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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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Collinearity between genetic and physical maps (markers that are distant from the “line of best fit” are not collinear).
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fig4: Collinearity between genetic and physical maps (markers that are distant from the “line of best fit” are not collinear).

Mentions: We examined the collinearity of genetic and physical maps for various chromosomes (Figure 4). Markers on chromosomes 3, 5, 7, and 10 were highly co-linear in terms of physical location. Chromosomes 1, 2, 4, 8, and 9 moderately agreed with the watermelon reference sequence. Chromosome 11 showed the highest disagreement between the genetic and physical map on either side of the chromosome; it contained a large segment that was not collinear with the physical map. We observed 17 major genome rearrangements or disagreements across all chromosomes.


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)

Collinearity between genetic and physical maps (markers that are distant from the “line of best fit” are not collinear).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Collinearity between genetic and physical maps (markers that are distant from the “line of best fit” are not collinear).
Mentions: We examined the collinearity of genetic and physical maps for various chromosomes (Figure 4). Markers on chromosomes 3, 5, 7, and 10 were highly co-linear in terms of physical location. Chromosomes 1, 2, 4, 8, and 9 moderately agreed with the watermelon reference sequence. Chromosome 11 showed the highest disagreement between the genetic and physical map on either side of the chromosome; it contained a large segment that was not collinear with the physical map. We observed 17 major genome rearrangements or disagreements across all chromosomes.

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