Structure and Origin of the Locus and Its Role in Evolution of Grain Color in Maize.

Selection for yellow- and white-grain types has been central to postdomestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the () phytoene synthase gene, less is known about the role of the dominant white endosperm factor (). We show that the locus contains multiple, tandem copies of a () gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that is exclusive to maize, where it is prevalent in white-grain () varieties. Moreover, copy number varies extensively among alleles (from 1 to 23 copies), and confers a proportional range of expression in diverse organs. We propose that this dynamic source of quantitative variation in expression was created in maize shortly after domestication by a two-step, transposon-mediated process. First, a chromosome segment containing and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitor locus on chromosome 9. Second, a subsequent interaction of transposons at the new locus created a 28-kb tandem duplication, setting up expansion of copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at the locus generated phenotypic variation that provided a foundation for breeding and selection of white-grain color in maize.