Evaluation Of Genomic Structure Of Zhejiang Indigenous Pig Breeds

The indigenous pig breeds in Zhejiang Province located in the southeast of China are well known for their highly prolific performance and disease resistance. They are domestic breeds from Zhejiang Province, with characteristics of low growth rate, poor feed conversion efficiency but early puberty and good meat quality. According to the latest classification, Chinese indigenous pig breeds, the indigenous pig breeds in Zhejiang Province are now classified into seven breeds (including Bibu, Chalu, Chun’an, Jiaxing, Jinhua, Lanxi and Shenxian) (Resource, 2011). From now on, the investigations primarily focused on Jinhua pigs. A fundamental survey on the whole-genome genetic markers of all seven Zhejiang indigenous pig breeds has been lacking. As a result of immoderate introduction of Western pig breeds to avoid high-fat meat, some indigenous pig breed, such as Chalu was progressively marginalized and faced near-extinction. Therefore, an estimation of genetic variation and population structure of Zhejiang indigenous pig breeds is necessary for animal genetic studies and breed conservation. The results are as follows:(1) Genome variants detection. We detected genetic variants of 361 Zhejiang indigenous pigs from seven breeds. Total of 108603 SNPs were identified in the whole-genome level of these pigs and distributed uniformly across chromosomes. These results are helpful to know the genome information of Zhejiang indigenous pig breeds and enrich the database of genetic markers of Chinese indigenous pigs.(2) Genetic diversity and population structure analysis. The analysis of genetic diversity includes three parameters. The expected heterozygosity value was ranged from 0.372 to 0.382 as compared to 0.389 to 0.395 of Western pig. Parameters obtained from allelic richness (AR) and proportion of polymorphic markers (PN) indicated that the genetic diversity of Chinese pigs was higher than Western pigs, with the highest and lowest values found in Chalu pig (Ar=1.97, Pn=0.99) and Landrace (Ar=1.82, Pn=0.84), respectively. Both Neighbour-joining (NJ) tree and principal component analysis (PCA) could distinguish breeds from one another while STUCTURE analysis showed smaller differentiation among Western pigs than Chinese pigs. Overall, the indigenous pigs showed a larger average genetic distance among populations than Western pigs, supporting the rationality of Chinese breed subdivision.(3) Analysis of Linkage disequilibrium. This study provided an overview of LD patterns against physical distance in seven Chinese indigenous pig breeds and three Western pig breeds and found that Western pigs exhibit long LD within populations against short LD than the indigenous pigs. The Average LD decay over distance is much shorter in Chinese pigs compared with Western pigs with average r2 at 0.3 value ranged from 188.2kb to 280.6kb for the Chinese pigs and 680.3kb to752.8kb for the Western ones. We believe that our findings will lay a good foundation for the development of a national plan for the conservation and utilization of these pig breeds.