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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

Manhattan plot of hapFLK analysis over the entire genome with 5 clusters.Blue (red) line indicates the upper (lower) 0.05% of hapFLK distribution, for, (A) within all breeds, (B) within white breeds, and, (C) Within brown breeds.
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pone.0130497.g003: Manhattan plot of hapFLK analysis over the entire genome with 5 clusters.Blue (red) line indicates the upper (lower) 0.05% of hapFLK distribution, for, (A) within all breeds, (B) within white breeds, and, (C) Within brown breeds.

Mentions: Based on the hapFLK values distribution, a total of 41 regions (17 in all layers, 12 in white layers and 12 in brown layers) were detected as selection signatures (S8 Table). All these regions were in either the upper or the lower 0.05% of the distribution, which represent regions with a fixed difference or fixed similarity between populations, respectively. The genome-wide distribution of hapFLK values with 5 haplotype clusters obtained for each group—all, white and brown—are depicted in Fig 3A, 3B and 3C, respectively. Annotation was carried out for all regions with extreme hapFLK values, i.e. potential selective sweeps. The lists of genes for selective sweeps detected with hapFLK are available in the supplementary tables (S9, S10 and S11 Tables). The annotation list is enriched with genes of biological interest involved in various pathways such as nerve development (p = 0.027), growth factor receptor (p = 0.008), RNA metabolic process (p = 0.042) and skeletal muscle cell differentiation (p = 0.032), all of which could be related to production traits indirectly. The lists of pathways and gene ontologies under which were detected under selection in this study are available in the supplementary tables (S12, S13 and S14 Tables). We identified four genes that were related to the breeding goals of chickens with the hapFLK method. IGF-1R and STAT5B are associated with growth and carcass traits [37,38]. BPIFB8 and SOX10, which are associated with egg natural defense [39] and dark brown mutational phenotype [40] respectively (more details is available in Table 2). Several QTL, which were related to the breeding goals of egg-layer chickens were detected as well, for traits such as drumstick and thigh morphology, carcass weight and shank length. A complete list of all QTL with more details is available in Table 4.


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)

Manhattan plot of hapFLK analysis over the entire genome with 5 clusters.Blue (red) line indicates the upper (lower) 0.05% of hapFLK distribution, for, (A) within all breeds, (B) within white breeds, and, (C) Within brown breeds.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0130497.g003: Manhattan plot of hapFLK analysis over the entire genome with 5 clusters.Blue (red) line indicates the upper (lower) 0.05% of hapFLK distribution, for, (A) within all breeds, (B) within white breeds, and, (C) Within brown breeds.
Mentions: Based on the hapFLK values distribution, a total of 41 regions (17 in all layers, 12 in white layers and 12 in brown layers) were detected as selection signatures (S8 Table). All these regions were in either the upper or the lower 0.05% of the distribution, which represent regions with a fixed difference or fixed similarity between populations, respectively. The genome-wide distribution of hapFLK values with 5 haplotype clusters obtained for each group—all, white and brown—are depicted in Fig 3A, 3B and 3C, respectively. Annotation was carried out for all regions with extreme hapFLK values, i.e. potential selective sweeps. The lists of genes for selective sweeps detected with hapFLK are available in the supplementary tables (S9, S10 and S11 Tables). The annotation list is enriched with genes of biological interest involved in various pathways such as nerve development (p = 0.027), growth factor receptor (p = 0.008), RNA metabolic process (p = 0.042) and skeletal muscle cell differentiation (p = 0.032), all of which could be related to production traits indirectly. The lists of pathways and gene ontologies under which were detected under selection in this study are available in the supplementary tables (S12, S13 and S14 Tables). We identified four genes that were related to the breeding goals of chickens with the hapFLK method. IGF-1R and STAT5B are associated with growth and carcass traits [37,38]. BPIFB8 and SOX10, which are associated with egg natural defense [39] and dark brown mutational phenotype [40] respectively (more details is available in Table 2). Several QTL, which were related to the breeding goals of egg-layer chickens were detected as well, for traits such as drumstick and thigh morphology, carcass weight and shank length. A complete list of all QTL with more details is available in Table 4.

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