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Molecular Plant Breeding 2013, Vol.4, No.38, 297
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Figure 2 LD between 141 SSR markers
Note: The diagonal represents LD between each site and itself; The R^2 in the upper right represents the correlation between alleles
at two loci, the P-value in the lower right indicates the extent of linkage equilibrium; Level of significance is indicated by colors
a decrease in the effective recombination rate, while
bottlenecks and selection will reduce the number of
haplotypes in domesticated rice, all of which would
inflate LD in the species (Mather et al., 2007). Further
more, the 184 rice germplasm accession used in the
experiment could be clustered into three major
subpopulations and which could be further divided
into 7 subpopulations as we had reported previously
(Xiao et al., 2012), as various aspects of population
structure are thought to influence LD, LD arises in
structured populations when allelic frequencies differ
at two loci across subpopulations (Oraguzie et al.,
2007).
In cultivated barley genome-wide LD extended from
10 cm to 15 cM when evaluated with SSRs
(Malysheva-otto et al., 2006) markers, and the pattern
of LD was extremely population dependent.