Abstract
Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high-throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber (Cucumis sativus L.). The GBS data, derived from 1234 cucumber accessions, provided more than 23 K high-quality single-nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10.6 kb). The SNP markers were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the NPGS cucumber collection. These results, providing detailed genetic analysis of the U.S. cucumber collection, complement NPGS descriptive information regarding geographic origin and phenotypic characterization. We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies (GWAS). Finally, we developed a molecularly informed, publicly accessible core collection of 395 accessions that represents at least 96% of the genetic variation present in the NPGS. Collectively, the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection, and will provide a valuable resource for genetic analyses, gene discovery, crop improvement, and germplasm preservation.
Highlights
Improvements in crop yield, ability to withstand abiotic and biotic stresses, and superior product quality all depend on genetic variation for key agronomic and horticultural traits
How do we evaluate the extent and nature of variation that exists within the collection? How can we access that variation for crop improvement? the past decade has ushered in powerful genomic tools that allow for high throughput, high resolution, genetic characterization, while providing breeders more efficient access to, and use of, the diversity available within collections
Since Turkey is a country straddling Asia and Europe, we put accessions from Turkey as an independent group. We genotyped these cucumber accessions, as well as two non-cucumber but closely related accessions plant introductions (PIs) 618817 (C. myriocarpus) and PI 282446 (C. heptadactylus), using the GBS technology, which generated a total of ~1.35 billion reads of 101 bp in length
Summary
Improvements in crop yield, ability to withstand abiotic and biotic stresses, and superior product quality all depend on genetic variation for key agronomic and horticultural traits. In search of such variation, breeders frequently turn to germplasm collections to find new sources of valuable characteristics, especially resistances to diseases, insects, and environmental stresses such as heat, drought, salt, or cold. To facilitate these breeding efforts and maintain critical diversity for future generations, many national and international institutions have developed extensive germplasm collections to provide repositories of genetic variation. The importance of such collections as a critical first step to conserve biological variation, especially in light of genetic erosion resulting from habitat loss, adoption of modern varieties, and climate change, is increasingly recognized as
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