Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

doi:10.1016/S2095-3119(20)63474-8

Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (9): 2483-2490.DOI: 10.1016/S2095-3119(20)63474-8

收稿日期:2020-06-15 出版日期:2021-09-01 发布日期:2021-07-20

Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

WU Ping-xian^1*, ZHOU Jie^1*, WANG Kai¹, CHEN De-juan¹, YANG Xi-di¹, LIU Yi-hui³, JIANG An-an¹, SHEN Lin-yuan¹, JIN Long¹, XIAO Wei-hang¹, JIANG Yan-zhi², LI Ming-zhou¹, ZHU Li¹, ZENG Yang-shuang³, XU Xu³, QIU Xiao-tian⁴, 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 Sichuan Animal Husbandry Station, Chengdu 610041, P.R.China
⁴ National Animal Husbandry Service, Beijing 100125, P.R.China

Received:2020-06-15 Online:2021-09-01 Published:2021-07-20
Contact: Correspondence TANG Guo-qing, E-mail: tyq003@163.com
About author:WU Ping-xian, E-mail: wupingxianxian@163.com; ZHOU Jie, E-mail: 1048185949@qq.com; * These authors contributed equally to this study.
Supported by:
This study was supported by grants from the Sichuan Science and Technology Program, China (2020YFN0024), the Sichuan Innovation Team of Pig, Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province (sccxtd-2020-08), the National Key R&D Program of China (2018YFD0501204), the National Natural Science Foundation of China (31530073 and C170102), and the the China Agricultural Research System of MOF and MARA (CARS-35-01A).

摘要/Abstract

摘要：

旨在基于简化基因组测序（Genotyping-by-sequencing，GBS）技术进一步挖掘与大白猪初生重（Birth weight，BW）和达百公斤日龄（Days to 100 kg，D100）性状相关的分子遗传标记，并挖掘同时影响两个性状的多效基因。简化基因组测序数据相较于SNP芯片分型数据能够获得更多的SNP位点信息，能够有效的提高全基因组关联分析的检测力。本研究采集600头大白猪的耳组织样品，提取基因组DNA，并利用GBS测序技术进行测序，测序共获得487.34Gb Clean data，测序结果经质量控制和基因型填充后，利用全基因组关联分析（Genome-wide association study，GWAS）鉴定影响大白猪BW和D100的SNP位点和候选基因，采用GEMMA软件对大白猪BW和D100性状进行全基因组关联分析。结果显示，通过GATK软件初步检测共获得10 445 924个SNPs，经过严格的质量控制后共获得279 787个高质量的SNPs位点，并利用Beagle 5.1软件对该基因型数据进行基因型填充。基于填充后的GBS数据采用全基因组关联分析，在基因组显著水平上鉴定到30个SNPs（P<1.79E-07）与D100相关；在建议显著水平上鉴定到22和2个SNPs（P<3.57E-06）分别与D100和BW相关。通过全基因组关联分析筛选到一个显著的SNPs（SSC12: 46,226,512 bp）同时影响BW和D100，暗示了基因在不同性状间具有的一因多效性。本文依据候选基因的相关分子生物学功能，最终确定了2个基因（NSRP1和DOCK7）作为影响猪生长性状的最有希望的候选基因。本研究结果为猪BW和D100性状提供了重要的遗传变异位点和候选基因，可以为猪生长性状基因组选择提供重要遗传信息。

Abstract:

Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS). A total of 30 genome-wide SNPs (P<1.79E–07) were identified for D100. Furthermore, a total of 22 and 2 suggestive SNPs (P<3.57E–06) were detected for D100 and BW, respectively. Of these, one locus located on SSC12 (position: 46 226 512 bp) were evaluated to affect both BW and D100 in Yorkshire pigs, indicating the pleiotropism in different traits. Considering the function of candidate genes, two genes, NSRP1 and DOCK7, were suggested as the most promising candidate genes involved in growth traits. Thus, use of GBS is able to identify novel variants and potential candidate genes for BW and D100, and provide an opportunity for improving pig growth traits using genomic selection in pigs.

Key words: genotyping-by-sequencing , GWAS , birth weight , days to 100 kg , Yorkshire pigs

. [J]. Journal of Integrative Agriculture, 2021, 20(9): 2483-2490.

WU Ping-xian, ZHOU Jie, WANG Kai, CHEN De-juan, YANG Xi-di, LIU Yi-hui, JIANG An-an, SHEN Lin-yuan, JIN Long, XIAO Wei-hang, JIANG Yan-zhi, LI Ming-zhou, ZHU Li, ZENG Yang-shuang, XU Xu, QIU Xiao-tian, LI Xue-wei, TANG Guo-qing. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing[J]. Journal of Integrative Agriculture, 2021, 20(9): 2483-2490.

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Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

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