Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization

Zhao, Pengju; Yu, Ying; Feng, Wen; Du, Huarui; Yu, Jian; Kang, Hao; Zheng, Xianrui; Wang, Zhiquan; Liu, George E.; Ernst, Catherine W.; Ran, Xueqin; Wang, Jiafu; Liu, Jianfeng

doi:10.1093/gigascience/giy058

Cited by 49 publications

(57 citation statements)

References 60 publications

(62 reference statements)

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“…Chickens from neighboring geographical locations and from similar altitudes are gathered together. Gene exchanges are likely to be correlated with geographical location, which is consistent with results from previous studies [14,24,[31][32][33]. Population genomics analysis, including PCA, NJ tree, and structure, reveal that red jungle fowl can be separated into two branches, possibly because there have been different venues for domestication [17,34,35].…”

Section: Discussionsupporting

confidence: 87%

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Sun

Zhang

et al. 2020

BMC Genomics

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Background: Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype. Results: Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis. Conclusions: These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.

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Section: Discussionsupporting

confidence: 87%

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Sun

Zhang

et al. 2020

BMC Genomics

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“…We found that a gene could elucidate the genetic basis of coat color phenotype of ASP population. In previous studies about pig coat color, MC1R gene was under positive selection (Li et al, 2010;Zhao et al, 2018). In this study, the MC1R gene was also found under selection based on cross approaches.…”

Section: Discussionmentioning

confidence: 62%

Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig

et al. 2020

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Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, wholegenome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (F ST) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color (MC1R), salivary secretion (STATH), reproduction (SPIRE2, OSBP2, LIMK2, FANCA, and CABS1), olfactory transduction (OR5K4), and growth (NPY1R, NPY5R, and SELENOM). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.

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“…The strictly organized breeding program was adopted to improve and develop livestock breeds, Britain, in particular, was the main center of the early improvement of pig breeds and cultivated the famous Yorkshire pigs [34]. FRA-Y was regarded as the pigs most likely to contain ancestries of Chinese local pigs [35]. Canada and the United States are far from the origin country of the Yorkshire-Britain and FRA-Y, CAN-Y and USA-Y were thus used in the study.…”

Section: Discussionmentioning

confidence: 99%

Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs

Zhang

Huang

et al. 2019

Animals

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Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.

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Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization

Cited by 49 publications

References 60 publications

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig

Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs

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