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Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL.

Bickel RD, Kopp A, Nuzhdin SV - PLoS Genet. (2011)

Bottom Line: Here, we take advantage of these features to identify and characterize the sequence polymorphisms that comprise major effect QTL alleles segregating at the bric-a-brac locus.We show that natural bric-a-brac alleles with large effects on cuticular pigmentation reflect a cumulative impact of polymorphisms that affect three functional regions: a promoter, a tissue-specific enhancer, and a Polycomb response element.Our results establish that a single QTL can act through a confluence of multiple molecular mechanisms and that sequence variation in regions flanking experimentally validated functional elements can have significant quantitative effects on transcriptional activity and phenotype.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America. rbickel2@unl.edu

ABSTRACT
Many agriculturally, evolutionarily, and medically important characters vary in a quantitative fashion. Unfortunately, the genes and sequence variants accounting for this variation remain largely unknown due to a variety of biological and technical challenges. Drosophila melanogaster contains high levels of sequence variation and low linkage disequilibrium, allowing us to dissect the effects of many causative variants within a single locus. Here, we take advantage of these features to identify and characterize the sequence polymorphisms that comprise major effect QTL alleles segregating at the bric-a-brac locus. We show that natural bric-a-brac alleles with large effects on cuticular pigmentation reflect a cumulative impact of polymorphisms that affect three functional regions: a promoter, a tissue-specific enhancer, and a Polycomb response element. Analysis of allele-specific expression at the bric-a-brac locus confirms that these polymorphisms modulate transcription at the cis-regulatory level. Our results establish that a single QTL can act through a confluence of multiple molecular mechanisms and that sequence variation in regions flanking experimentally validated functional elements can have significant quantitative effects on transcriptional activity and phenotype. These findings have important design and conceptual implications for basic and medical genomics.

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Association mapping of female A6 pigmentation at the bab locus.(A) P-values from a Spearman rank correlation for each polymorphism identified in the bab locus. The dotted and solid red lines indicate FDR values of 0.3 and 0.4 respectively. 3 functional regions containing most associated polymorphisms (shaded blue rectangles) are shown in greater detail above. The sex-specific abdominal CRE (in region 1), Polycomb response element (region 2), and the bab2 promoter (region 3) are indicated by red bars. The yellow region contains an excess of linked polymorphisms, but is attributed to cryptic structure in our samples. (B) Black line shows the proportion of all polymorphisms in 5 kb sliding windows that are significantly associated with variation in pigmentation (FDR <.4), plotted against the midpoint of the window. Overlayed in yellow is Fst between samples collected in separate years (see text for details).
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pgen-1001275-g002: Association mapping of female A6 pigmentation at the bab locus.(A) P-values from a Spearman rank correlation for each polymorphism identified in the bab locus. The dotted and solid red lines indicate FDR values of 0.3 and 0.4 respectively. 3 functional regions containing most associated polymorphisms (shaded blue rectangles) are shown in greater detail above. The sex-specific abdominal CRE (in region 1), Polycomb response element (region 2), and the bab2 promoter (region 3) are indicated by red bars. The yellow region contains an excess of linked polymorphisms, but is attributed to cryptic structure in our samples. (B) Black line shows the proportion of all polymorphisms in 5 kb sliding windows that are significantly associated with variation in pigmentation (FDR <.4), plotted against the midpoint of the window. Overlayed in yellow is Fst between samples collected in separate years (see text for details).

Mentions: We identified 6766 sequence variants, including 5566 single nucleotide polymorphisms (SNPs) and 1211 insertion/deletion (indel) polymorphisms, in the bab region. After removing polymorphisms with frequencies below 5%, which are difficult to associate with phenotypic variation, 3821 polymorphism (SNPs and indels) remained. We tested each polymorphism individually for an association with female pigmentation, and identified 266 polymorphisms that showed significant association at the false discovery rate (FDR) <0.4 (p<.033) (Spearman rank correlation, qvalue correction) [11] (Figure 2A). All associated polymorphisms are located in non-coding DNA.


Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL.

