A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds.

IF 2.2 2区农林科学 Asian-Australasian Journal of Animal Sciences Pub Date : 2020-09-01 Epub Date: 2019-10-21 DOI:10.5713/ajas.19.0411

Yao Jiang, Shaoqing Tang, Wei Xiao, Peng Yun, Xiangdong Ding

{"title":"A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds.","authors":"Yao Jiang, Shaoqing Tang, Wei Xiao, Peng Yun, Xiangdong Ding","doi":"10.5713/ajas.19.0411","DOIUrl":null,"url":null,"abstract":"Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB).Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multitrait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874).Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits.Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.","PeriodicalId":8558,"journal":{"name":"Asian-Australasian Journal of Animal Sciences","volume":null,"pages":null},"PeriodicalIF":2.2000,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7468174/pdf/","citationCount":"8","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Asian-Australasian Journal of Animal Sciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.5713/ajas.19.0411","RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2019/10/21 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}

引用次数: 8

Abstract

Objective: Genome-wide association study and two meta-analysis based on GWAS performed to explore the genetic mechanism underlying variation in pig number born alive (NBA) and total number born (TNB).

Methods: Single trait GWAS and two meta-analysis (single-trait meta analysis and multitrait meta analysis) were used in our study for NBA and TNB on 3,121 Yorkshires from 4 populations, including three different American Yorkshire populations (n = 2,247) and one British Yorkshire populations (n = 874).

Results: The result of single trait GWAS showed that no significant associated single nucleotide polymorphisms (SNPs) were identified. Using single-trait meta analysis and multi-trait meta analysis within populations, 11 significant loci were identified associated with target traits. Spindlin 1, vascular endothelial growth factor A, forkhead box Q1, msh homeobox 1, and LHFPL tetraspan submily member 3 are five functionally plausible candidate genes for NBA and TNB. Compared to the single population GWAS, single-trait Meta analysis can improve the detection power to identify SNPs by integrating information of multiple populations. The multiple-trait analysis reduced the power to detect trait-specific loci but enhanced the power to identify the common loci across traits.

Conclusion: In total, our findings identified novel genes to be validated as candidates for NBA and TNB in pigs. Also, it enabled us to enlarge population size by including multiple populations with different genetic backgrounds and increase the power of GWAS by using meta analysis.

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

4个不同遗传背景猪群体繁殖性状的全基因组关联研究。

目的:通过全基因组关联研究和基于GWAS的两项meta分析，探讨猪出生活数(NBA)和总出生数(TNB)变异的遗传机制。方法:采用单性状GWAS和两项荟萃分析(单性状荟萃分析和多性状荟萃分析)对4个种群3121只约克郡的NBA和TNB进行研究，其中包括3个不同的美国约克郡种群(n = 2247)和1个英国约克郡种群(n = 874)。结果:单性状GWAS结果显示，未发现显著相关的单核苷酸多态性(snp)。通过群体内单性状和多性状荟萃分析，鉴定出11个与目标性状相关的显著基因座。Spindlin 1、血管内皮生长因子A、forkhead box Q1、msh homobox 1和LHFPL tetraspan亚家族成员3是NBA和TNB的五个功能上合理的候选基因。与单种群GWAS相比，单性状Meta分析可以整合多种群的信息，提高snp的检测能力。多性状分析降低了识别性状特异性位点的能力，但提高了识别性状间共有位点的能力。结论:总的来说，我们的发现确定了新的基因，作为猪NBA和TNB的候选基因。此外，通过纳入不同遗传背景的多个群体，可以扩大群体规模;通过meta分析，可以提高GWAS的效力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

Asian-Australasian Journal of Animal Sciences AGRICULTURE, DAIRY & ANIMAL SCIENCE-

自引率

0.00%

发文量

审稿时长

3 months

期刊介绍： Asian-Australasian Journal of Animal Sciences (AJAS) aims to publish original and cutting-edge research results and reviews on animal-related aspects of the life sciences. Emphasis will be placed on studies involving farm animals such as cattle, buffaloes, sheep, goats, pigs, horses, and poultry. Studies for the improvement of human health using animal models may also be publishable. AJAS will encompass all areas of animal production and fundamental aspects of animal sciences: breeding and genetics, reproduction and physiology, nutrition, meat and milk science, biotechnology, behavior, welfare, health, and livestock farming systems.