Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens

Li, D. F.; Liu, W. B.; Liu, J. F.; Yi, Guoqiang; Lian, Ling; Qu, Lujiang; Li, J. Y.; Xu, Guanlong; Yang, Ning

doi:10.3382/ps.2012-02275

Cited by 16 publications

(16 citation statements)

References 45 publications

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“…The 806 significant core regions (S2 Table) identified in this study was much more than previous report because of the high density SNP chip and genome recombination events [33, 34]. We further compared significant core haplotypes with other haplotypes in these regions and found that the former possess the larger extent of homozygosity than the later.…”

Section: Discussionmentioning

confidence: 59%

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Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

Liu

Sun

et al. 2016

PLoS ONE

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Chicken is recognized as an excellent model for studies of genetic mechanism of phenotypic and genomic evolution, with large effective population size and strong human-driven selection. In the present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions employing 600K SNP Chicken chip in an F2 population of 1,534 hens, which was derived from reciprocal crosses between White Leghorn and Dongxiang chicken. Results indicated that a total of 49,151 core regions with an average length of 9.79 Kb were identified, which occupied approximately 52.15% of genome across all autosomes, and 806 significant core regions attracted us mostly. Genes in candidate regions may experience positive selection and were considered to have possible influence on beneficial economic traits. A panel of genes including AASDHPPT, GDPD5, PAR3, SOX6, GPC1 and a signal pathway of AKT1 were detected with the most extreme P-values. Further enrichment analyses indicated that these genes were associated with immune function, sensory organ development and neurogenesis, and may have experienced positive selection in chicken. Moreover, some of core regions exactly overlapped with genes excavated in our previous GWAS, suggesting that these genes have undergone positive selection may affect egg production. Findings in our study could draw a comparatively integrate genome-wide map of selection signature in the chicken genome, and would be worthy for explicating the genetic mechanisms of phenotypic diversity in poultry breeding.

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Section: Discussionmentioning

confidence: 59%

“…So far, the EHH test has been applied to detect selective signatures of different animals in many researches [13,14,15,16], and proved to be particularly effective among the various statistics [17,18]. Measuring the characteristics of haplotypes, it could identify selection signatures.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

Liu

Sun

et al. 2016

PLoS ONE

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“…Research by Li et al (2012) suggested that genes related to chicken resistance traits are located on chromosome 16, and at the same time, they also located both the egg laying performance and growth performance genes. In our study, the objective genes were LHCGR, ESR2, and DRD2, located on chromosomes 3, 5, and 24, respectively, and our results agree with those of Li et al (2013).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, many investigations have used genome-wide association studies (GWAS) to identify special loci used during chicken domestication (van Kaam et al, 1999;Useche et al, 2001;Akey et al, 2002;Reich et al, 2003;Rubin et al, 2010;Gu et al, 2011;Xie et al, 2012;Li et al, 2012Li et al, , 2013. Rubin et al (2010) used whole-genome re-sequencing methods to analyze chicken selection loci and the results revealed that there are 7,000,000 single nucleotide polymorphisms (SNPs), including 1300 deficiency loci, and during chicken domestication specific loci are involved in specialization into broiler (meat-producing) and layer (eggproducing) chicken.…”

Section: Introductionmentioning

confidence: 99%

Verification of specific selection SNPs between broiler and layer chicken in Chinese indigenous chicken breeds

D¹,

Yd²,

Zhu³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The direction of production for indigenous chicken breeds is currently unknown and this knowledge, combined with the development of chicken genome-wide association studies, led us to investigate differences in specific loci between broiler and layer chicken using bioinformatic methods. In addition, we analyzed the distribution of these seven identified loci in four Chinese indigenous chicken breeds, Caoke chicken, Jiuyuan chicken, Sichuan mountain chicken, and Tibetan chicken, using DNA direct sequencing methods, and analyzed the data using bioinformatic methods. Based on the results, we suggest that Caoke chicken could be developed for meat production, while Jiuyuan chicken could be developed for egg production. As Sichuan mountain chicken and Tibetan chicken exhibited large polymorphisms, these breeds could be improved by changing their living environment.