Bickel RD, Kopp A, Nuzhdin SV - PLoS Genet. (2011)

Association mapping of female A6 pigmentation at the bab locus.(A) P-values from a Spearman rank correlation for each polymorphism identified in the bab locus. The dotted and solid red lines indicate FDR values of 0.3 and 0.4 respectively. 3 functional regions containing most associated polymorphisms (shaded blue rectangles) are shown in greater detail above. The sex-specific abdominal CRE (in region 1), Polycomb response element (region 2), and the bab2 promoter (region 3) are indicated by red bars. The yellow region contains an excess of linked polymorphisms, but is attributed to cryptic structure in our samples. (B) Black line shows the proportion of all polymorphisms in 5 kb sliding windows that are significantly associated with variation in pigmentation (FDR <.4), plotted against the midpoint of the window. Overlayed in yellow is Fst between samples collected in separate years (see text for details).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3020931&req=5

pgen-1001275-g002: Association mapping of female A6 pigmentation at the bab locus.(A) P-values from a Spearman rank correlation for each polymorphism identified in the bab locus. The dotted and solid red lines indicate FDR values of 0.3 and 0.4 respectively. 3 functional regions containing most associated polymorphisms (shaded blue rectangles) are shown in greater detail above. The sex-specific abdominal CRE (in region 1), Polycomb response element (region 2), and the bab2 promoter (region 3) are indicated by red bars. The yellow region contains an excess of linked polymorphisms, but is attributed to cryptic structure in our samples. (B) Black line shows the proportion of all polymorphisms in 5 kb sliding windows that are significantly associated with variation in pigmentation (FDR <.4), plotted against the midpoint of the window. Overlayed in yellow is Fst between samples collected in separate years (see text for details).
Mentions: We identified 6766 sequence variants, including 5566 single nucleotide polymorphisms (SNPs) and 1211 insertion/deletion (indel) polymorphisms, in the bab region. After removing polymorphisms with frequencies below 5%, which are difficult to associate with phenotypic variation, 3821 polymorphism (SNPs and indels) remained. We tested each polymorphism individually for an association with female pigmentation, and identified 266 polymorphisms that showed significant association at the false discovery rate (FDR) <0.4 (p<.033) (Spearman rank correlation, qvalue correction) [11] (Figure 2A). All associated polymorphisms are located in non-coding DNA.

Bottom Line: Here, we take advantage of these features to identify and characterize the sequence polymorphisms that comprise major effect QTL alleles segregating at the bric-a-brac locus.We show that natural bric-a-brac alleles with large effects on cuticular pigmentation reflect a cumulative impact of polymorphisms that affect three functional regions: a promoter, a tissue-specific enhancer, and a Polycomb response element.Our results establish that a single QTL can act through a confluence of multiple molecular mechanisms and that sequence variation in regions flanking experimentally validated functional elements can have significant quantitative effects on transcriptional activity and phenotype.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Science, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America. rbickel2@unl.edu

ABSTRACT
Many agriculturally, evolutionarily, and medically important characters vary in a quantitative fashion. Unfortunately, the genes and sequence variants accounting for this variation remain largely unknown due to a variety of biological and technical challenges. Drosophila melanogaster contains high levels of sequence variation and low linkage disequilibrium, allowing us to dissect the effects of many causative variants within a single locus. Here, we take advantage of these features to identify and characterize the sequence polymorphisms that comprise major effect QTL alleles segregating at the bric-a-brac locus. We show that natural bric-a-brac alleles with large effects on cuticular pigmentation reflect a cumulative impact of polymorphisms that affect three functional regions: a promoter, a tissue-specific enhancer, and a Polycomb response element. Analysis of allele-specific expression at the bric-a-brac locus confirms that these polymorphisms modulate transcription at the cis-regulatory level. Our results establish that a single QTL can act through a confluence of multiple molecular mechanisms and that sequence variation in regions flanking experimentally validated functional elements can have significant quantitative effects on transcriptional activity and phenotype. These findings have important design and conceptual implications for basic and medical genomics.

Show MeSH