Yao Jiang, Shaoqing Tang, Wei Xiao, Peng Yun, Xiangdong Ding
{"title":"4个不同遗传背景猪群体繁殖性状的全基因组关联研究。","authors":"Yao Jiang, Shaoqing Tang, Wei Xiao, Peng Yun, Xiangdong Ding","doi":"10.5713/ajas.19.0411","DOIUrl":null,"url":null,"abstract":"<p><strong>Objective: </strong>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).</p><p><strong>Methods: </strong>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).</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","PeriodicalId":8558,"journal":{"name":"Asian-Australasian Journal of Animal Sciences","volume":"33 9","pages":"1400-1410"},"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":"{\"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\":\"<p><strong>Objective: </strong>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).</p><p><strong>Methods: </strong>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).</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>\",\"PeriodicalId\":8558,\"journal\":{\"name\":\"Asian-Australasian Journal of Animal Sciences\",\"volume\":\"33 9\",\"pages\":\"1400-1410\"},\"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}","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}
A genome-wide association study of reproduction traits in four pig populations with different genetic backgrounds.
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.
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.
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