Acta Veterinaria et Zootechnica Sinica ›› 2023, Vol. 54 ›› Issue (6): 2297-2307.doi: 10.11843/j.issn.0366-6964.2023.06.010

• ANIMAL GENETICS AND BREEDING • Previous Articles     Next Articles

Population Structure and Genetic Diversity Analysis of Neijiang Pigs Based on Low-coverage Whole Genome Sequencing

ZHAO Zhenjian1,2, WANG Shujie1,2, CHEN Dong1,2, JI Xiang1,2, SHEN Qi1,2, YU Yang1,2, CUI Shengdi1,2, WANG Junge1,2, CHEN Ziyang1,2, TANG Guoqing1,2*   

  1. 1. Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China;
    2. Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
  • Received:2022-11-18 Online:2023-06-23 Published:2023-06-16

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Abstract: The study aimed to better understand the population structure and genetic diversity of Neijiang pigs, make a better protection and utilization of the genetic resources of Neijiang pig. The SNPs of 133 Neijiang pigs (12 boars, 121 sows) was detected based on low-coverage whole genome sequencing. Two sets of SNPs data, with different calling rates 90% or 95%, were obtained and named as NJ90 and NJ95. Population structure of Neijiang pigs was analyzed by population stratification, genetic distance, genetic relationship and boar genome family. The population genetic diversity was estimated by allele frequency, effective number of alleles, proportion of polymorphic and heterozygosity. Finally, the inbreeding coefficient of population was evaluated by different methods. The results showed as follows: 1) NJ90 contained 135 760 SNPs. The allele frequency, effective number of alleles, and proportion of polymorphic were 0.87, 1.27, and 0.76, respectively. The observed heterozygosity and expected heterozygosity were 0.15 and 0.21. NJ95 contained 32 266 SNPs. The allele frequency, effective allele number, and proportion of polymorphic were 0.79, 1.44, and 0.74, respectively. The observed heterozygosity and expected heterozygosity was 0.30 and 0.31. 2) The results of NJ90 showed that the average genetic distance of the population was 0.20, and the average kinship coefficient was 0.9%. The results of NJ95 showed that the average genetic distance of the population was 0.25, and the average kinship coefficient was 0.7%. 3) According to the boars of NJ90 and population clustering as well as kinship, the population could be divided into 6 families. 4) According to SNPs homozygosity, the average inbreeding coefficients of NJ90 and NJ95 were 0.27 and 0.01, respectively. According to the runs of homozygosity, the average inbreeding coefficients of NJ90 and NJ95 were 6.65% and 0.02%. In conclusion, the Neijiang pigs are relative abundant in genetic diversity, far in genetic distance and kinship, and low in inbreeding degree. The population can be divided into 6 families according to boars clustering and kinship analysis, which has a good basis for the protection, exploration and utilization of genetic resource. Moreover, low-coverage whole genome sequencing can cover genome information in a wider range, which is of more reference value for population genetic diversity and genetic structure analysis.

Key words: low-coverage whole genome sequencing, Neijiang pig, population structure, genetic diversity

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