基于全基因组重测序对晋汾白猪单核苷酸多态性位点鉴定和筛选

doi:10.11843/j.issn.0366-6964.2023.07.010

摘要/Abstract

摘要： 旨在鉴定晋汾白猪单核苷酸多态性位点（SNP）并分析其特征，筛选特异性SNPs。本研究对30头晋汾白猪（9头公猪和21头母猪）耳组织DNA进行全基因组重测序，利用GATK和VEP软件检测变异位点和进行注释分类。整合晋汾白猪与其亲本的基因组重测序数据，基于等位基因频率检测晋汾白猪特异SNPs位点，并进行功能富集分析。经测序以及数据过滤后共获得约1 761.73 Gb的Clean reads，Q30均值为91.77%，平均比对率为75.61%，平均覆盖度为14.7 X。去冗余后共得到14 680 807个SNPs，大部分SNPs位于1号染色体和基因非编码区。基于等位基因频率筛选到87 366个晋汾白猪特异SNPs，主要分布于2号染色体和内含子区。此外，外显子区的错义突变SNPs位点分布于343个基因，这些基因显著富集于细胞器和细胞器组分等GO生物学过程，以及肠道免疫、脂肪酸降解等KEGG信号通路。利用全基因组重测序和生物信息学技术分析了晋汾白猪SNPs与其特征，并筛选了87 366个特异SNPs位点，将为晋汾白猪分子标记开发、种质鉴定、分子育种等工作奠定研究基础。

关键词: 晋汾白猪, 全基因组重测序, 单核苷酸多态性

Abstract: The aim of this study was to identify and analyze the single nucleotide polymorphism (SNP) and screen the specific SNPs in Jinfen White pigs. In this study, the whole genome of 30 ear DNA samples from 9 male and 21 female Jinfen White pigs were resequenced. The GATK software was used to detect the mutation sites, and VEP software was used for SNPs classification and annotation. The genome resequencing data of its parents, including Mashen pig, Taihu (Erhualian) pig, Landrace and Large white pig, were integrated to detect the specific SNPs loci of Jinfen White pig based on allele frequency. The biological functions of the genes including SNP loci were annotated by enrichment analysis. The results of whole genome resequencing of 30 Jinfen White pigs showed that about 1 761.73 Gb Clean reads were obtained by sequencing and data filtering, among which the average values of Q30 reached 91.77%. The average sample alignment rate was 75.61%, the average coverage depth was 14.7 X. A total of 14 680 807 SNPs were identified after filtering, most SNPs were distributed on Chr1 and in the non-coding region of the gene. Subsequently, 87 366 specific SNPs of Jinfen White pigs were screened based on allele frequencies, most of which were located on Chr2 and distributed in the intron. In addition, the missense mutant SNPs located in the exon region belonged to 343 genes, which were significantly enriched in organelles, organelle components, intestinal immune, fatty acid degradation pathway, et al. The SNPs were analyzed and 87 366 specific SNPs loci were also screened through whole genome resequencing and bioinformatics techniques. This study will provide a research basis for the development of molecular markers, pure breed identification and molecular breeding of Jinfen White pigs.

Key words: Jinfen White pig, whole genome resequencing, SNP

中图分类号:

S828.2

路畅, 董磊, 张万锋, 高鹏飞, 郭晓红, 蔡春波, 曹果清, 李步高. 基于全基因组重测序对晋汾白猪单核苷酸多态性位点鉴定和筛选[J]. 畜牧兽医学报, 2023, 54(7): 2761-2771.

LU Chang, DONG Lei, ZHANG Wanfeng, GAO Pengfei, GUO Xiaohong, CAI Chunbo, CAO Guoqing, LI Bugao. Identification and Screening of Single Nucleotide Polymorphism Loci in Jinfen White Pigs Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2761-2771.

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