Figure 2: Illustration of the 350-kb selective sweep region.
From: Analysis of elite variety tag SNPs reveals an important allele in upland rice
Nucleotide diversity (π) is the number of nucleotide differences per site between two randomly chosen sequences of upland and irrigated rice (see Methods). (a) Selective sweep signals around the Nced gene. The horizontal axis shows the coordinates on chromosome 12. For example, ‘1.4e+07’ refers to the coordinate ‘14,000,000’. The vertical axis indicates π values. The red, blue and black curves indicate π values of the T-type upland population, C-type upland population and irrigated population, respectively. The green vertical line marks the position of the Nced gene. (b) A 350-kb selective sweep region on chromosome 12; ‘12S’ and ‘12L’ indicate the short and long arms of chromosome 12, respectively. (c) Eleven genes in the 350-kb region; the yellow arrow is the Nced gene. (d) The protein-altering ETAS in Nced is indicated with a red asterisk.
