芯片和重测序在猪遗传结构研究中的应用比较

doi:10.11843/j.issn.0366-6964.2023.07.011

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (7): 2772-2782.doi: 10.11843/j.issn.0366-6964.2023.07.011

芯片和重测序在猪遗传结构研究中的应用比较

杨晴^1,2, 巩静^1,2, 赵雪艳^2,3, 朱晓东⁴, 耿立英¹, 张传生^1*, 王继英^2,3*

1. 河北科技师范学院动物科技学院, 秦皇岛 066600;
2. 山东省农业科学院畜牧兽医研究所山东省畜禽疫病防治与繁育重点实验室, 济南 250100;
3. 农业农村部畜禽生物组学重点实验室, 济南 250100;
4. 枣庄黑盖猪养殖有限公司, 枣庄 277100

收稿日期:2023-01-13 出版日期:2023-07-23 发布日期:2023-07-21
通讯作者: 王继英,主要从事猪遗传育种研究,E-mail:jnwangjiying@163.com;张传生,主要从事动物遗传育种与繁殖研究,E-mail:cszhang1976@126.com
作者简介:杨晴(1997-),女,河南郑州人,硕士生,主要从事猪遗传育种与繁殖研究,E-mail:yangoh123@163.com
基金资助:
山东省农业良种工程项目（2020LZGC012；2022LZGCQY007）；山东省生猪产业技术体系（SDAIT-08-03）；枣庄市自主创新及成果转化项目（2022GH-27）；国家生猪产业技术体系（CARS-35）

Comparison of Array and Resequencing in Pig Genetic Structure Studies

YANG Qing^1,2, GONG Jing^1,2, ZHAO Xueyan^2,3, ZHU Xiaodong⁴, GENG Liying¹, ZHANG Chuansheng^1*, WANG Jiying^2,3*

1. College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066600, China;
2. Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China;
3. Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs, Jinan 250100, China;
4. Zaozhuang Heigai Pig Breeding Co. Ltd., Zaozhuang 277100, China

Received:2023-01-13 Online:2023-07-23 Published:2023-07-21

摘要/Abstract

摘要： 旨在比较芯片与测序SNP分型技术、标记密度对遗传多样性、系统发生树和近交系数等分析结果的影响，探讨遗传结构分析中低成本、高效的分型方法和适宜的SNP密度。本研究以35头枣庄黑盖猪的CAUPorcineSNP50芯片数据和重测序数据为基础，以重测序数据为"原材料"构建了随机34K、均匀34K、均匀340K和均匀3 400K 4个SNP面板，利用CAUPorcineSNP50芯片和各SNP面板的SNP标记分析了枣庄黑盖猪的遗传多样性、系统发生树和基因组近交系数。结果表明：1）利用芯片SNP标记分析的观察杂合度（observed heterozygosity，H_O）（0.385 9 vs.0.320 0~0.324 1）、期望杂合度（expected heterozygosity，H_E）（0.381 3 vs. 0.333 5~0.334 6）、遗传距离（0.305 7 vs. 0.279 8~0.280 6）等遗传多样性指标值均高于各测序SNP面板，利用芯片SNP标记构建的系统发生树与各测序SNP面板存在较大不同，这可能是由于芯片设计中倾向于选择高MAF的SNP位点等原因所导致。2）各测序SNP面板对H_O（0.320 0~0.324 1）、H_E（0.333 5~0.334 6）、遗传距离（0.279 8~0.280 6）和系统发生树分析影响较小，但对纯合性片段（runs of homozygosity，ROH）的数目（784~106 547）和长度（0.20~13.51 Mb）及基因组近交系数F_ROH（0.127~0.263）影响很大。目前畜禽基因组近交系数分析采用的50 K左右基因组SNP芯片有利于检测大片段ROH，对中小片段的ROH检测力差，故估计的基因组近交系数可能比实际值偏低。综上所述，不同SNP分型技术对遗传多样性、系统发生树和ROH的分析结果影响较大。测序组中，不同SNP密度对遗传多样性、系统发生树分析结果影响较小，但对ROH以及F_ROH分析结果影响很大。

关键词: SNP芯片, 重测序, 遗传多样性, 系统进化树, 基因组近交系数

Abstract: This study aimed to compare the effects of SNP genotyping techniques (array and sequencing) and marker densities on the analysis results of genetic diversity, phylogenetic tree and genomic inbreeding coefficient, and explore low-cost and efficient genotyping method and appropriate SNP density in genetic structure study. The data of the CAUPorcine SNP50 array and the resequencing data of 35 Zaozhuang Heigai pigs were used in this study. In this study, using resequencing data as "raw materials", 4 SNP panels of random 34K, even 34K, even 340K and even 3 400K were constructed. The genetic diversity, phylogenetic tree and genomic inbreeding coefficient of Zaozhuang Heigai pigs were analyzed using SNP data of CAUPorcine SNP50 array and several sequencing panels. The results showed that:1) The index values of genetic diversity, including observed heterozygosity (H_O) (0.385 9 vs. 0.320 0-0.324 1), expected heterozygosity (H_E) (0.381 3 vs. 0.333 5-0.334 6), and genetic distance (0.305 7 vs. 0.279 8-0.280 6), estimated by array SNPs were higher than those by the SNPs of sequencing panels, and the phylogenetic tree constructed by array SNPs was of much difference from those by the SNPs of sequencing panels. These may be caused by the tendency of choosing higher minor allele frequency (MAF) SNPs in array design. 2) All sequencing panels had small impact on the analysis results of H_O (0.320 0-0.324 1), H_E (0.333 5-0.334 6), genetic distance (0.279 8-0.280 6) and phylogenetic tree, but had great impact on the number (784-106 547) and length (0.20-13.51 Mb) of runs of homozygosity (ROH) and genomic inbreeding coefficient (F_ROH) (0.127-0.263). Currently used 50 K genome-wide SNP arrays in the analysis of inbreeding coefficient of livestock and poultry is good at detection of large fragments of ROHs, but weak in identification small and medium ones. So the genomic inbreeding coefficient estimated by them may be lower than the actual value. In summary, different SNP genotyping techniques have a significant impact on the analysis results of genetic diversity, phylogenetic tree, and ROH. In the sequencing group, different SNP densities had a small impact on genetic diversity and phylogenetic tree analysis results, but had a significant impact on ROH and F_ROH analysis results.

Key words: SNP array, resequencing, genetic diversity, phylogenetic tree, genomic inbreeding coefficient

中图分类号:

S828.2

杨晴, 巩静, 赵雪艳, 朱晓东, 耿立英, 张传生, 王继英. 芯片和重测序在猪遗传结构研究中的应用比较[J]. 畜牧兽医学报, 2023, 54(7): 2772-2782.

YANG Qing, GONG Jing, ZHAO Xueyan, ZHU Xiaodong, GENG Liying, ZHANG Chuansheng, WANG Jiying. Comparison of Array and Resequencing in Pig Genetic Structure Studies[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2772-2782.

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芯片和重测序在猪遗传结构研究中的应用比较

Comparison of Array and Resequencing in Pig Genetic Structure Studies

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