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Evidence for a Selective Sweep on Chromosome 1 of Cultivated Sorghum

A.M. Casa, S.E. Mitchell, M.T. Hamblin, and S. Kresovich, Institute for Genomic Diversity, Cornell Univ., Ithaca, NY 14853; J.D. Jensen and C.F. Aquadro, Dep. of Molecular Biology and Genetics, Cornell Univ., Ithaca, NY 14853; A.H. Paterson, Plant Genome Mapping Laboratory and Comparative Grass Genomics Center, Univ. of Georgia, Athens, GA 30602. DNA sequences were deposited in GenBank under accession numbers DQ459071, DQ462793–DQ463100

View larger version (8K): [in this window] [in a new window]   Fig. 1. Dot plot showing areas of sequence similarity between Sorghum bicolor BAC c0156b06 and rice chromosome 3. The x axis shows the rice genome coordinates (nucleotides), and sorghum coordinates are on the y axis. Note that the sorghum BAC sequence is in opposite orientation to the rice sequence (i.e., lower right line in the diagonal corresponds to sorghum gene 1 on Table 2). Arrows on the right side of the figure span the sorghum retrotransposon insertions.

View larger version (16K): [in this window] [in a new window]   Fig. 2. Diversity, divergence, and population differentiation (Fst) for 10 loci in a 99 kb region flanking Xcup15 in cultivated and wild Sorghum bicolor lines. The y axis shows levels of diversity (x100) and divergence (x100) and S. bicolor BAC c0156b06 coordinates (bp) are on the x axis (actual numbers were multiplied by 100 to obtain the reported numbers). Solid and dashed trend lines represent diversity and divergence, respectively. Cultivated and wild sorghum accessions are denoted by open squares and circles, respectively. The solid gray line with asterisks shows Fst values, a measure of population differentiation between cultivated and wild lines. Loci sampled are designated by numbers and letters along the lines (see Table 3). The asterisk to the right of the graph denotes average divergence levels between cultivated sorghum and S. propinquum based on genome-wide estimates. The arrow head along the x axis indicates the approximate location of SSR locus Xcup15.

View larger version (38K): [in this window] [in a new window]   Fig. 3. Haplotypes observed in the Xcup15 region of cultivated and wild sorghum excluding locus 9–10b. Numbers across the top of the figure indicate the site coordinate within the BAC sequence (bp), and the shaded area denotes the position of the derived fixed nucleotide difference between cultivated and wild sorghum accessions. Dots indicate sequence identity to reference sequence. Segregating nucleotide sites are shown only for accessions with no missing data. Insertion–deletion polymorphisms were excluded from the analysis. Mutations unique to S. propinquum are not shown.