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Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits.

Morris GP, Rhodes DH, Brenton Z, Ramu P, Thayil VM, Deshpande S, Hash CT, Acharya C, Mitchell SE, Buckler ES, Yu J, Kresovich S - G3 (Bethesda) (2013)

Bottom Line: Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood.Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness.These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208.

ABSTRACT
Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.

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Genome-wide mapping of testa presence in a RIL biparental family. Manhattan plots for a linear model using 263 recombinant inbred lines genotyped at 265,487 SNPs, (A) scanning genome-wide and (B) with a detailed view at Tannin1 locus on chromosome 4, with Tannin1 indicated by the red bar. Other flavonoid-related genes are indicated by the blue bars, whereas all other annotated genes in the detailed view are indicated in green.
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fig3: Genome-wide mapping of testa presence in a RIL biparental family. Manhattan plots for a linear model using 263 recombinant inbred lines genotyped at 265,487 SNPs, (A) scanning genome-wide and (B) with a detailed view at Tannin1 locus on chromosome 4, with Tannin1 indicated by the red bar. Other flavonoid-related genes are indicated by the blue bars, whereas all other annotated genes in the detailed view are indicated in green.

Mentions: Given that complex association signals made the precise mapping of tan1-a in an association population difficult, we considered whether the reduced genetic and allelic heterogeneity of a biparental family would allow precise mapping of Tannin1 using linear models. We phenotyped testa pigmentation (tannin presence) in a population of 263 RILs that we genotyped at 265,487 SNPs. There is a single locus associated with the pigmented testa in this family that is precisely colocalized with Tannin1 on chromosome 4, with the most significant SNP being the tan1-a SNP (Figure 3). To determine whether this gene resolution mapping in RILs is likely to be a typical result, we also mapped two other flavonoid pigmentation traits (coleoptile color and adult plant color) that are segregating in this RIL family. We mapped coleoptile color to a region around 54 Mb on chromosome 6 (Figure S2). This peak colocalizes with the classical Rs1 locus and a priori candidate gene Sb06g025060, a putative basic helix-loop-helix (bHLH) transcription factor, and a sorghum co-ortholog of Arabidopsis TRANSPARENT TESTA8 and maize B1/R1 anthocyanin regulators (File S3). However, the most significant SNP (S6_53849573) is 220 kb upstream of Sb06g025060, and no promising a posteriori candidate genes are found at S6_53849573, suggesting gene resolution was not achieved in this case. Adult plant color maps to 58 Mb on chromosome 6, colocalized with the classical P locus (Doggett 1988; Mace and Jordan 2010) and a large cluster of putative reductase genes that are homologous to Arabidopsis TRANSPARENT TESTA3 and BANYULS and maize ANTHOCYANINLESS1 (File S1). Here again, the most significant SNP (S6_57865283) is not colocalized precisely with the a priori candidates (TT3/BANYULS cluster) but 260 kb upstream (Figure S3).


Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits.

Morris GP, Rhodes DH, Brenton Z, Ramu P, Thayil VM, Deshpande S, Hash CT, Acharya C, Mitchell SE, Buckler ES, Yu J, Kresovich S - G3 (Bethesda) (2013)

Genome-wide mapping of testa presence in a RIL biparental family. Manhattan plots for a linear model using 263 recombinant inbred lines genotyped at 265,487 SNPs, (A) scanning genome-wide and (B) with a detailed view at Tannin1 locus on chromosome 4, with Tannin1 indicated by the red bar. Other flavonoid-related genes are indicated by the blue bars, whereas all other annotated genes in the detailed view are indicated in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3815067&req=5

fig3: Genome-wide mapping of testa presence in a RIL biparental family. Manhattan plots for a linear model using 263 recombinant inbred lines genotyped at 265,487 SNPs, (A) scanning genome-wide and (B) with a detailed view at Tannin1 locus on chromosome 4, with Tannin1 indicated by the red bar. Other flavonoid-related genes are indicated by the blue bars, whereas all other annotated genes in the detailed view are indicated in green.
Mentions: Given that complex association signals made the precise mapping of tan1-a in an association population difficult, we considered whether the reduced genetic and allelic heterogeneity of a biparental family would allow precise mapping of Tannin1 using linear models. We phenotyped testa pigmentation (tannin presence) in a population of 263 RILs that we genotyped at 265,487 SNPs. There is a single locus associated with the pigmented testa in this family that is precisely colocalized with Tannin1 on chromosome 4, with the most significant SNP being the tan1-a SNP (Figure 3). To determine whether this gene resolution mapping in RILs is likely to be a typical result, we also mapped two other flavonoid pigmentation traits (coleoptile color and adult plant color) that are segregating in this RIL family. We mapped coleoptile color to a region around 54 Mb on chromosome 6 (Figure S2). This peak colocalizes with the classical Rs1 locus and a priori candidate gene Sb06g025060, a putative basic helix-loop-helix (bHLH) transcription factor, and a sorghum co-ortholog of Arabidopsis TRANSPARENT TESTA8 and maize B1/R1 anthocyanin regulators (File S3). However, the most significant SNP (S6_53849573) is 220 kb upstream of Sb06g025060, and no promising a posteriori candidate genes are found at S6_53849573, suggesting gene resolution was not achieved in this case. Adult plant color maps to 58 Mb on chromosome 6, colocalized with the classical P locus (Doggett 1988; Mace and Jordan 2010) and a large cluster of putative reductase genes that are homologous to Arabidopsis TRANSPARENT TESTA3 and BANYULS and maize ANTHOCYANINLESS1 (File S1). Here again, the most significant SNP (S6_57865283) is not colocalized precisely with the a priori candidates (TT3/BANYULS cluster) but 260 kb upstream (Figure S3).

Bottom Line: Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood.Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness.These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208.

ABSTRACT
Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.

Show MeSH
Related in: MedlinePlus