Genome-wide Analysis Of Selective Regions And Copy Number Variations Among Nine Chinese And Western Pig Breeds

Pig domestication is occurred about 10000 years ago. During the domesticaiton, many factors including climate, environment, human needs and different selection would have huge influence on the formation of pig breeds, making great diversity among pigs in different areas. There were evidences showed that domestication on Asian pigs and European pigs were in independent ways, which means huge phenotypic changes would be caused by different selection in these areas. And due to the independent domesticaiton, great phenotypic differences were observed between Chinese and European domesitc pigs. Thus, analyzing genomic variations and regions under different selection by SNP Beadchip data of Chinese and wester pig breeds, searching the candidate genes for different traits, could uncover the genetic basis underlying the morphologic characteristics of Chinese indigenous pig breeds and differences between Chinese and western pigs. In this study, the Illumina Porcine SNP 60 Beadchip of 302 pigs and sequencing data of 13 Chinese and European wild boars were used to analyze genomic selective regions and copy number variations, and some important candidate genes were identified in strong seletive regions and copy number variation regions.(1) The Illumina Porcine SNP60 Beadchip was used to analyze 272 individuals including 6 Chinese breeds(Tongcheng pigs, Laiwu pigs, Luchuan pigs, Bama pigs, Ningxiang pigs and Wuzhishan pigs) and 3 western breeds(Yorkshire pigs, Landrace pigs and Duroc pigs). Using STRUCTURE and DAPC method to analyze the population structure of these breeds and conducted Neighbor-Joining Tree of all individuals. The results showed that the domestication of Asian and European pigs were relatively independent process, but there were still some genetic exchanges. The genetic distance between Tongcheng and Ningxiang pigs is closer than other breeds.(2) Analyzing and comparing the signature of selection between Chinese and western pig breeds, we found very few overlapped regions among them. Different from the three western breeds showing common selective regions, the signatures of selection detected in Chinese pig breeds were much more scattered, indicating that domestical patterns between Chinese and western pig breeds were different.(3) The selective signature of Chinese pig breeds were detected on chromosome 1, 6, 8, 13 and 14, and genes in these selective regions were mainly participate in immune system and stress response. This revealed the specific domestication of Chinese local pig breeds.(4) In selective regions detected in Chinese pig breeds, we observed the ESR2 gene, which is significantly associated with litter size as previous reports. In this gene, a G>A SNP showed high allele difference between Chinese and western pigs. CALB1 gene is another reproductive related gene found in selective regions. The A>C SNP of this gene showed great allele difference between Chinese domestic breeds and Chinese wild boars, indicating that this mutation might be generated during domestication, and may generally affect the reproductive traits in nowadays Chniese domestic breeds.(5) The Illumina Porcine SNP60 Beadchip was used to analyze 302 individuals including 6 Chinese breeds, 3 western breeds and one hybrid(Tongcheng ×Duroc crossbred pigs). A total of 1272 CNVs were assessed by PennCNV on 18 pairs of autosomal chromosomes and 348 CNVRs were acquired by aggregating overlapping CNVs, including 88 gain, 243 loss and 17 both(loss and gain within the same region) events. According to the location of these CNVRs, we drew a map of genomic CNVRs in 18 pairs of autosomal chromosomes of pigs.(6) Quantitative real time PCR(qPCR) was used to validate 12 CNVRs chosen from the 348 CNVRs detected in the study. These 12 CNVRs represent different predicted status of copy numbers(i.e., loss, gain and both) and different CNVR frequencies. Nine(75%) of them were in agreement with the prediction by PennCNV.(7) The Gene Ontology(GO) analysis revealed that CNV genes mainly participated in cellular component morphogenesis, cell differentiation, muscle cell development, cell adhesion, and other basic metabolic processes.(8) A great difference was found in the CNVR numbers among the nine breeds, and CNVRs were much more in Chinese breeds than western breeds. Three Chinese indigenous breeds(Luchuan, Tongcheng and Laiwu pigs) harbor the maximum number of CNVRs.This research analyzed genome-wide selective regions and copy number variations in Chinese and western pig breeds by SNP chip data, identified several important candidate genes which played importan roles in immune, reproductive traits, and uncovered some genetic basis of the differences between Chinese and western pigs.