The Genome Database for Rosaceae (GDR, https://www.rosaceae.org/) and the Genome Database for Vaccinium (GDV, https://www.vaccinium.org/), are databases that support genomics, genetics and breeding in under-represented crops like small fruits. These fruit crops include Fragaria (strawberry), Rubus (red raspberry, black raspberry, and blackberry) in GDR, and Vaccinium (blueberry and cranberry) in GDV. Data include curated genome sequences, genetic maps, markers, QTL, genes, transcripts, germplasm, and publications, made accessible to browse, query and download through easy-to-use web interfaces and tools. One of the objectives of a 2022-funded SCRI- project ‘Advanced National Database Resources for Specialty Crop Research and Improvement’ is to collect, curate, and integrate all types of genomics, genetics, and breeding big data in easy-to-use and robust crop-specific databases. In this presentation, we summarize our progress towards curating and making available phenotype and genotype data for strawberry. We also present a strawberry Crop Ontology we have developed with input from crop researchers and breeders from North America and Europe. Public availability of phenotypic and genotypic data in GDR, GDV, and GRIN-GLOBAL will allow easy access to this data to use in genome-wide association studies. Crop Ontology will enable digital capture and trait data integration across locations and projects.
A major focus in plant breeding has been the improvement of crops through various traits that affect disease resistance and yield. However, the focus on productivity has led to an inattentiveness to other traits that specifically affect produce quality. An example of a critical fruit quality trait is its flavor, contributing to our perception of aromatic volatiles. Even at nanomolar concentrations, aromatic volatiles can be perceived by the olfactory system and influence the liking of the fruit. The focus of this study was to investigate the genetic aspect of the branched-chain amino acid (BCAA) volatiles, derived from L-valine, L-isoleucine and L-leucine, in tomato fruits. It is generally considered that these BCAA-derived volatiles contribute positively to overall liking, because these are essential amino acids required by the human diet. To identify quantitative trait loci (QTLs) affecting the biosynthetic pathway for 11 BCAA-derived volatiles, a Genome-Wide Association Study (GWAS) was conducted using a diverse and unique panel of 167 tomato accessions. The GWAS was run using the FarmCPU model in GAPIT-R, with a total of 21,893,681 SNPs, 2,735,297 INDELs, and 154 structural variants across the genome. Furthermore, a weighted gene co-expression network analysis (WGCNA) was conducted in parallel to identify modules of co-expressed genes that cluster with known genes that affect the BCAA-derived volatile pathway. A total of 113 QTLs were identified from GWAS and 3024 co-expressed genes were identified from the WGCNA. Candidate genes were screened based on annotated biochemical function, overlap within the GWAS QTLs, and gene expression in the red-ripe fruits. This led to the identification of two candidate genes, one on the long arm of chromosome 1 and another on the long arm of chromosome 11. These genes are being knocked-out using CRISPR-Cas9, and current progress is aimed to confirm the validity and function of these genes in the near-future.
Understanding the genetic composition and diversity of plant collections is crucial for their effective management and utilization in breeding programs. Cultivated strawberry (Fragaria x ananassa) is a significant global crop, contributing substantially to the U.S. agricultural economy with more than $3 billion in production value. The USDA-ARS National Clonal Germplasm Repository (NCGR) maintains a collection of cultivated and wild Fragaria accessions, which provide a valuable source of disease-resistance and other quality traits for the improvement of cultivated strawberry. Despite the recognized importance of genetic diversity, an in-depth assessment of genetic relationships within the USDA-ARS collection remains incomplete. To address these gaps, we genotyped 1,876 cultivated and wild Fragaria accessions from NCGR using a strawberry 5K DArTag marker panel. The evaluation of microhaplotype-based missing data rates revealed an increase in percent of missing data with an increased distance from the cultivated strawberry. This trend is expected because the 5K panel was developed based on the octoploid cultivated strawberries. Among the species studied, the higher ploidy accessions representing F. x vescana, F. x ananassa, F. virginiana, F. cascadensis, and F. chiloensis exhibited the least missing data, with percentages of 2.6%, 5.0%, 7.5%, 10.2%, 14.7%, respectively. Conversely, diploid accessions mostly Asian F. daltoniana, F. nubicola, F. viridis (Eurasian), F. pentaphylla, and F. nilgerrensis displayed the highest percentages of missing data, with 87.1%, 82.5%, 80.2%, 80.2%, 79.9%, respectively. Utilizing the microhaplotypes derived from the 5K panel, a total of 17,925 SNPs were identified after quality filtering, which were then used to assess the ancestry and genomic diversity of the Fragaria species housed within the USDA-ARS collection. We performed PCA and UPGMA analyses, and found distinct species clusters for each putative taxonomic assignment, suggesting high concordance between sample genotype and species identity. Finally, species-specific loci were then identified and genomic diversity analyses were performed for species represented with more than five accessions. Our findings clarified the identity and diversity of Fragaria within the USDA-ARS germplasm collection, aiding in germplasm conservation efforts and informing future breeding initiatives.
