research. In this study, we performed whole-genome sequencing (WGS) on 445 peach genetic resources using the Illumina NovaSeq 6000 platform at a sequencing depth of 15´ coverage. Single nucleotide polymorphisms (SNPs) were identified from the WGS data and used to establish a core collection of peach genetic resources. Additionally, these SNPs will be utilized in a genome-wide association study (GWAS) to investigate key agronomic traits, including fruit shape, pollen fertility, flower morphology, maturity timing and so on. SNP filtration was conducted based on the following criteria: (1) SNPs with a missing rate exceeding 30% were removed, and (2) SNPs with a minor allele frequency (MAF) below 0.05 were excluded. As a result, 944,670 high-confidence SNPs were identified across the peach genetic resources. Based on this dataset, we established a core collection consisting of 150 accessions that retained over 99% of the total genetic diversity observed within the 445 peach genetic resources. Furthermore, we developed a high-resolution melting (HRM) marker derived from WGS-identified SNPs, which enables differentiation between round and flat peach fruit shapes. The SNP regions that can distinguish the fruit shape (round and flat shape) identified in this study were confirmed to be the same regions as the results of previously reported papers. Collectively, we successfully constructed a peach core collection through WGS analysis and developed a HRM marker for fruit shape classification. Also, our results produced in this study should be valuable for peach breeding program, identifying of agriculturally important genes, GWAS analyses, and further genomic studies in peach.

Although peach production worldwide has been increasing for decades, peach production in the United States continues to decline in the face of changing climate, disease pressures, and reduced consumption. Novel and diverse germplasm is required to improve peach breeding efforts with the goal of developing new cultivars better adapted to these challenges. Unfortunately, current peach SNP genotyping platforms are expensive and need to be outsourced to specialized laboratories. The purpose of this project is to use SNPs generated using Capture-Seq technology to evaluate the diversity of potential new sources of breeding material in comparison with germplasm from different regions of the world. In addition, our goal is to create a panel of SNP-based markers that can be used in-house for future studies. Capture-Seq technology yielded 134,424 SNPs when comparing P. persica (221 genotypes) and related Prunus species (29 genotypes). A PCA from these SNPs yielded different clusters representing Asian, Australian, European, and North American germplasm. AMOVA indicated that, among P. persica samples, 21.3% of the genetic variation was between regions with 78.7% of the variation present within regions. STRUCTURE analysis showed differences between regional groups, where the Asian group composition was different to the other regions, North American and European group composition were similar to each other, and the Australian group composition had a large percentage of genotypes sharing a group mostly present in Asia. This study confirms that Australia’s peach populations could be a valuable source of novel germplasm to bolster worldwide peach breeding efforts. Furthermore, a panel of informative SNP markers can be converted into KASP markers, which can be used in-house for numerous applications, including genetic fingerprinting, MAS, GWAS, among others.

‘Hamlin 1-4-1’ sweet orange (Citrus sinensis L. Osbeck) is one of the major varieties cultivated in Florida and is of relevant importance for the orange juice industry as an early maturing variety. While this cultivar does not produce juice of sufficient quality to meet USDA Grade A orange juice standards, it performs relatively well in semitropical climates characterized by high temperatures and humidity levels. To provide the bioinformatics tools required to support the genetic improvement of modern citrus varieties, we present the de novo and fully phased ‘Hamlin’ genome. The DNA of the plant was sequenced using two different platforms. PacBio technology was adopted to generate long reads sequencing, while Oxford Nanopore was employed to produce ultra-long reads. Hi-C technique was used to capture chromosome conformation and facilitate the correct assembly of contigs into two haplotypes. RNA samples were collected from five different tissues (leaves, petals, ovaries, peel, and bark) and sequenced with the Illumina platform. These RNA sequences enabled the identification and annotation of as many functional genes as possible. The results of this study will provide the genomic information required to compare the ‘Hamlin 1-4-1 genome with the more commonly grown industry standard ‘Valencia’ and to investigate the differences between the genomes of these two clonally derived sweet oranges. These data will also aid in comparing budlines of Hamlin and other sweet orange accessions that appear to be HLB tolerant. This research will facilitate the detection of DNA variants related to traits of interest and their integration in new germplasm resources. In addition, it will allow breeders to get further insights into mutations that may have occurred to new budlines originating from ‘Hamlin’.

