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Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

Gholami M, Reimer C, Erbe M, Preisinger R, Weigend A, Weigend S, Servin B, Simianer H - PLoS ONE (2015)

Bottom Line: We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively.A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B.We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10).

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.

ABSTRACT
An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

No MeSH data available.


Related in: MedlinePlus

Allele frequency in different breeds for 2 Mbp around the intended region.Red box indicates, for (A) TGFB2 gene (Chr3: 18,690,003–18,753,123), (B) H3F3C gene (Chr3: 16,483,162–16,487,393) and (C) 60Kb region on chromosome 10 (6,799,776–6,738,610).
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pone.0130497.g005: Allele frequency in different breeds for 2 Mbp around the intended region.Red box indicates, for (A) TGFB2 gene (Chr3: 18,690,003–18,753,123), (B) H3F3C gene (Chr3: 16,483,162–16,487,393) and (C) 60Kb region on chromosome 10 (6,799,776–6,738,610).

Mentions: As an example, in Fig 5A we demonstrate allele frequencies at SNP positions around the TGFB2 gene (Chr3: 18,690,003–18,753,123) which was detected as a gene under selection by FST [20] due to a reduction of diversity within the WL breed. However, since this reduction exists only within the WL breed this can also be explained by drift alone. By taking the population tree into consideration, FLK does not detect any signals in this region. Another example is the region around the H3F3C gene (Chr3: 16,483,162–16,487,393) which was detected to be under selection by FLK. Allele frequencies around this region shows that a huge diversity exists between some breeds (Fig 5B). We detect an outlier with FLK in particular because WR1 and WR2 show very different patterns of allele frequencies in this region although they are closely related in the population tree. However FST was not able to detect any signal here, since FST treats each population as an independent evidence for sweep detection and does not consider the huge difference between WL, RIR and WR breeds. There are as well cases in which all three methods (FST, FLK and hapFLK) were able to detect the region under selection. An example is a 60Kb region on chromosome 10 (6,799,776–6,738,610). Fig 5C shows allele frequencies around this region.


Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.

Gholami M, Reimer C, Erbe M, Preisinger R, Weigend A, Weigend S, Servin B, Simianer H - PLoS ONE (2015)

Allele frequency in different breeds for 2 Mbp around the intended region.Red box indicates, for (A) TGFB2 gene (Chr3: 18,690,003–18,753,123), (B) H3F3C gene (Chr3: 16,483,162–16,487,393) and (C) 60Kb region on chromosome 10 (6,799,776–6,738,610).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494984&req=5

pone.0130497.g005: Allele frequency in different breeds for 2 Mbp around the intended region.Red box indicates, for (A) TGFB2 gene (Chr3: 18,690,003–18,753,123), (B) H3F3C gene (Chr3: 16,483,162–16,487,393) and (C) 60Kb region on chromosome 10 (6,799,776–6,738,610).
Mentions: As an example, in Fig 5A we demonstrate allele frequencies at SNP positions around the TGFB2 gene (Chr3: 18,690,003–18,753,123) which was detected as a gene under selection by FST [20] due to a reduction of diversity within the WL breed. However, since this reduction exists only within the WL breed this can also be explained by drift alone. By taking the population tree into consideration, FLK does not detect any signals in this region. Another example is the region around the H3F3C gene (Chr3: 16,483,162–16,487,393) which was detected to be under selection by FLK. Allele frequencies around this region shows that a huge diversity exists between some breeds (Fig 5B). We detect an outlier with FLK in particular because WR1 and WR2 show very different patterns of allele frequencies in this region although they are closely related in the population tree. However FST was not able to detect any signal here, since FST treats each population as an independent evidence for sweep detection and does not consider the huge difference between WL, RIR and WR breeds. There are as well cases in which all three methods (FST, FLK and hapFLK) were able to detect the region under selection. An example is a 60Kb region on chromosome 10 (6,799,776–6,738,610). Fig 5C shows allele frequencies around this region.

Bottom Line: We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively.A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B.We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10).

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.

ABSTRACT
An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.

No MeSH data available.


Related in: MedlinePlus