A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.
Bottom Line: Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes.This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids.In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits.
Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.Show MeSH
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Mentions: A significant association at 5% FDR was identified between zeaxanthin and an insertion in the 3′ end (3′TE indel marker) of the crtRB1 gene (GRMZM2G152135) on chromosome 10 (P-value 1.11 × 10−6). At 10% FDR, signals for β-carotene/(β-cryptoxanthin+zeaxanthin) were detected by crtRB1 InDel4, a coding region indel, and SNP ss196501627, with P-values of 2.23 × 10−7 and 3.51 × 10−7, respectively. crtRB1 encodes a nonheme dioxygenase that hydroxylates β-rings of carotenoids. Significant associations with β-carotene, ratios of β-carotene/β-cryptoxanthin and β-carotene/β-cryptoxanthin+zeaxanthin, and total carotenoid content were previously reported for crtRB1 (Yan et al. 2010). The MLMM analysis produced an optimal model that contained only crtRB1 InDel4, which, when included as a covariate in GWAS, removed other signals in the region (Figure 6, Figure S13, Figure S14, Table S8F).
Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.