Aneuploidy refers to a condition in which a cell or organism that has an abnormal chromosome number compared to the base chromosome number. This can cause gene dosage imbalances and a potential decrease in fitness. Most potato (Solanum tuberosum) cultivars are tetraploid (2n=4x=48) with a base chromosome number of 12. In this study, we analyzed 1,014 potato genotypes, 422 from two autotetraploid bi-parental full-sib populations and 592 from a diversity panel. We used allele SNP fluorescent intensity data for each individual to determine their ploidy and identify aneuploid individuals using the R package Qploidy. This package estimates the copy number by evaluating the standardized B allele frequencies (BAF) distributions across a sample, chromosome, or chromosome arm. Within the mapping populations, 41% of the members were aneuploids, compared to only 17% of the in the diversity panel; with an average of 27% aneuploidy level across all individuals included in the study. However, the frequency of aneuploidy for any given chromosome was 3%. As a measure of fitness, we compared 19 phenotypic traits related to tuber yield and quality in one of the full-sib mapping populations. There were significant differences between aneuploid and euploid family members for six traits. Aneuploid genotypes had significantly lower total tuber weight/plant, marketable tuber weight/plant, non-marketable tuber number/plant, tuber density, and overall appearance, while having higher percentage of tubers with heat sprouts compared to euploid family members. Chromosome additions were more common than chromosome losses in aneuploid individuals accounting for 57% and 39% of the aneuploid chromosomes, respectively. By analyzing this large potato genotypic dataset (most autotetraploids), we gained a better understanding of patterns of aneuploidy and their impact on crop performance in polyploid crops.

Salix pellita (satiny willow) is a state-threatened shrub willow species which is native to Minnesota and offers appealing ornamental traits. The natural distribution of this taxon in Minnesota is limited primarily by habitat loss. Because the disjunct populations of this species in Minnesota are in decline and because no prior efforts have been made to conserve this taxon, horticultural practices and cultivation could offer a preservation outlet for satiny willow. Prior to this project, Salix pellita was not represented in any germplasm repository in the United States. This study uses GBS (genotyping by sequencing) to characterize diversity among, between, and within wild collected Salix pellita populations from Minnesota, Michigan, and New Hampshire. Diversity metrics Fis, Fst , pairwise Fst and He were used to categorize genetic diversity. High Fis was found within most populations, which can be attributed to population isolation and small population size. Pairwise Fst between state populations (MN-MI, MN-NH, MI-NH) showed high levels of genetic differentiation, which can be attributed to the lack of gene flow between these populations. Ultimately, these metrics will be used to establish a genetically diverse ex situ collection of Salix pellita.

Phytophthora capsici is one of the top ten oomycete plant pathogens infecting a wide range of economically important crops. P. capsici was first reported to infect chile pepper (Capsicum annuum L.) in New Mexico Agricultural Research Station in Las Cruces, NM, and is currently a major threat on chile pepper production worldwide. The pathogen affects multiple plant parts at all stages of growth leading to death and significant economic losses. The diseases caused by P. capsici are difficult to eliminate which can be attributed to its broad host range, complexity of the inheritance of disease resistance, its global distribution, and diversity of the pathogen population. This study aims to analyse global distribution and diversity of P. capsici isolates infecting different hosts including Cucumis sativus, Cucurbita pepo, Capsicum annuum, Cucurbita maxima, Piper nigrum, Solanum lycopersicum, and Theobroma cacao by examining mitochondrial genes (secY, cox2, nad9, rps10) using Clustal Omega. Phylogenetic analyses based on different mitochondrial genes revealed diversity of P. capsici isolates. Based on secY, cox2, and nad9 genes, clustering patterns are found based on both the host from which they were isolated from and their geographical origin, while for rps10 gene, most of the isolates are found in one cluster. Notably, a separate analysis focusing on P. capsici isolates collected from C. annuum showed five isolates from South Korea (P15103, P1514, P15157, P15160, and P15161) clustered together, as did three isolates from New Mexico (P10199, P1091, and P3605). Similarly, isolates P10736 and P3941 from China, along with P15155 and P6741 from South Korea, consistently clustered together across all four genes analyzed. Future genetic diversity studies will include analysing the pangenome of P. capsici isolates from Texas, Florida, Arizona, Illinois, New Jersey, and New Mexico, USA; and screening of C. annuum recombinant inbred lines using different isolates with varying levels of virulence. Understanding genetic makeup of isolates may provide insights of their pathogenicity. Meanwhile, the results of screening of C. annuum recombinant inbred lines will aid in understanding the inheritance of disease resistance. Altogether, these approaches can contribute to the development of more effective and sustainable disease management strategies against P. capsici.