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“…Since natural selection removes variation from the population, and linked sites hitch-hike with the selected variant, signatures of selection should manifest themselves as regions of reduced diversity (Maynard Smith and Haigh 1974). Genome scans have been performed in the chicken to search for domestication sweeps (Wong, Liu et al 2004;Rubin, Zody et al 2010), in domestic populations (Elferink, Megens et al 2012;Li, Liu et al 2012;Zhang, Wang et al 2012;Fan, Ng et al 2013;Gholami, Erbe et al 2014), and in chickens adapted to altitude (Wang, Li et al 2015). These studies have been successful in identifying some plausible candidates.…”

Section: Feralisation and Selective Sweep Mappingmentioning

confidence: 99%

Genomics of chicken domestication and feralisation

Johnsson¹

2015

Linköping Studies in Science and Technology. Dissertations

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Domestication can serve as a study system of rapid evolutionary change with wideranging effects on traits in animals. The chicken was domesticated from the Red Junglefowl and has diverged in behaviour, morphology and life history traits. Conversely, feralisation is a more recent process when domestic animals are again exposed and respond to an environment outside of human husbandry. Linkage-based quantitative trait locus (QTL) mapping has been used to localise genetic variants that affect domestication traits in the chicken genome. Because of the limited resolution of linkage mapping, the QTL regions associated with domestication traits are often broad and contain many genes. One approach to help sort out potential causative genes is to measure gene expression as an intermediary molecular phenotype. In this dissertation, expression quantitative trait locus (eQTL) mapping of gene expression traits is used to search for potential causative genes for domestication traits in the chicken. Expression quantitative trait loci were mapped across the whole genome in bone and hypothalamus samples, and targeted at QTL regions in the base of the comb. These studies have resulted in candidate quantitative trait genes, supported by genetic and gene expression evidence, for relative comb mass, bone allocation, egg production and fearful behaviour as measured in an open field test. Secondly, a population genomics approach was used to study the molecular basis of feralisation in a free-range feral chicken population from the Pacific island of Kauai. Mitochondrial DNA sequences and phenotypic observations establish the hybrid origin of this population as a mixture of wild and domestic chickens. Genome-wide mapping of pooled heterozygosity highlight regions that may be involved in adaptation to the feral environment. The expression QTL results bring us closer to knowledge about the molecular basis of domestication traits in the chicken, suggesting plausible candidate genes and opening up for functional studies of individual loci. The population genomic study shows that feralisation has a mostly different genomic architecture than domestication, and suggests phenotypic effects, based on overlap with domestication QTL regions, for some of the identified regions. 2 Populärvetenskaplig sammanfattningDomesticering är när en vild population ger upphov till en tam population i människans vård, och är ett exempel på snabb evolutionär förändring som påverkar många ärftliga egenskaper hos djur. Feralisering, å andra sidan, är när tama djur åter utsätts för vilda omgivningar. De stora ärftliga skillnader som uppstått under domesticering gör att jämförelsen mellan vilda och tama djur kan användas som genetiskt studiesystem för flera kvantitativa egenskaper. Hos feraliserade djur kan man se vad som händer med tamdjurs egenskaper och genetiska varianter i en vild miljö.Den här avhandlingen handlar om den genetiska grunden för domesticering och feralisering. Den omfattar arbeten som belyser, i tur och ordning: hönskammens storlek; benets ...

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Whole-genome scan for signatures of recent selection reveals loci associated with important traits in White Leghorn chickens

Cited by 16 publications

References 45 publications

Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

Genome-Wide Detection of Selective Signatures in Chicken through High Density SNPs

Verification of specific selection SNPs between broiler and layer chicken in Chinese indigenous chicken breeds

Genomics of chicken domestication and feralisation

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