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High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

Reddy UK, Nimmakayala P, Levi A, Abburi VL, Saminathan T, Tomason YR, Vajja G, Reddy R, Abburi L, Wehner TC, Ronin Y, Karol A - G3 (Bethesda) (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000 ureddy@wvstateu.edu.

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Related in: MedlinePlus

Principal component analysis (PCA) based on the first two components showing distribution of sweet, semi-wild, and wild watermelons by using 1563 single nucleotide polymorphisms (SNPs) generated by genotyping by sequencing (GBS). See Table S1 for a list of accessions and Table S2 for respective eigen values to locate individual accessions on the graph.
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fig1: Principal component analysis (PCA) based on the first two components showing distribution of sweet, semi-wild, and wild watermelons by using 1563 single nucleotide polymorphisms (SNPs) generated by genotyping by sequencing (GBS). See Table S1 for a list of accessions and Table S2 for respective eigen values to locate individual accessions on the graph.

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.


High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.

Reddy UK, Nimmakayala P, Levi A, Abburi VL, Saminathan T, Tomason YR, Vajja G, Reddy R, Abburi L, Wehner TC, Ronin Y, Karol A - G3 (Bethesda) (2014)

Principal component analysis (PCA) based on the first two components showing distribution of sweet, semi-wild, and wild watermelons by using 1563 single nucleotide polymorphisms (SNPs) generated by genotyping by sequencing (GBS). See Table S1 for a list of accessions and Table S2 for respective eigen values to locate individual accessions on the graph.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232547&req=5

fig1: Principal component analysis (PCA) based on the first two components showing distribution of sweet, semi-wild, and wild watermelons by using 1563 single nucleotide polymorphisms (SNPs) generated by genotyping by sequencing (GBS). See Table S1 for a list of accessions and Table S2 for respective eigen values to locate individual accessions on the graph.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000 ureddy@wvstateu.edu.

Show MeSH
Related in: MedlinePlus