The Detection Of Seven Copy Number Variations And The Functions In Xiang Pig Breed

To investigate the polymorphisms of copy number variation(Copy Number Variation, CNV) and its relationship with the growth and reproduction traits of Xiang pig, 213 CNVRs(copy number variation regions) were deduced based on the genotyping data by Illumina Porcine SNP 60 k chip taking 120 native pigs of Xiang and Kele pig breeds as samples. 7 CNVRs(42, 77, 103, 105, 149, 165 and 188) were detected by real-time PCR methods in Xiang pig to research the regulation mechanism of reproduction and growth. The main results of this study included:1、Verification of candidate CNV: Seven CNVRs were confirmed in Xiang pig polulation, and CNVR77 was the new CNVR.2、Quantitative analysis in small sample of Xiang pig: The copy numbers of CNVR42, CNVR77, CNVR103 and CNVR105 were not significantly different between the prolific and low-fertility Xiang pig herds(P > 0.05), and the main copies was increased. However, CNVR149, CNVR165, CNVR188 were significantly different between the prolific and low-fertility Xiang pig herds. CNVR149,CNVR165, CNVR188 could be taken as a candidate CNV to distinguish the prolific and low-fertility Xiang pig herds.3、Quantitative analysis in large populations of Xiang pig: The results showed an increased frequency of CNVR149 in both of two Xiang pig herds, although it was slightly higher in the low-fertility one. A reduced CNVR165 copy number was observed in the prolific Xiang pig population, whereas an increased CNVR165 copy number was primarily found out from the low-fertility Xiang pig herd. The copy number of CNVR188 was increased in the prolific Xiang pig herd but decreased in the low one. Correlation analysis indicated that the copy numbers of CNVR149,CNVR165 and CNVR188 weakly correlated with the litter size at the third parity inXiang pig. CNVR149 weakly correlated with the body width and chest girth.CNVR188 weakly correlated with the chest girth and cannon circumference.4、The comparison of CNV in three additional indigenous Guizhou breeds: For CNVR42, CNVR77, CNVR103, CNVR105, copy numbers gain were predominant in Kele, Nuogu and Yorkshire pigs. This result was consistent with that in Xiang pigs.However, copy numbers of CNVR103 and CNVR105 were significantly different among five pig breeds. Therefore, CNVR103 and CNVR105 have polymorphism in pig herds. The copy number of CNVR149 was primarily increased in Nuogu and Yorkshire breeds, which was identical to that in Xiang pigs. For CNV165, copy number of gain was predominant in the Rongchang, Nuogu and Yorkshire breeds, and this trend was consistent with that in the low-fertility herd of Xiang pigs. In contrast,many samples at CNVR165 loci showed copy number loss in both Kele and the prolific Xiang pig herds. For CNVR188, copy number gain type was predominant in Kele, Nuogu and Yorkshire pigs, and it was consistent with that in the prolific Xiang pig herd. Thus, CNVR149, CNVR165, CNVR188 showed polymorphism in five pig breeds.5 、 Bioinformatics analysis: There were no genes in CNVR42, CNVR77.CNVR149 includes the ATP-binding cassette(ABC) carrier 4 gene(ABCC4). ABCC4 appears as a functional carrier of prostaglandins regulated by oxytocin in the bovine endometrium, and its protein was present throughout the estrous cycle. The lipase member I(LIPI) gene is present in the identified CNVR165 region. LIPI can catalyze the production of fatty acids and lysophosphatidic acid(LPA) from phosphatidic acid.The LIPI mRNA transcript has been detected in the mouse ovary. CNVR188 includes bone morphogenetic protein receptor, type II(BMPR2), BMPR2 can improve follicular maturity during the preovulatory period.6、The detection of gene expression level: The correlationship between the CNV copy types in genome and the expression mRNA levels of genes showed that the copy number variations of CNVR149, CNVR165, CNVR188 were positively related with the mRNA expression level of ABCC4, LIPI, BMPR2 genes.In this paper, Seven CNVRs were analyzed and confirmed. Noteworthy, threeCNVRs, CNVR149, CNVR165 and CNVR188, appeared to be changeable among pig breeds. Correlation analysis indicated that the copy numbers of CNVR149, CNVR165 and CNVR188 weakly correlated with the litter size at the third parity in Xiang pig breed. Based on detection results for mRNA expression level, polymorphisms of three CNVRs might have a positive regulatory role in the reproductive performance of Xiang Pig. These research results would provide the foundation for the regulation mechanism of the growth and development of pigs and the pig breeding.