title: Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci.
abstract: We investigated the effects of human selection for yellow endosperm color, representing increased 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 inbred lines. Many polymorphic sites showed strong association with the endosperm color phenotype at Y1, but no detectable association was found at PSY2. Nucleotide diversity 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 upregulation of expression in endosperm have been incorporated into yellow maize.
authors.affiliation: Department of Plant and Soil Sciences, University of Delaware, and Delaware Biotechnology Institute, Newark, DE 19716, USA. kapal918@yahoo.com
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Palaisa
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Mark
authors.initials: M
authors.lastname: Williams
authors.forename: Antoni
authors.initials: A
authors.lastname: Rafalski
mesh_terms: D001483:Base Sequence; D002338:Carotenoids / Q000235:genetics*; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D005091:Exons; D017343:Genes, Plant; D014644:Genetic Variation; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000235:genetics*; D005810:Multigene Family; D010641:Phenotype; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D012641:Selection, Genetic; D003313:Zea mays / Q000201:enzymology* / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D009097:Multienzyme Complexes; D002338:Carotenoids; C022399:phytoene synthetase complex