Title |
Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon
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Published in |
BMC Genomics, September 2014
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DOI | 10.1186/1471-2164-15-767 |
Pubmed ID | |
Authors |
Padma Nimmakayala, Amnon Levi, Lavanya Abburi, Venkata Lakshmi Abburi, Yan R Tomason, Thangasamy Saminathan, Venkata Gopinath Vajja, Sridhar Malkaram, Rishi Reddy, Todd C Wehner, Sharon E Mitchell, Umesh K Reddy |
Abstract |
A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication. |
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