The USDA National Plant Germplasm System is a network of germplasm repositories dedicated to conserving genetic diversity of crops and their wild relatives. The USDA grapevine (Vitis) repository contains 5000 unique accessions representing 36 species, and is divided between two locations: Davis, CA and Geneva, NY. While this material is available for distribution to researchers and breeders, there is currently limited characterization data to help requestors identify accessions with unique and valuable traits, particularly for fruit quality. Thus, we began a germplasm screening project to measure fruit quality traits of 481 unique accessions from both locations spanning three years (2022-2024). Fruit samples were juiced, filtered through cheesecloth, and analyzed for Brix, titratable acidity, and available nitrogen. Additionally, composition of phenolic compounds was assessed using liquid chromatography-mass spectrometry (LC-MS), and aromas were detected using solid phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS). Overall, there was a wide range of diversity in fruit quality traits across the collection. Brix values ranged from 8.5 to 30.1 (average=17.8), and titratable acidity ranged from 2.7 to 25.6 g mol-1 Tartaric acid equivalents (average=8.2). The phenolic compounds commonly detected in grape juice included the anthocyanins malvidin 3-O-glucoside and peonidin 3-O-glucoside, the hydroxycinnamic acid caftaric acid, and the flavonols quercetin 3-O-glucuronide and isoquercetin. Analysis of aromatic compounds revealed accessions that contained higher amounts of linalool, β-myrcene, and geraniol, which are associated with a “Muscat” flavor profile, while others contained methyl anthranilate, which is associated with a “Foxy” flavor profile. We hope this fruit quality dataset not only proves to be a valuable asset to researchers utilizing the USDA Vitis repository, but may also open new directions of exploration into improved grape flavor, nutrition, and quality.
Genetic diversity is invaluable to the sustainability of American horticulture. In the case of tart cherry, production in the United States is precariously reliant on a single cultivar, ‘Montmorency.’ Our research explores diverse genetic resources in tart cherry to promote utilization of high quality and locally adapted cultivars for plant breeding and improved production. Tart cherry nutritional quality is of particular interest to consumers. The United States Department of Agriculture Tart Cherry collection in Geneva, New York maintains 100 cultivars of tart cherry, including their wild relatives. Over a five-year period, we assayed fruit quality traits, including Brix, titratable acidity, and phenolic content. Total soluble solids (TSS) ranged from 10.9 to 20.7% (average=14.8%) and acidity (TA) ranged from 5.3 to 32.1 g/L (average=16.3%). The sugar/acid ratio ranged from 3.7 to 27.6 (average=10.2). Individual fruit weight ranged from 0.2 to 8.6 g (average of 5.0 g) and pit weight percentage ranged from 6-32% (average=11%). Total anthocyanin content varied from 75.2 to 3760.0 μg/g, with an average of 771.4 μg. We also evaluated bloom phenology over a three-year period. The distribution of bloom ranged from 56.7 to 134.4 GDD, with an average value of 86.0 Growing Degree Days (GDD ). ‘Montmorency’ bloom was above average with values around 95.8 GDD. Sweet cherries (63.5 – 90.6 GDD) tended to bloom much earlier than tart cherries (64.9 –118.0 GDD) and P. fruticosa, the wild progenitor of the tart cherry, bloomed the latest with a range of 85.3 to 134.4 GDD. For Brix, acidity, and phenolic content, ‘Montmorency’ falls significantly below average, though it has a balanced sugar/acid ratio. ‘Montmorency’ is lacking in anthocyanin content which is increasingly relevant for the juice industry. It tends to bloom later than other tart cherries evaluated, though there are some more extreme late bloomers. This data will be available through GRIN-Global, the USDA germplasm database to facilitate future research and breeding.
Hydrangea quercifolia, oakleaf hydrangea, a flowering shrub native to woodlands of the southeastern United States. Oakleaf hydrangea has immense ornamental potential with four-season interest, including traits like showy panicles, striking foliage textures, red fall color, and exfoliating bark. Cultivars are often derived from wild selections either directly or only a few generations removed. Full genetic and phenotypic variation has not been evaluated for the species, and little is known about the diversity in horticulturally important traits for oakleaf hydrangea. For this study, growth and plant architecture of wild-collected oakleaf hydrangea seedlings were observed at the Otis L. Floyd Nursery Research Center in McMinnville Tennessee over a 3-year period. Seedlings from 14 populations of oakleaf hydrangea spanning the species’ native range were planted in a randomized complete block design containing six blocks and nine replications per block. Two-way ANOVA was used to partition variation in height, width, growth rate, and number of stems into sources attributable to block, population, and block × population. There were significant differences among populations for growth rate, size, and number of stems in all years. Southern populations were smaller than northern populations and showed a slower growth rate. Genetic and phenotypic variation shown among populations will guide conservation efforts and supplement breeding efforts for oakleaf hydrangea.
