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A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR, Buckler ES, DellaPenna D, Gore MA, Rocheford T - Genetics (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.

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Related in: MedlinePlus

GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1.2-Mb region on chromosome 10 that encompasses crtRB1. The vertical lines are –log10P-values for all tested SNPs in this region. Triangles are the r2 values of each SNP relative to the peak polymorphism (indicated in red) at 136,059,748 bp. The black vertical dashed lines indicate the start and stop positions of crtRB1 (GRMZM2G152135). (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region, as in A. The peak polymorphism from the unconditional GWAS (crtRB1 InDel4; 136,059,748 bp) was included as a covariate in the unified mixed model to control for the crtRB1 effect.
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fig6: GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1.2-Mb region on chromosome 10 that encompasses crtRB1. The vertical lines are –log10P-values for all tested SNPs in this region. Triangles are the r2 values of each SNP relative to the peak polymorphism (indicated in red) at 136,059,748 bp. The black vertical dashed lines indicate the start and stop positions of crtRB1 (GRMZM2G152135). (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region, as in A. The peak polymorphism from the unconditional GWAS (crtRB1 InDel4; 136,059,748 bp) was included as a covariate in the unified mixed model to control for the crtRB1 effect.

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).


A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR, Buckler ES, DellaPenna D, Gore MA, Rocheford T - Genetics (2014)

GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1.2-Mb region on chromosome 10 that encompasses crtRB1. The vertical lines are –log10P-values for all tested SNPs in this region. Triangles are the r2 values of each SNP relative to the peak polymorphism (indicated in red) at 136,059,748 bp. The black vertical dashed lines indicate the start and stop positions of crtRB1 (GRMZM2G152135). (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region, as in A. The peak polymorphism from the unconditional GWAS (crtRB1 InDel4; 136,059,748 bp) was included as a covariate in the unified mixed model to control for the crtRB1 effect.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig6: GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1.2-Mb region on chromosome 10 that encompasses crtRB1. The vertical lines are –log10P-values for all tested SNPs in this region. Triangles are the r2 values of each SNP relative to the peak polymorphism (indicated in red) at 136,059,748 bp. The black vertical dashed lines indicate the start and stop positions of crtRB1 (GRMZM2G152135). (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of β-carotene to β-cryptoxanthin plus zeaxanthin and LD estimates (r2) across the crtRB1 chromosome region, as in A. The peak polymorphism from the unconditional GWAS (crtRB1 InDel4; 136,059,748 bp) was included as a covariate in the unified mixed model to control for the crtRB1 effect.
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).

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.

Show MeSH
Related in: MedlinePlus