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: The lut1 gene (GRMZM2G143202) on chromosome 1 contains an intronic SNP (ss196425306; 86,844,203 bp) that was significantly associated with α-carotene/zeinoxanthin, zeinoxanthin, and zeinoxanthin/lutein (P-values 8.95 × 10−8 to 3.47 × 10−10). The lut1 gene encodes CYP97C, a cytochrome P450-type monooxygenase responsible for hydroxylating the ε-ring of zeinoxanthin to yield lutein (Tian et al. 2004; Quinlan et al. 2012). The only other statistically significant SNP (ss196425308; 86,945,134 bp) in this region was located ∼100 kb downstream of lut1 and was in perfect LD (r2 = 1) with the peak SNP (ss196425306) in lut1. To further resolve the signals in the lut1 region, the MLMM procedure was run on these three carotenoid traits, with all SNPs on chromosome 1 considered for inclusion into the optimal models. All optimal models contained only the peak GWAS SNP in the lut1 intron (Figure 3, Figure S5, Figure S6, Table S8C).
Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.