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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

Distribution of genome-wide recombination rate (GWRR) and observed nucleotide diversity (π) along chromosomes in the watermelon genome. In each plot, the horizontal axis (in Mb) represents the physical distance (PD) along the reference chromosomes and the vertical axis (cM/Mb) represents the genetic-to-physical distance ratio (green) and log −2 transformed values of nucleotide diversity (π).
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fig5: Distribution of genome-wide recombination rate (GWRR) and observed nucleotide diversity (π) along chromosomes in the watermelon genome. In each plot, the horizontal axis (in Mb) represents the physical distance (PD) along the reference chromosomes and the vertical axis (cM/Mb) represents the genetic-to-physical distance ratio (green) and log −2 transformed values of nucleotide diversity (π).

Mentions: Observed nucleotide diversity was mapped against the physical map to show the pattern of distribution. Nucleotide diversity varied within and across the chromosomes. Mean and SD of nucleotide diversity (observed and expected) for cultivated and semi-wild watermelon are provided in Table 1. The difference in nucleotides between semi-wild and cultivated watermelon was largest for the chromosome 3 as compared with the other chromosomes, so this chromosome harbors mutations and genes of importance for the process of domestication. Moreover, nucleotide diversity was the least in chromosome 3, which supports this chromosome harboring signals of domestication (Figure 5).


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)

Distribution of genome-wide recombination rate (GWRR) and observed nucleotide diversity (π) along chromosomes in the watermelon genome. In each plot, the horizontal axis (in Mb) represents the physical distance (PD) along the reference chromosomes and the vertical axis (cM/Mb) represents the genetic-to-physical distance ratio (green) and log −2 transformed values of nucleotide diversity (π).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: Distribution of genome-wide recombination rate (GWRR) and observed nucleotide diversity (π) along chromosomes in the watermelon genome. In each plot, the horizontal axis (in Mb) represents the physical distance (PD) along the reference chromosomes and the vertical axis (cM/Mb) represents the genetic-to-physical distance ratio (green) and log −2 transformed values of nucleotide diversity (π).
Mentions: Observed nucleotide diversity was mapped against the physical map to show the pattern of distribution. Nucleotide diversity varied within and across the chromosomes. Mean and SD of nucleotide diversity (observed and expected) for cultivated and semi-wild watermelon are provided in Table 1. The difference in nucleotides between semi-wild and cultivated watermelon was largest for the chromosome 3 as compared with the other chromosomes, so this chromosome harbors mutations and genes of importance for the process of domestication. Moreover, nucleotide diversity was the least in chromosome 3, which supports this chromosome harboring signals of domestication (Figure 5).

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