Sequence diversity and linkage disequilibrium surrounding the maize Y1 locus on chromosome 6

We investigated the effects of human selection for yellow endosperm color, representing elevated carotenoid content, on two maize genes, the Y1 phytoene synthase, and PSY2, a putative second phytoene synthase. Multiple polymorphic sites were identified at Y1 and PSY2 in 75 white and yellow maize inbreds. Many polymorphic sites showed strong association with the endosperm color phenotype at Y1, but no detectable association was found at PSY2. Nucleotide diversity (π) was equivalent for whites and yellows at PSY2 but was 19-fold less in yellows than in whites at Y1, consistent with the white ancestral state of the gene. The strong sequence haplotype conservation within yellows at Y1 and a significant, negative Tajima's D both verified positive selection for yellow endosperm. We propose that two independent gain of function events associated with insertions into the promoter of the Y1 gene and that up-regulation of expression in endosperm has been incorporated into yellow corn.; Because we predict that selection has occurred relatively recently in the history of maize, we set out to discover just how far the signature of selection for the yellow endosperm phenotype continues. To this end, we analyzed patterns of sequence diversity and linkage disequilibrium in 9 low copy regions located at varying distances from the Y1 gene. The association of informative SNPs with endosperm color phenotype, strong linkage disequilibrium, and significantly reduced diversity within the yellow endosperm haplotypes portrayed a 600 kb+ selective sweep on one end of Y1 and a rapid decline in patterns of conservation and LD on the other. The asymmetric selective sweep surrounding Y1 is likely to have occurred as a result of differences in recombination rates in the regions proximal and distal to the gene.; The orientation of the Y1 gene relative to the physical map was determined through shotgun sequencing assembly and long range PCR. The 3′ end of the gene is the side of the BAC contig that evinces the more pronounced selective sweep; however, the MLO homolog immediately adjacent to the 3′ end of Y1 shows patterns not indicative of this extension. Explanations for the dramatic differences in diversity at the MLO relative to its bordering regions include diversifying selection at the MLO, a higher mutation rate, or that each introgression of yellow endosperm was linked to a different MLO variant. The long range patterns of LD and reduced diversity within this region of chromosome 6 do suggest that the whole genome scan is suitable for genes that have experienced directional selection in recent breeding history.