Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Abstract

Both yellow and white corn occurs among ancestral open pollinated varieties. More recently, breeders have selected yellow endosperm variants of maize over ancestral white phenotypes for their increased nutritional value resulting from the up-regulation of the Y1 phytoene synthase gene product in endosperm tissue. As a result, diversity within yellow maize lines at the Y1 gene is dramatically decreased as compared to white corn. We analyzed patterns of sequence diversity and linkage disequilibrium in nine low copy regions located at varying distances from the Y1 gene, including a homolog of the barley Mlo gene. Patterns consistent with a selective sweep, such as significant associations of informative single-nucleotide polymorphisms with endosperm color phenotype, linkage disequilibrium, and significantly reduced diversity within the yellow endosperm haplotypes, were observed up to 600 kb downstream of Y1, whereas the upstream region showed a more rapid recovery. The starch branching enzyme 1 (sbe1) gene is the first region downstream of Y1 that does not have a highly conserved haplotype in the yellow endosperm germplasm.

Fig. 1.

The arrangement of the identified low copy regions surrounding the Y1 gene on the BAC physical contig. Horizontal lines indicate individual BAC clones. BACs 1-3 represent the BACs with low copy BAC ends, whereas BAC 4 is the Y1-containing BAC that was shotgun sequenced. BACs 2 and 5 are the BACs whose ends border the Y1 gene. The arrow indicates the orientation of the Y1 gene. BAC clone sizes and physical distances are approximated from the CB map (see Materials and Methods).

Fig. 2.

Significance of associations between informative SNPs within the low copy regions and endosperm color phenotype. P values were calculated by using Fisher's exact test. The points above the solid horizontal line represent SNP association significant at P < 0.001. The dashed line represents P < 0.001 after Bonferroni correction (n = 133). The horizontal axis is not to scale, but distances in kilobases and gene symbols are indicated.

Fig. 3.

Ratios of yellow to white diversity values (π_yellow/π_white) in the surrounding regions of Y1. Standard error bars are plotted. Three of the points on the graph, at positions -550, 0, and 685, were genetically mapped relative to one another, and the number of recombinants between the respective regions is indicated.