Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

doi:10.1016/S2095-3119(20)63488-8

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (7): 1898-1906.DOI: 10.1016/S2095-3119(20)63488-8

收稿日期:2020-05-14 出版日期:2021-07-01 发布日期:2021-06-02

Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

WANG Kai^1*, WU Ping-xian^1*, CHEN De-juan¹, ZHOU Jie¹, YANG Xi-di¹, JIANG An-an1, MA Ji-deng¹, TANG Qian-zi¹, XIAO Wei-hang¹, JIANG Yan-zhi², ZHU Li¹, QIU Xiao-tian³, LI Ming-zhou¹, LI Xue-wei¹, TANG Guo-qing¹

¹ Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P.R.China
² College of Life Science, Sichuan Agricultural University, Ya’an 625014, P.R.China
³ National Animal Husbandry Service, Beijing 100125, P.R.China

Received:2020-05-14 Online:2021-07-01 Published:2021-06-02
Contact: Correspondence TANG Guo-qing, E-mail: tyq003@163.com, tanggq@sicau.edu.cn
About author:WANG Kai, E-mail: 614351818@qq.com; * These authors contributed equally to this study.
Supported by:
The study was supported by the grants from the Sichuan Science and Technology Program, China (2020YFN0024), the earmarked fund for the China Agriculture Research System (CARS-35-01A), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (C170102), and the Sichuan Innovation Team of Pig, China (sccxtd-2021-08).

摘要/Abstract

摘要：

长白猪和大白猪是重要的商品猪品种。在长期的育种过程中，由于两种猪的育种目标不同，经过强烈的人工选择，长白猪和大白猪在猪基因组上有不同的选择信号，这些选择信号反映了它们特定的表型特征。因此本研究旨在通过全基因组选择信号扫描检测长白猪和大白猪之间的选择痕迹差异，从而为长白猪和大白猪的育种历史提供基础数据支持。在本研究中我们使用了Z转换的FST（Z(FST)）和Z转换的杂合度（ZHp）两种方法对长白猪和大白猪进行全基因组扫描。在扫描过程中我们使用滑动窗口（40-kb窗口和20-kb步长）来检验FST值和杂合度，然后对FST值和杂合度进行Z转换，当滑动窗口的Z(FST)>5或ZHp<-2.8时，我们将该窗口确定为显著窗口，然后基于该窗口的基因组范围搜索候选基因。我们使用Z(FST)的方法找到了17个显著窗口，基于这些窗口找到15个注释元件，其中包括13个基因，比如UGP2基因, RAB3C基因和TLL1基因；我们使用ZHp的方法鉴别了363个显著窗口，基于这些窗口找到208个注释元件，其中包括140个基因，比如PPP3CA基因，PTPN13基因和MAPK10基因。功能分析和相关研究结果表明，大部分候选基因与基础代谢、抗病、细胞过程和生化信号有关，有几个与机体形态和器官有关。研究结果表明由于长期的人工选择，长白猪和大白猪在猪基因组上有明显不同的选择足迹。本研究基于全基因组重测序数据对长白猪和大白猪进行全基因组选择信号扫描，与其他研究相比，我们鉴别出了两个品种特定的差异基因组区域和候选基因，这些结果可以帮助研究者更好的了解人工选择对长白猪和大白猪的选择作用以及为这两个品种的现代育种提供新的方向。

Abstract:

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs. Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST (Z(FST)) method, and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity (ZHp) method. The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism, disease resistance, cellular processes, and biochemical signals, and several were related to body morphology and organs. They included PPP3CA, which plays an essential role in the transduction of intracellular Ca²⁺-mediated signals, and WWTR1, which plays a pivotal role in organ size control and tumor suppression. These results suggest that genes associated with body morphology were subject to selection pressure during domestication, whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding. Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.

Key words: pig , variation , whole-genome sequence , selection signature , phenotypic trait

. [J]. Journal of Integrative Agriculture, 2021, 20(7): 1898-1906.

WANG Kai, WU Ping-xian, CHEN De-juan, ZHOU Jie, YANG Xi-di, JIANG An-an, MA Ji-deng, TANG Qian-zi, XIAO Wei-hang, JIANG Yan-zhi, ZHU Li, QIU Xiao-tian, LI Ming-zhou, LI Xue-wei, TANG Guo-qing. Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs[J]. Journal of Integrative Agriculture, 2021, 20(7): 1898-1906.

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Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

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