Erhualian (E), Meishan (MS) and Mi (MI) pigs are excellent indigenous pig breeds in Chinese Taihu Basin, which have made great contributions to the genetic improvement of commercial pigs. Investigation of the genetic structure and inbreeding level of the 3 pig breeds is of great significance for the sustainable breeding of commercial pigs. The length and number of runs of homozygosity (ROH) as well as the frequency of genomes covered by ROH can be used as indicators to evaluate the level of inbreeding and the origin of the population. In this study, the ROH characteristics of E, MS, MI and Landrace (L) pigs were analyzed by SLAF-seq data, and the inbreeding coeffcient based on ROH (FROH) was calculated. In addition, we have identified candidate genes in the genomic regions associated with ROH. A total of 10568 ROH were detected in 116 individuals of 4 pig breeds. The analysis showed that there were significant differences in genetic structure between 3 Taihu Basin pig breeds and L, and the genetic structure of E and MI was similar. The results of FROH showed that the inbreeding level of MS was the highest (0.25±0.07), while E and MI were lower than L. Compared with the other 3 pig populations, MS showed a higher frequency of long ROH (>5 Mb), indicating higher inbreeding in MS in recent generations. A large number of candidate genes related to reproductive traits are located in the genomic regions with a high frequency of ROH, and these genes are expected to be used as candidate genes in marker-assisted selection (MAS) breeding programs. Our findings can provide theoretical support for genetic conservation and genetic improvement of 3 pig breeds in Chinese Taihu Basin.

TONG Shi-feng;ZHU Mo;XIE Rui;LI Dong-feng;ZHANG Li-fan;LIU Yang

Department of Animal Genetics,Breeding and Reproduction,College of Animal Science and Technology,Nanjing Agricultural University,Nanjing 210095,P.R.China;Key Laboratory of Urban Agriculture,Ministry of Agriculture and Rural Affairs,Shanghai 200240,P.R.China

农业科学学报（英文）

[1]TONG Shi-feng;ZHU Mo;XIE Rui;LI Dong-feng;ZHANG Li-fan;LIU Yang-.Genome-wide detection for runs of homozygosity analysis in three pig breeds from Chinese Taihu Basin and Landrace pigs by SLAF-seq data)[J].农业科学学报（英文）,2022(11):3293-3301

Erhualian,Meishan,coeffcient

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