皖岳黑猪基因组遗传变异分析及特征SNPs挖掘

doi:10.11843/j.issn.0366-6964.2023.07.012

摘要/Abstract

摘要： 旨在揭示皖岳黑猪全基因组遗传变异情况，筛选皖岳黑猪特征分子标记SNP位点。本研究随机选取体重达110 kg的24头皖岳黑猪进行全基因组重测序，检测皖岳黑猪全基因组变异类型、分析群体遗传多样性参数；结合公共数据库信息，下载北京黑猪、杜洛克、大白猪、蓝塘猪、民猪、深县黑猪的SNPs信息，利用挑选最大分类能力方法，将7个品种133个个体的SNPs分成两个数据集，进行皖岳黑猪特征位点选择，并对筛选到的SNPs进行基因功能注释。全基因组重测序分析结果显示，皖岳黑猪群体共获得31 534 384个SNPs，43 673个SVs，3 258个CNVRs，并筛选出33个皖岳黑猪特异位点；对33个SNP位点所注释基因进行功能富集分析，发现它们与生长（SUSD4、NELL1、GPC6）、繁殖（KHDRBS2、CRISP1）、免疫（NECTIN1）、神经调节及环境适应性（GRIK4）相关；群体遗传结构分析结果显示，皖岳黑猪有效群体较小为4.2，个体间的遗传距离在0.157 4~0.287 3之间，平均为0.243 5±0.022 2；皖岳黑猪群体期望杂合度为0.320，观察杂合度为0.328，多态性标记比例为0.788，多态性较为丰富；皖岳黑猪基因组ROH总长度在14.6~178.0 Mb，平均ROH长度为（61±9.4） Mb，群体近交系数较低，为0.025±0.004。综上，皖岳黑猪基因组遗传变异位点丰富，证明了皖岳黑猪在选育过程中保留了较丰富的遗传多样性，个体间遗传距离较远。结果为皖岳黑猪的持续选育提供了科学参考。

关键词: 皖岳黑猪, 全基因组重测序, 基因组遗传变异, 特征SNPs, 遗传结构

Abstract: This study aimed to reveal the genome-wide genetic variation of Wangyue black pigs, screen the SNP loci for molecular markers characteristic. Twenty-four Wangyue black pigs weighing 110 kg were randomly selected and re-sequenced at whole-genome level, and genome-wide variation types was detected and population genetic diversity parameters was analyzed; Combined with the public database information, the SNPs informations of Beijing black pigs, Duroc, Large White pigs, Lantang pigs, Min pigs and Shenxian black pigs were downloaded, and the SNPs of 133 individuals of 7 breeds were divided into two datasets by using the method of selecting the maximum classification ability, and the characteristic sites of Wanyue black pigs were selected, and the gene function of the screened SNPs were annotated. The variation information scanning results showed that a total of 315 343 84 SNPs, 43 673 SVs and 3 258 CNVRs were obtained. A feature database of black pigs in Anhui was constructed, and finally 33 specific sites of Wanyue black pigs were screened, and the genes involved in 33 SNPs were functionally enriched, and it was found that these genes were related to growth (SUSD4, NELL1, GPC6), reproduction (KHDRBS2, CRISP1), immunity (NECTIN1), neuromodulation and environmental adaptation (GRIK4); The results of the relevant parameters of the genetic structure of the population showed that the genetic distance between individuals was between 0.157 4-0.287 3, with an average of 0.243 5±0.022 2; the effective population size was 4.2, the expected heterozygosity was 0.320, the observed heterozygosity was 0.328, the polymorphism marker ratio was 0.788, the total individual ROH length was 14.6-178.0Mb, the average ROH length was (61±9.4) Mb, and the inbreeding coefficient of the population was 0.025±0.004, with a low inbreeding coefficient. In summary, the abundant genomic variation resources of Wanyue black pig indicate that Wanyue black pig retains rich genetic diversity in the breeding process, and most of the individuals have a long genetic distance, which is a characteristic and valuable germplasm resource. This study provides scientific reference for the further breeding of Wanyue black pig.

Key words: Wanyue black pig, whole-genome re-sequencing, genome genetic variation, characteristic SNP sites, genetic structure

中图分类号:

S828.2

王静琳, 刘阳光, 徐启隆, 陈朔, 邓在双, 程诗雨, 丁月云, 郑先瑞, 殷宗俊, 张晓东. 皖岳黑猪基因组遗传变异分析及特征SNPs挖掘[J]. 畜牧兽医学报, 2023, 54(7): 2783-2793.

WANG Jinglin, LIU Yangguang, XU Qilong, CHEN Shuo, DENG Zaishuang, CHENG Shiyu, DING Yueyun, ZHENG Xianrui, YIN Zongjun, ZHANG Xiaodong. Genome Structures Variant Analysis and Feature SNPs Screening of Wanyue Black Pig[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2783-2793.

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