基于SNP芯片监测通城猪的保种效果

doi:10.11843/j.issn.0366-6964.2022.08.010

Abstract

Abstract: This study aimed to analyze the population structure and genetic diversity of Tongcheng pig conservation population based on SNP chip information and to monitor the conservation effect. In this study, "Zhongxin No.1" 50K SNP chip was used to scan the whole genome SNPs of 68 Tongcheng pigs, and the population conservation effect was evaluated from two aspects:1) Population structure. Based on the analysis of population stratification, genetic distance, kinship, and boar genome family, the population structure among Tongcheng pigs were studied; 2) Genetic diversity. Allele frequency, effective number of alleles, polymorphism information content, proportion of polymorphic loci, heterozygosity, nucleotide diversity, and other polymorphism and heterozygosity-related parameters were employed to estimate genetic diversity and to analyze effective population size and runs of homozygosity (ROH). Based on these parameters, comprehensive evaluation of population conservation effects was conducted. The results showed that:1) The conservation population exhibited no obvious stratification with the genetic distance of 0.27, and they had a medium kinship 0.17; 2) The genome allele frequency was 0.77; the effective number of alleles was 1.52; the mean polymorphism information content was 0.31; the proportion of polymorphic markers was 88.28%; the observed heterozygosity was 0.32; and the expected heterozygosity was 0.31. The effective population size of Tongcheng pigs before the 20th generation was 105, and the effective population size of the current generation was 94. There were 184 ROHs in total. The average ROH length was 23.71 Mb, of which 28.80% was between 15 and 20 Mb in length. The genomic inbreeding coefficient was 0.04%, indicating a low level of inbreeding. Taken together, the results show that the conservation population of Tongcheng pigs is a pure breed without stratification, and Tongcheng pigs had rich genetic diversity with remarkable population conservation effect.

Key words: Tongcheng pig, conservation, population structure, genetic diversity

CLC Number:

S828.2

YUAN Jiao, XU Guoqiang, ZHOU Xiang, XU Sanping, LI Sheng, LI Wangming, LIU Bang. SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2514-2523.

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SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs

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