Analysis Of Lingkage Disequilibrium And Estimation Of Effective Population Size In Southern Chinese Indigenous Pig Breeds

Linkage disequilibrium(LD) and Effective population size, which are two of important parameters in the quantitative genetics and evolution researches, could provide efficient directions for animal breeding and breed conservation. With the development of molecular biology, high-density SNP chip has being widely used in a variety of plant and animal research, such as LD, genomic selection, genome-wide association analysis and so on. Based on Illumina Porcine SNP60 K Bead Chip, we estimated LD and Effective population size of 11 pig breeds, including 10 Southern Chinese indigenous breeds and 1Western commercial breed.In this study, 11 diverse populations, Gaoligongshan(GLGS), Bamaxiang(BMX),Dahuabai(DHB), Lantang(LT), Guizhonghua(GZH), Baoshan(BS), Saba(SB),Diannanxiaoer(DNXE), Yuedonghei(YDH), Meihua(MH) and DUROC(DR), were genotyped by using Illumina Porcine SNP60 K Bead Chip. After quality control, 33606,26877, 25094, 25299, 25839, 36803, 35579, 29632, 38736, 32495 and 33032 SNP markers were remained for the next analysis in the 11 pig breeds.LD between two adjacent SNP markers was measured by the pairwise r2. In our results,r2 decreased with the marker distances increase, but we also found a few of pair markers with long distance were of high LD level. Besides, the average r2 of GLGS, BMX, DHB,LT, GZH, BS, SB, DNXE, YDH, MH and DR were 0.153, 0.223, 0.319, 0.218, 0.206,0.261, 0.193, 0.280, 0.449 and 0.516, respectively. LD of the western commercial breed was higher than that of Southern Chinese indigenous breeds in short marker distance, but it was gradually reversed with the marker distance increase. In addition, LD of MH was highest and that of GLGS was lowest in Southern Chinese indigenous breeds. Furthermore,the r2, effected by lots of factors, was significant different between two different chromosomes. In the evolution, the selection intensity for SSC10, SSC11 and SSC12 are smallest, while SSC14 and SSC15 are largest.Nine kinds of SNPs pair with distances 0.05, 0.1, 0.2, 0.5, 1, 2, 5, 10, 25 Mb were chosen to estimated the effective population size of 11 pig breeds since 2 generations ago.The results show that the effective population size were decreased in the past generations,but DR was gradually higher than the Southern Chinese indigenous breeds with the generation decreased. The corresponding effective population size in 2 generations ago was approximately 24, 15, 12, 14, 22, 17, 6, 19, 10, 8 and 46 for GLGS, BMX, DHB, LT, GZH,BS, SB, DNXE, YDH, MH and DR pig breeds, respectively.Meanwhile, we could conclude that the selection intensity of Southern Chinese indigenous was MH>DHB?LT?YDH>SB?BS?BMX?GZH>DNXE?GLGS, and it results from geographical distribution. The genetic diversity of DNXE and GLGS were richest among all breeds.