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

摘要/Abstract

摘要： 旨在分析徽县青泥黑猪遗传多样性和遗传结构，为其作为新遗传资源申报、保护与利用提供参考。本研究以甘肃省2个已知地方猪种（八眉猪、合作猪各20头）和待鉴定新猪种（徽县青泥黑猪28头）共68头猪为研究对象，利用"中芯一号"50K SNP芯片检测全基因组范围内单核苷酸多态性（single nucleotide polymorphisms，SNPs），采用多种软件分析徽县青泥黑猪遗传多样性、遗传结构、群体分化指数及亲缘关系。结果显示：共检测到55 156个SNPs，质控后剩余49 279个SNPs；徽县青泥黑猪的有效群体含量（N_e）、期望杂合度（H_e）、观察杂合度（H_o）、多态标记比例（P_N）和核苷酸多样性（P_i）分别为2.2、0.370 7、0.386 4、0.915 7、0.378 6，均高于合作猪和八眉猪，且徽县青泥黑猪的连锁不平衡系数较低，衰减速度较快；PCA显示，3个群体分别聚类，根据PC1（PC1>0）可将HX群体和HZ、BM群体区分开，进化树分析发现徽县青泥黑猪独自聚为一支，八眉猪和合作猪聚为另一大支，随后逐渐分离，群体结构显示，当K=3时，徽县青泥黑猪呈现出与八眉猪、合作猪不同的进化路线，但徽县青泥黑猪血缘较为混杂；徽县青泥黑猪与八眉猪、合作猪之间的群体分化指数分别为0.123 6和0.159 8，表明各猪种之间存在一定程度的遗传分化；IBS矩阵和G矩阵分析发现，徽县青泥黑猪大部分个体之间亲缘关系较远，少数个体亲缘关系较近。本研究基于"中芯一号"50K SNP芯片数据分析了徽县青泥黑猪的遗传多样性及遗传结构，发现徽县青泥黑猪遗传多样性高于八眉猪和合作猪，独立聚类，且与八眉猪、合作猪之间有明显的遗传分化，初步认为是甘肃地方新猪种，徽县青泥黑猪部分个体之间存在近交风险，需要加强保种，该研究为深入挖掘徽县青泥黑猪新遗传资源及合理保种利用提供参考。

关键词: 徽县青泥黑猪, SNP芯片, 遗传多样性, 遗传结构, 亲缘关系

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

中图分类号:

S828.2

宋科林, 闫尊强, 王鹏飞, 程文昊, 李杰, 白雅琴, 孙国虎, 滚双宝. 基于SNP芯片分析徽县青泥黑猪遗传多样性和遗传结构[J]. 畜牧兽医学报, 2024, 55(3): 995-1006.

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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