基于全基因组重测序数据的新疆褐牛基因组结构变异检测及群体结构分析

doi:10.11843/j.issn.0366-6964.2024.08.016

摘要/Abstract

摘要：

旨在鉴定新疆褐牛基因组结构变异(structure variation，SVs)特征，并在此基础上探索新疆褐牛培育过程中受到影响的结构变异。本研究基于全基因组重测序数据，利用Manta、Delly、Lumpy三款软件对新疆褐牛及其父母本(瑞士褐牛、哈萨克牛)以及中国西门塔尔牛基因组结构变异进行检测，之后利用主成分分析、构建系统发育树和遗传分化指数(F_ST)将新疆褐牛基因组与其余3个品种进行比较分析。结果显示，4个牛品种共检测出54 969个SVs，缺失型变异占比最高(56.59%)，插入型变异占比最少(0.03%)。从数量上看，这些SVs在染色体上的分布呈现出随染色体号变大而逐渐减少的趋势。不同品种间存在共有变异和品种特有变异，其中地方品种哈萨克牛拥有的特有SVs数量最多。主成分分析和系统发育树结果发现，新疆褐牛同哈萨克牛和瑞士褐牛具有较近的亲缘关系。经选择信号分析、基因注释和富集分析，挖掘出了一批与产奶性状(PI4K2A、ELOVL3、ECHS1、SCD、TCF7L2、PNLIPRP2、BTRC、PLCE1)、生长发育(BMP6、TLL2、MAPK9、ROR2)、适应性(PRKCB)以及免疫(GSTO2、GSTO1)相关的关键基因。本研究从结构变异上解析新疆褐牛的特征，并揭示一些新疆褐牛培育过程中高度分化的基因，为推动新疆褐牛的遗传改良提供了基础资料。

关键词: 结构变异, 全基因组重测序, 群体结构分析, 新疆褐牛

Abstract:

The aim of this study was to characterize the structural variations (SVs) in the genome of Xinjiang brown cattle, and on this basis, to explore the structural variations affected during the breeding process of Xinjiang brown cattle. Based on the whole genome resequencing data, the structural variation in the genomes of Xinjiang Brown cattle, their parents (Swiss brown cattle and Kazakh cattle) and Chinese Simmental cattle was examined using 3 software programs, Manta, Delly and Lumpy, and then analyzed the genomes of Xinjiang Brown cattle in comparison with the remaining 3 breeds using principal component analysis, construction of phylogenetic tree and fixation index (F_ST). The results showed that a total of 54 969 SVs were detected in the 4 cattle breeds, with the highest percentage of deletion-type variants (56.59%) and the lowest percentage of insertion-type variants (0.03%). Quantitatively, the distribution of these SVs on chromosomes showed a tendency of decreasing with larger chromosome numbers. Shared and breed-specific variants existed among different breeds, with the local breed Kazakh cattle possessing the highest number of specific SVs. The results of principal component analysis and phylogenetic tree revealed that Xinjiang brown cattle were closely related to Kazakh and Swiss brown cattle. A number of key genes related to milk production traits (PI4K2A, ELOVL3, ECHS1, SCD, TCF7L2, PNLIPRP2, BTRC, PLCE1), growth and development (BMP6, TLL2, MAPK9, ROR2), adaptability (PRKCB) and immunity (GSTO2, GSTO1) were mined out by selective signaling analysis, gene annotation and enrichment analysis. This study analyzed the characteristics of Xinjiang brown cattle in terms of structural variation and revealed some highly differentiated genes in the breeding process of Xinjiang brown cattle, which provided basic information for promoting the genetic improvement of Xinjiang brown cattle.

Key words: structural variation, whole genome resequencing, population structure analysis, Xinjiang brown cattle

中图分类号:

S823.2

张涛, 李佳芪, 胥磊, 王丹, 张梦华, 张涛, 闫梦婕, 王玮韬, 范守民, 黄锡霞. 基于全基因组重测序数据的新疆褐牛基因组结构变异检测及群体结构分析[J]. 畜牧兽医学报, 2024, 55(8): 3427-3435.

Tao ZHANG, Jiaqi LI, Lei XU, Dan WANG, Menghua ZHANG, Tao ZHANG, Mengjie YAN, Weitao WANG, Shoumin FAN, Xixia HUANG. Detection and Population Structure Analysis of Genomic Structural Variation in Xinjiang Brown Cattle Based on Whole Genome Resequencing Data[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(8): 3427-3435.

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