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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0884    [Accepted] Published online May 12, 2020.
SNP-based analysis of the genetic structure of Liangshan pig population
Bin Liu1,2  , Linyuan Shen1,2  , Zhixian Guo1,2  , Mailing Gan1,2  , Ying Chen3  , Runling Yang4  , Lili Niu1,2  , Dongmei Jiang1,2  , Zhijun Zhong5  , Xuewei Li1,2  , Shunhua Zhang1,2,*  , Li Zhu1,2,* 
1College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
2Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province,Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
3Sichuan Province General Station of Animal Husbandry, Chengdu 610066, China
4Agriculture and Rural Bureau of Mabian Yi Autonomous County, Mabian, 614600, China
5Sichuan Academy of Animal Sciences, Chengdu 610066, China
Correspondence:  Shunhua Zhang,Email: zhangsh1919@163.com
Li Zhu, Tel: +86-13982083385, Email: zhuli7508@163.com
Received: 18 November 2019   • Revised: 24 January 2020   • Accepted: 14 April 2020
To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study.
We used 50K SNP chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm.
The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (PN) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823 ± 0.0259, and the average genetic distance of the 14 boars was 0.2723 ± 0.0384. Thus it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%.
This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.
Keywords: SNP chip; Liangshan pig; inbreeding coefficient; genetic distance; genetic diversity

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