Bigleaf hydrangea (Hydrangea macrophylla) is an economically important ornamental shrub produced worldwide for the floral trade, as a container crop, and as a landscape plant. Powdery mildew (PM), caused by Golovinomyces orontii, is a widespread disease of bigleaf hydrangea impacting production and salability of plants. However, mechanisms of resistance to PM of bigleaf hydrangea are still largely unexplored. The purpose of this study was to investigate whole-plant response to PM infection and identify differentially expressed genes (DEGs) that contribute to the PM disease response in bigleaf hydrangea. Mature plants of four cultivars (‘Blushing Bride’, ‘Endless Summer’, ‘Nigra’, and ‘Veitchii’) were chosen based on their variable responses to natural PM infection. Powdery mildew was collected by harvesting naturally infected leaves from field plants and applied via spray inoculation averaging ~20ml per plant, with inoculum rate being 1 x 104 CFUmL-1, to six replicate plants per cultivar; one plant per cultivar was sprayed with water as a control. Whole plant response (% of plant tissue infected) was measured visually on a scale of 0-100% disease severity weekly starting from 29 Nov 2023 to 14 Feb 2024 and used to calculate Area Under the Disease Progress Curve (AUDPC). Plant tissue was sampled at 12 different time points, from 1 hour after inoculation (HAI) to 5 days after inoculation (DAI) using a leaf disc puncher and immediately flash frozen in liquid nitrogen. RNA was extracted using a Qiagen RNeasy Plant Mini kit and sequenced using NovaSeq. Adapters were removed from raw reads using fastp (0.23.4) and trimmed reads were aligned to the ‘Endless Summer’ reference genome using STAR (2.7.11b). STAR bam files were sorted with samtools (1.21) and featurecounts (2.0.6) was used for the gene model counting. DESeq was used to identify DEGs between ‘Veitchii’ and ‘Nigra’. There were significant differences among cultivars for AUDPC, with disease severity ranging between 7.7 and 19.2%. Bigleaf hydrangea ‘Nigra’ and ‘Endless Summer’ were the most susceptible to PM infection and ‘Veitchii’ the most tolerant. There were 11,629 DEGs total with 6,145 upregulated compared to ‘Veitchii’ and 5,484 downregulated compared to ‘Nigra’. DEGs were sorted by their P-adjust value followed by the Log 2-fold change. Many of the top 25 strongest DEGs include genes for plant stress such as serine threonine-protein kinase, PAN_AP, and leucine-rich repeat family proteins. These genes are currently being tested for expression levels among bigleaf hydrangea cultivars.

Tomato is one of the economically important agricultural crops worldwide. Approximately 80% of tomatoes are consumed fresh, while 20% are used in various processed food products. The tomato production in the United States (US) contribute and $2.8 billion to the national economy annually. However, virus infections are a major threat to tomato production and fruit quality. Tomato brown rugose fruit virus (ToBRFV) which was reported in 2014 and has spread in more than 50 countries since then, is a highly infectious and stable Tobamovirus spreads mechanically and can stay on a surface for weeks. Its ability to overcome existing resistance genes in tomato is the main concern, emphasizing the urgent need to identify tolerance or resistance in tomatoes cultivars. Besides this, horse nettle virus A (HNVA), recently reported to infect tomatoes in Oklahoma was previously limited to a weed named horse nettle (Solanum carolinense), and exhibits a concerning host shift, causing symptoms such as curling, cupping, and brown discoloration of leaves in tomatoes plants. The objective of this study was to evaluate commercially cultivated tomato cultivars in the US for resistance against both ToBRFV and HNVA. The tomato seedlings were inoculated mechanically with ToBRFV and HNVA and were observed and scored weekly at 7-, 14-, 21-, and 28-days post-inoculation (dpi) on a severity scale of 0 to 3 where 0,1, 2, and 3 correspond to no symptoms, mild, mildly severe and severe symptoms respectively. At 28 dpi, representative plants were tested using virus-specific RT-PCR assays to confirm systemic infection. The findings suggest that there are no resistant cultivars against ToBRFV while there are some showing tolerance based on the symptom severity scores. For HNVA, 22 cultivars have been screened so far and were mostly tolerant but not resistant. These results provide insights into the interaction of these emerging viruses with widely grown tomato cultivars and help us to identify tolerant cultivars to inform the growers and the variation in disease severity which would be valuable for breeders to guide future breeding strategies aimed at ToBRFV and HNVA resistance.

