Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment

doi:10.1016/S2095-3119(20)63255-5

Journal of Integrative Agriculture ›› 2020, Vol. 19 ›› Issue (10): 2514-2522.DOI: 10.1016/S2095-3119(20)63255-5

所属专题：动物科学合辑Animal Science

收稿日期:2019-07-31 出版日期:2020-10-01 发布日期:2020-09-08

Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment

ZHENG Yao^1*, CHEN Cai^1*, CHEN Wei¹, WANG Xiao-yan¹, WANG Wei¹, GAO Bo¹, Klaus WIMMERS², MAO Jiu-de³, SONG Cheng-yi¹

¹ Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, P.R.China
² Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf 18196, Germany
³ Life Science Center, University of Missouri, Columbia, MO, 65211, USA

Received:2019-07-31 Online:2020-10-01 Published:2020-09-08
Contact: Correspondence SONG Cheng-yi, Tel: +86-514-87979034, E-mail: cysong@yzu.edu.cn
About author:ZHENG Yao, E-mail: zhengyao3225@outlook.com; CHEN Cai, E-mail: chencai9596@hotmail.com; * These authors contributed equally to this study.
Supported by:
This work was supported by the National Natural Science Foundation of China (31872977 and 31572364), the Jiangsu Agricultural Science and Technology Innovation Fund (CX(19)2016), and the Priority Academic Program Development of Jiangsu Higher Education Institutions, China.

摘要/Abstract

Abstract:

Despite one SINE retrotransposon insertion polymorphism (sRTIP) in the vertebrae development-associated (VRTN) gene was identified in pigs, the structural variations (SVs) in VRTN gene and its proximal flank regions were largely unknown. VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole-genome shotgun contings (WGS) database, and aligned to identify the SVs with Clustalx, and retrotransposons in VRTN gene were annotated by RepeatMasker, the splicing patterns of VRTN gene were predicted by Genescan, and large SVs were evaluated by PCR. A total of 12 small SVs and three large SVs in intron of VRTN, derived from SINE insertion polymorphisms, were identified, and two of them (VRTN-sRTIP2 and VRTN-sRTIP3) were not reported before. These VRTN-sRTIPs may affect the splicing patterns of VRTN. They displayed polymorphisms in most detected eight breeds. VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs, while VRTN-sRTIP1 showed genetic equilibrium in Erhualian pigs. Three VRTN-sRTIPs were identified, and displayed polymorphisms in pigs, and two of them were not reported before. These SVs provide a useful molecular markers for genetic analysis in pigs, and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.

Key words: VRTN gene , structural variations , SINE insertion polymorphism , pig

. [J]. Journal of Integrative Agriculture, 2020, 19(10): 2514-2522.

ZHENG Yao, CHEN Cai, CHEN Wei, WANG Xiao-yan, WANG Wei, GAO Bo, Klaus WIMMERS, MAO Jiu-de, SONG Cheng-yi. Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment[J]. Journal of Integrative Agriculture, 2020, 19(10): 2514-2522.

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Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment

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