High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.
Bottom Line: We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity.LD decay was estimated for various chromosomes.We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.
Affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000 email@example.com.Show MeSH
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Mentions: PCA of the 1563 SNPs revealed two dimensions, clustering according to cultivated, semi-wild, and wild accessions (Figure 1 and Table S2). We constructed 11 NJ trees with various chromosome-specific SNPs separately to resolve the differences among sweet, semi-wild, and wild watermelon and to understand the effect of various chromosome-specific SNPs on the clustering pattern. All chromosome-specific phylograms clearly separated wild, semi-wild, and sweet watermelon types into distinct clusters, so domestication of sweet watermelon is a genome-wide process. Chromosome-specific trees resolved sweet watermelons into a variable number of subclusters ranging from 2 to 10 (Figure S1A and Figure S1B). Despite no clear pattern of clustering based on geographic distribution, most of the US cultivars were grouped into a subcluster in all chromosome-specific trees.
Affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000 firstname.lastname@example.org.