Focus on the role of National Clean Plant Networks and other agencies (potentially including private parties), and discuss best practices.

Jerusalem artichoke (Helianthus tuberosus L.) (sunchoke) presents a resilient and low-input crop alternative with potential for both biomass and tuber production. However, a comprehensive understanding of varietal performance in specific environments like Ohio is essential to unlock its full agricultural potential. This study evaluated the growth and yield performance of five Sunchoke varieties (Beaver Valley, Dwarf Sunray, Jack's Copperclad, Supernova, and White Fuseau) in Ohio, during the 2024 growing season. Plant height, tuber number, root system weight, and morphological characteristics were assessed. Variations were observed among the varieties in terms of growth and yield. "Dwarf Sunray" exhibited the highest growth rate, while "Jack's Copperclad" had the lowest. "White Fuseau" yielded the highest tuber count and weight, approximately nine times more than "Jack's Copperclad". Tuber production was positively correlated with root system weight. Varieties also differed in branching patterns, flowering time, tuber shape, and tuber color. This study provides preliminary data for selecting varieties suitable for further research and evaluation in Ohio. The study emphasizes the importance of considering root system development for improved tuber yield and suggests future research should focus on the genetic basis of trait variations and varietal performance under diverse conditions.

With an economic value exceeding $68 billion USD, grapes are third in global horticultural crop production, with production across 93 countries. Recurring incidents of extreme weather conditions are forcing growers to alter conventional production practices. Reduced production areas, shifts in pest management, decreased water availability, increased temperature stress, and extreme weather events have all negatively impacted global grape production. There is a need to develop resilient grape cultivars that can survive the vagaries of nature. In the late 1800s, American horticulture scientist Thomas Volney Munson utilized 10 of the 13 Vitis spp. native to Texas and SW USA to develop cultivars that were adapted to the North American environment and resistant to the pests and pathogens of this area. Munson introduced 300 cultivars, of which 87 remain today. These cultivars have the potential to offer improved fruit quality combined with pest and pathogen resistance, traits that are sought after in modern grape breeding programs. Due to the wide range of parental material used to improve these native grapes, Munson’s cultivars offer a largely untapped genetic resource. By performing whole genome sequencing on the remaining 87 cultivars and the parental lines, we aim to develop a pangenome encompassing the full range of genetic diversity within the remaining Munson cultivars. This study will help clarify the lineage and shed light on any discrepancies in the records. The genomic characterization of the Munson cultivars will also aid in identifying potential resistance genes in these cultivars. This work is expected to secure profitable and resilient production of grapes in the US.

Freezing injuries account for an estimated 15 % of global grape production losses annually, posing a significant challenge to sustainable viticulture. This study investigated phenotypic variation correlated with cold hardiness in two biparental mapping populations to explore potential markers for selecting cold‐hardy genotypes. Quantitative trait locus (QTL) mapping was also performed to identify loci that could accelerate the development of environmentally resilient grape cultivars. We examined two F₁ families—312 hybrids from V. riparia × V. vinifera ‘Fresno Seedless’ and 302 hybrids from V. amurensis × V. vinifera ‘Valley Pearl’. Differential thermal analysis (DTA) was used to assess bud cold tolerance, and we recorded additional traits including bud water content, trunk and cane diameters, and post–bud‐break phenology. Significant variation was observed in cold hardiness and all measured phenotypes. High‐quality genetic linkage maps were generated for both populations, providing a solid foundation for subsequent QTL analysis and marker development. This research offers a sustainable strategy for breeding cold‐hardy grape cultivars that maintain productivity under harsh conditions and speeds breeding efforts in support of climate‐adaptive viticulture.