Animal Bioscience

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
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Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population

  • Liu, Bin (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Shen, Linyuan (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Guo, Zhixian (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Gan, Mailing (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Chen, Ying (Sichuan Province General Station of Animal Husbandry) ;
  • Yang, Runling (Agriculture and Rural Bureau of Mabian Yi Autonomous County) ;
  • Niu, Lili (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Jiang, Dongmei (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Zhong, Zhijun (Sichuan Academy of Animal Sciences) ;
  • Li, Xuewei (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Zhang, Shunhua (College of Animal Science and Technology, Sichuan Agricultural University) ;
  • Zhu, Li (College of Animal Science and Technology, Sichuan Agricultural University)
  • Received : 2019.11.18
  • Accepted : 2020.04.14
  • Published : 2021.07.01
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Abstract

Objective: 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. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: 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%. Conclusion: 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

Acknowledgement

This study was supported by the Sichuan Science and Technology Support Program (No. 2016NYZ0050; No. SCSZTD-3-008), the National Natural Science Foundation of China (No. 31530073), and the earmarked fund for China Agriculture Research System (No. CARS-36-05B).

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