title: A genome scan for selection signatures in pigs.
abstract: Identifying signatures of selection can provide a straightforward insight into the mechanism of artificial selection and further uncover the causal genes related to the phenotypic variation. Based on Illumina Porcine60KSNP chip data, four complementary methods, Long-Range Haplotype (LRH), Tajima's D, Cross Population Extend Haplotype Homozygosity Test (XPEHH) and FST, were implemented in this study to detect the selection signatures in the whole genome of one typical Chinese indigenous breed, Rongchang, one Chinese cultivated breed, Songliao, and two western breeds, Landrace and Yorkshire. False Discovery Rate (FDR) was implemented to control the false positive rates. In our study, a total of 159, 127, 179 and 159 candidate selection regions with average length of 0.80 Mb, 0.73 Mb, 0.78 Mb and 0.73 Mb were identified in Landrace, Rongchang, Songliao and Yorkshire, respectively, that span approximately 128.00 Mb, 92.38 Mb, 130.30 Mb and 115.40 Mb and account for approximately 3.74-5.33% of genome across all autosomes. The selection regions of 11.52 Mb shared by Landrace and Yorkshire were the longest when chosen pairs from the pool of the four breeds were examined. The overlaps between Yorkshire and Songliao, approximately 9.20 Mb, were greater than those of Yorkshire and Rongchang. Meanwhile, the overlaps between Landrace and Songliao were greater than those of Landrace and Rongchang but less than those of Songliao and Ronchang. Bioinformatics analysis showed that the genes/QTLs relevant to fertility, coat color, and ear morphology were found in candidate selection regions. Some genes, such as LEMD3, MC1R, KIT, TRHR etc. that were reported under selection, were confirmed in our study, and this analysis also demonstrated the diversity of breeds.
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
authors.forename: Julong
authors.initials: J
authors.lastname: Wei
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Chongqing Academy of Animal Science, Chongqing, P.R. China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Chongqing Academy of Animal Science, Chongqing, P.R. China.
authors.forename: Jinyong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Liu
authors.affiliation: Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College Animal Science and Technology, China Agricultural University, Beijing, P.R. China.
authors.forename: Xiangdong
authors.initials: X
authors.lastname: Ding
mesh_terms: D000818:Animals; D001947:Breeding; D002681:China; D019295:Computational Biology; D019143:Evolution, Molecular; D016678:Genome; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D013552:Swine / Q000145:classification* / Q000235:genetics*