利用50K芯片解析和田羊和策勒黑羊的遗传规律

doi:10.11843/j.issn.0366-6964.2022.04.006

摘要/Abstract

摘要： 旨在探究和田羊和策勒黑羊遗传规律的不同，筛选优异基因及其分子标记，推动新疆南疆绵羊品种遗传资源的开发和利用。本研究分别选取健康、成年和田母羊84只、策勒黑羊41只，采集耳组织，放入75%的酒精。基于酚氯仿法提取DNA，经电泳和核酸仪检测，制备Illumina Ovine SNP50芯片。用Plink1.07对基因组数据进行质量控制，质控标准：剔除检出率小于90%、最小等位基因频率(MAF)< 5%、哈代温伯格平衡P<1×10^-6的SNPs。对两个品种进行PCA群体分类，HapFLK分析取前1%的P值所对应SNPs，经过绵羊基因组Oar_v4.0注释基因，对候选基因进行GO和KEGG分析。结果表明：1)和田羊和策勒黑羊经不同程度的选育后，在遗传结构上存在差异，但与藏羊群体相比，二者的分化程度不高。2)获得候选基因167个。基于和田羊和策勒黑羊在生产性能的差异，在基因组水平对两个品种的遗传规律进行解析，发现绵羊毛生长相关的基因有KRT82、KRT84等；毛色相关的基因KIT等；生长发育相关的基因AMHR2、SP1、OARDACVR1B、ADIPOQ等；环境适应性相关的基因PDGFRA、ADIPOQ等。通过基因组选择性清扫的方法，对和田羊和策勒黑羊在不同生产性状进行基因组水平差异解析，发现两个品种在毛质性状、毛色、尾型上存在差异，而繁殖相关性状差异较小。综上所述，本研究利用绵羊基因组芯片比较了和田羊和策勒黑羊遗传结构的不同，寻找了相关的优异基因，为南疆地区绵羊种质资源保护和分子选育提供参考。

关键词: 50K芯片, 遗传规律, 选择信号

Abstract: The aim of this study was to investigate the differences in genetic patterns between Hetian and Qira Black sheep, to screen superior genes and their molecular markers, and to promote the development and utilization of genetic resources of sheep breeds in southern Xinjiang. In this study, 84 healthy, adult Hetian ewes and 41 Qira Black sheep were selected, respectively, and ear tissues were collected and put into 75% alcohol. DNA was extracted based on phenol-chloroform method, and Illumina Ovine SNP50 was prepared by electrophoresis and nucleic acid instrumentation. For genomic data, quality control was performed with Plink1.07, and quality control criteria: exclusion of SNPs with detection rate less than 90%, minimum allele frequency (MAF)<5%, and Hardy-Weinberg equilibrium P<1×10^-6. PCA populations of both breeds were classified, and HapFLK analysis was performed to take the SNPs corresponding to the top 1% of P values, and after sheep genome Oar_v4.0 annotation of genes, the GO and KEGG analyses were performed on the candidate genes. The results showed that: 1) Hetian sheep and Qira Black sheep differed in genetic structure after different degrees of selection and breeding, but they were not highly differentiated compared with the Tibetan sheep population. 2) A total of 167 candidate genes were obtained, and based on the differences in production performance between Hetian sheep and Qira Black sheep, the genetic patterns of the two breeds were resolved at the genomic level, and genes related to sheep wool growth were found to be KRT82 and KRT84, etc., wool color-related genes KIT, etc., growth and development-related genes AMHR2, SP1, OARDACVR1B, ADIPOQ, etc., and environmental adaptation-related genes PDGFRA, ADIPOQ, etc. Genome-level differences between Hetian and Qira Black sheep in different production traits were resolved by genomic selective sweeping, and it was found that the two breeds differed in wool quality traits, coat color, and tail type, while the differences in reproduction-related traits were small. In conclusion, the sheep genome microarrays was used to compare the differences in genetic structure of Hetian and Qira Black sheep and to search for the related superior genes, which would provide reference for the conservation of sheep germplasm resources and molecular selection and breeding in Southern Xinjiang region.

Key words: 50K chip, genetic pattern, selection signal

中图分类号:

S826.2

张成龙, 郑浪漫, 刘春洁, 高庆华, 刘书东. 利用50K芯片解析和田羊和策勒黑羊的遗传规律[J]. 畜牧兽医学报, 2022, 53(4): 1051-1063.

ZHANG Chenglong, ZHENG Langman, LIU Chunjie, GAO Qinghua, LIU Shudong. Analysis of Genetic Law of Hetian and Qira Black Sheep Using Illumina Ovine SNP50 Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(4): 1051-1063.

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