Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.

Natural Genetic Diversity of Nutritive Value Traits in the Genus Cynodon

The Cynodon spp. collection maintained by United States Department of Agriculture National Plant Germplasm System (USDA-NPGS) has limited information on nutritive value (NV) traits. In this study, crude protein (CP), phosphorous concentration (P), in vitro digestible organic matter (IVDOM), and neutral detergent fiber (NDF) were determined to (i) estimate genetic parameters for NV, (ii) obtain genetic values for the whole population across two harvests, (iii) estimate genotype by harvest interaction (GHI) for NV traits, and (iv) select accessions exhibiting improved NV traits compared to ‘Tifton 85′. The experiment was setup as a row-column design with two replicates and augmented representation of controls: Tifton 85, ‘Jiggs’, and ‘Coastal’. The whole-population was harvested twice, and data were analyzed using linear mixed models with repeated measures. In addition, a selected population of 15 genotypes were evaluated across 11 harvests to determine the extent of GHI. Genetic parameters revealed the presence of significant genetic variability, indicating potential improvements for NV through breeding. Specifically, P and IVDOM presented large variation, while NDF had lower diversity but some accessions exhibited lower NDF than Tifton 85. Low GHI, except for IVDOM, indicated genotypic stability and potential for selecting improved accessions under fewer harvests. Breeding line 240, PI-316510, and PI-3166536 presented superior NV than Tifton 85.

Genetic characterisation of the petal spot phenotype for Gossypium arboreum accession PI 408798

The occurrence of floral petal spots is common among flowering plants and plays a major role in attracting pollinators. Cotton genotypes having large red petal spots are frequent in the United States Department of Agriculture, National Plant Germplasm System Gossypium arboreum (L.) collection. One accession, PI 408798, showed a unique faint red petal spot phenotype. To genetically characterise this trait, a F₂ population of 226 plants was developed by crossing PI 408798 with G. arboreum accession PI 529714 that lacked pigmented petal spots. From the population, 161 plants showed the presence of faint red petal spots; whereas, 65 plants lacked pigmented petal spots. These data supported the single dominant gene model for the presence of floral petal spots. Accession PI 408798 will provide an important genetic resource to characterise the genes involved in the pathway controlling floral pigmentation.

DNA Content and Ploidy Estimation of Festuca ovina Accessions by Flow Cytometry

ABSTRACTFestuca ovina is a fine fescue that is used as a low-input turfgrass. The ploidy levels of F. ovina accessions held by the USDA National Plant Germplasm System (NPGS) are unknown, limiting the use of the germplasm in breeding programs. The objective of this study was to determine DNA content and estimate ploidy of these 127 accessions. Among the accessions, we identified a wide range of ploidy levels from diploid to octoploid. We also found the accessions with higher ploidy levels usually had larger seed size. These results will be informative to plant breeders and researchers using germplasm from the F. ovina collection and point to challenges in maintaining polyploid, outcrossing germplasm seed stocks in common nurseries.

New genetic sources for orange color in cucumber (Cucumis sativus L.) fruit flesh

Most cucumber varieties have fruits with white flesh, which is devoid of ß-carotene and has a low concentration of total carotenoids. Carotenoids are important nutrients for humans and animals. Thus, developing cucumber varieties with orange flesh could provide a new nutritionally enhanced food source. Some cucumbers with yellow and orange flesh have been described, but there are others that have not been studied. Here, we used three cucumber PI lines, reported to produce colored fruits, from the USDA National Plant Germplasm System to generate three F2 populations. Fruits from the F2 populations with colored flesh (green, yellow, or orange) were pooled, and an equal number of fruits with white flesh were pooled. RNA was isolated from the pools and used for RNA sequencing to determine gene expression differences and to identify SNPs in each pool. The orange color of the cucumber fruits was confirmed to be due to ß-carotene. There were no clear expression patterns for genes of the carotenoid biosynthesis pathway that would suggest that their expression controlled the coloration of fruits. Mutations in carotenoid biosynthesis genes also did not explain the variation. However, we detected a SNP in the homolog of the Or gene that is responsible for ß-carotene accumulation in orange cauliflower. This genetic basis is different from that of previously studied orange cucumbers, but our results suggest that Or is not the only factor. These results provide the basis for future studies for breeding orange cucumbers for commercial or home garden production.

Identification of Historic Homestead and Orchard Apple Cultivars in Wyoming

Thousands of apple trees were planted in Wyoming’s orchards and homesteads in the 1800s, many of which are still alive today. Unfortunately, cultivar identity of these trees has mostly been lost or obscured. The purpose of this research was to identify heritage apple cultivars in Wyoming using genetic fingerprinting (microsatellite) techniques and to use this information to make recommendations on candidate cold-hardy cultivars for specialty crop and breeding programs. Leaf samples were collected from 510 heritage apple trees from 91 sites in 19 locales across Wyoming. Known cultivars from the U.S. Department of Agriculture (USDA)–National Plant Germplasm System, Seed Savers Exchange, and Washington State University apple collections were used as standards to determine cultivar identities. Overall, 328 (64%) of the previously unidentified apples trees were identified to 47 known cultivars. Fifteen of these known cultivars comprised more than 80% of the samples that were identified, with all 15 of those cultivars developed in states and countries with average temperatures or winter conditions similar to Wyoming. Seventy-one of the heritage trees were identified as the Wealthy cultivar. Other commonly identified cultivars were Haralson, Patten’s Greening, Yellow Transparent, Northwestern Greening, and McMahon. It is likely that a combination of popularity and cultivar origin affected the choice of cultivars that were grown in Wyoming. Although most original Wyoming heritage apple trees are reaching the end of their life span, many surviving trees continue to produce fruit. This strongly suggests that despite lower resistance to certain pathogens than many modern cultivars, these heritage trees should be considered for use today. The results provide insights into possible cultivars that could be grown in Wyoming and also in other states with similar harsh growing conditions.