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Long-Range Patterns of Diversity and Linkage Disequilibrium Surrounding the Maize Y1 Gene Are Indicative of an Asymmetric Selective Sweep
Kelly Palaisa, Michele Morgante, Scott Tingey, Antoni Rafalski and Ronald L. Phillips
Proceedings of the National Academy of Sciences of the United States of America
Vol. 101, No. 26 (Jun. 29, 2004), pp. 9885-9890
Published by: National Academy of Sciences
Stable URL: http://www.jstor.org/stable/3372552
Page Count: 6
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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.
Proceedings of the National Academy of Sciences of the United States of America © 2004 National Academy of Sciences