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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 α-carotene to zeinoxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of α-carotene to zeinoxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1-Mb region on chromosome 1 that encompasses lut1. The blue vertical lines are –log10P-values for SNPs that are statistically significant for the ratio of α-carotene to zeinoxanthin at 5% FDR, while the gray vertical lines are –log10P-values for SNPs that are nonsignificant at 5% FDR. Triangles are the r2 values of each SNP relative to the peak SNP (indicated in red) at 86,844,203 bp. The black horizontal dashed line indicates the –log10P-value of the least statistically significant SNP at 5% FDR. The black vertical dashed lines indicate the start and stop positions of lut1 (GRMZM2G14322.) (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region, as in A. The peak SNP from the unconditional GWAS (ss196425306; 86,844,203 bp) was included as a covariate in the unified mixed model to control for the lut1 effect.
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fig3: GWAS for the ratio of α-carotene to zeinoxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of α-carotene to zeinoxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1-Mb region on chromosome 1 that encompasses lut1. The blue vertical lines are –log10P-values for SNPs that are statistically significant for the ratio of α-carotene to zeinoxanthin at 5% FDR, while the gray vertical lines are –log10P-values for SNPs that are nonsignificant at 5% FDR. Triangles are the r2 values of each SNP relative to the peak SNP (indicated in red) at 86,844,203 bp. The black horizontal dashed line indicates the –log10P-value of the least statistically significant SNP at 5% FDR. The black vertical dashed lines indicate the start and stop positions of lut1 (GRMZM2G14322.) (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region, as in A. The peak SNP from the unconditional GWAS (ss196425306; 86,844,203 bp) was included as a covariate in the unified mixed model to control for the lut1 effect.

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).


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 α-carotene to zeinoxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of α-carotene to zeinoxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1-Mb region on chromosome 1 that encompasses lut1. The blue vertical lines are –log10P-values for SNPs that are statistically significant for the ratio of α-carotene to zeinoxanthin at 5% FDR, while the gray vertical lines are –log10P-values for SNPs that are nonsignificant at 5% FDR. Triangles are the r2 values of each SNP relative to the peak SNP (indicated in red) at 86,844,203 bp. The black horizontal dashed line indicates the –log10P-value of the least statistically significant SNP at 5% FDR. The black vertical dashed lines indicate the start and stop positions of lut1 (GRMZM2G14322.) (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region, as in A. The peak SNP from the unconditional GWAS (ss196425306; 86,844,203 bp) was included as a covariate in the unified mixed model to control for the lut1 effect.
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig3: GWAS for the ratio of α-carotene to zeinoxanthin content in maize grain. (A) Scatter plot of association results from a unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region. Negative log10-transformed P-values (left y-axis) from a GWAS for the ratio of α-carotene to zeinoxanthin and r2 values (right y-axis) are plotted against physical position (B73 RefGen_v2) for a 1-Mb region on chromosome 1 that encompasses lut1. The blue vertical lines are –log10P-values for SNPs that are statistically significant for the ratio of α-carotene to zeinoxanthin at 5% FDR, while the gray vertical lines are –log10P-values for SNPs that are nonsignificant at 5% FDR. Triangles are the r2 values of each SNP relative to the peak SNP (indicated in red) at 86,844,203 bp. The black horizontal dashed line indicates the –log10P-value of the least statistically significant SNP at 5% FDR. The black vertical dashed lines indicate the start and stop positions of lut1 (GRMZM2G14322.) (B) Scatter plot of association results from a conditional unified mixed model analysis of the ratio of α-carotene to zeinoxanthin and LD estimates (r2) across the lut1 chromosome region, as in A. The peak SNP from the unconditional GWAS (ss196425306; 86,844,203 bp) was included as a covariate in the unified mixed model to control for the lut1 effect.
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).

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