Structure and origin of theWhite Caplocus and its role in evolution of grain color in maize

Abstract

Selection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 21 teosinte accessions reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties.Moreover, Ccd1 copy number varies extensively among Wc alleles (from 1 to 23 copies), and confers a proportional range of Ccd1 expression in diverse organs. We propose that this dynamic source of quantitative variation in Ccd1 expression was created in maize shortly after domestication by a two-step, Tam3L transposon-mediated process. First, a chromosome segment containing Ccd1 and several nearby genes duplicated at a position 1.9 Mb proximal to the progenitor Ccd1r locus on chromosome 9. Second, a subsequent interaction of Tam3L transposons at the new locus created a 28-kb tandem duplication, setting up expansion of Ccd1 copy number by unequal crossing over. In this way, transposon-mediated variation in copy number at the Wc locus created phenotypic variation that provided a foundation for breeding and selection of white grain color in maize.

TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

“…We also analyzed the 8 bp TSD sequences located immediately adjacent to each DTA insertion. Duplicated TSD sequences were removed to avoid overrepresentation of non-transposition events (Arensburger et al, 2011) such as unequal crossing over (Tan et al, 2017). Finally, 9106 unique TSD sequences of B73 DTA insertions were aligned to reveal a TSD consensus sequence: 5 0 -STnnnnAS-3 0 , where S stands for C or G. This result is consistent with previous studies (Kondrychyn et al, 2009;Arensburger et al, 2011) showing that the plant Ac or Aclike transposons, which belong to the DTA superfamily, have a similar TSD consensus sequence.…”

A global perspective on carotenoids: Metabolism, biotechnology, and benefits for nutrition and health

“…The Arabidopsis thaliana CCD1 enzyme was initially found to act on a variety of carotenoids at their 9-10 and 9′-10′ double bonds [219], although further studies showed a relaxed double bond specificity [220]. In maize, CCD1 transcript abundance negatively correlates with carotenoid content in the grain endosperm [221][222][223]. By contrast, manipulation of CCD1 activity alters CCP levels [224] but not the carotenoid content of the other plant tissues [220,225,226].…”

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

“…a eQTL (expression QTL) indicates significant correlations between expression values and JL-QTL allelic effect estimates at >2 time points for at least one trait. *Due to the multi-gene array nature of the macrotransposon insertion-derived whitecap1 locus and its position 1.9 Mb away from the progenitor ccd1-r locus (Tan et al 2017),…”