基于SNP芯片分析徽县青泥黑猪遗传多样性和遗传结构

doi:10.11843/j.issn.0366-6964.2024.03.013

Abstract

Abstract: The aim of this study was to analyse the genetic diversity and genetic structure of the Huixian Qingni Black pig, and to provide reference for its declaration, protection and utilization as a new genetic resource. A total of 68 pigs from two known local pig breeds (20 each of Bamei pigs and Hezuo pigs) and a new pig breed to be identified (28 of Huixian Qingni Black pigs) in Gansu Province were used for the study. "Zhongxin-1"50K SNP chip was used to detect whole-genome single nucleotide polymorphisms (SNPs), and a variety of softwares were used to analyse the genetic diversity, genetic structure, population differentiation indices and relationship of the Huixian Qingni Black pig. The results showed that:a total of 55 156 SNPs were detected, with 49 279 SNPs remaining after quality control; The effective population size (N_e), expected heterozygosity (H_e), observed heterozygosity (H_o), proportion of polymorphic markers (P_N) and nucleotide diversity (P_i) of Huixian Qingni Black pigs were higher than Hezuo pigs and Bamei pigs at 2.2, 0.370 7, 0.386 4, 0.915 7 and 0.378 6, respectively, and the linkage disequilibrium coefficients of Huixian Qingni Black pigs were lower and decayed faster; PCA showed that the three populations were clustered respectively, and HX population could be distinguished from HZ and BM populations according to PC1 (PC1>0), and the evolutionary tree analysis revealed that the Huixian Qingni Black pigs clustered into a single branch, while the Bamei pigs and the Hezuo pigs clustered into another large branch, and then gradually separated, and the population structure showed that the Huixian Qingni Black pigs showed a different evolutionary route from the Bamei pigs and the Hezuo pigs when K=3, but the bloodlines of the Huixian Qingni Black pigs were more mixed; The population differentiation indices between the Huixian Qingni Black pigs and Bamei pigs, Hezuo pigs were 0.123 6 and 0.159 8, respectively, indicating that there was a certain degree of genetic differentiation among the pig breeds; The IBS matrix and G matrix analyses showed that most of the individuals in Huixian Qingni Black pigs were distantly related to each other, while a few individuals were more closely related to each other. In this study, we analysed the genetic diversity and genetic structure of Huixian Qingni Black pigs based on "zhongxin-1"50K SNP chips data, and found that the genetic diversity of Huixian Qingni Black pigs is higher than that of Bamei pigs and Hezuo pigs, independently clustering, and there is obvious genetic differentiation with Bamei pigs and Hezuo pigs. It is preliminarily considered to be a new local pig breed in Gansu. There is risk of inbreeding between some of the individuals of Huixian Qingni Black pig, which needs to be strengthened to preserve the breed, this study provided a reference for further excavation of new genetic resources of Huixian Qingni Black pigs and rational breeding conservation and utilization.

Key words: Huixian Qingni Black pig, SNP chip, genetic diversity, genetic structure, relationship

CLC Number:

S828.2

SONG Kelin, YAN Zunqiang, WANG Pengfei, CHENG Wenhao, LI Jie, BAI Yaqin, SUN Guohu, GUN Shuangbao. Analysis on Genetic Diversity and Genetic Structure Based on SNP Chips of Huixian Qingni Black Pig[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 995-1006.

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Analysis on Genetic Diversity and Genetic Structure Based on SNP Chips of Huixian Qingni Black Pig

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