Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs
Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large...
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Frontiers Media S.A.
2021-08-01
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Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.650370/full |
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language |
English |
format |
Article |
sources |
DOAJ |
author |
Yifeng Hong Yifeng Hong Jian Ye Jian Ye Linsong Dong Yalan Li Limin Yan Gengyuan Cai Gengyuan Cai Dewu Liu Cheng Tan Cheng Tan Zhenfang Wu Zhenfang Wu |
spellingShingle |
Yifeng Hong Yifeng Hong Jian Ye Jian Ye Linsong Dong Yalan Li Limin Yan Gengyuan Cai Gengyuan Cai Dewu Liu Cheng Tan Cheng Tan Zhenfang Wu Zhenfang Wu Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs Frontiers in Genetics genome-wide association study body length body height total teat number Large white pigs |
author_facet |
Yifeng Hong Yifeng Hong Jian Ye Jian Ye Linsong Dong Yalan Li Limin Yan Gengyuan Cai Gengyuan Cai Dewu Liu Cheng Tan Cheng Tan Zhenfang Wu Zhenfang Wu |
author_sort |
Yifeng Hong |
title |
Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs |
title_short |
Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs |
title_full |
Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs |
title_fullStr |
Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs |
title_full_unstemmed |
Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs |
title_sort |
genome-wide association study for body length, body height, and total teat number in large white pigs |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-08-01 |
description |
Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection. |
topic |
genome-wide association study body length body height total teat number Large white pigs |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.650370/full |
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doaj-b4d8d489522449c4b641d45207c9d3762021-08-02T09:04:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-08-011210.3389/fgene.2021.650370650370Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White PigsYifeng Hong0Yifeng Hong1Jian Ye2Jian Ye3Linsong Dong4Yalan Li5Limin Yan6Gengyuan Cai7Gengyuan Cai8Dewu Liu9Cheng Tan10Cheng Tan11Zhenfang Wu12Zhenfang Wu13College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaCollege of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, ChinaNational Engineering Research Center for Breeding Swine Industry, Wens Foodstuff Group Co., Ltd., Yunfu, ChinaBody length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96–15.02 Mb, SSC7: 97.18–98.18 Mb, SSC14: 128.29–131.15 Mb, SSC17: 15.39–17.27 Mb, and SSC17: 22.04–24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.https://www.frontiersin.org/articles/10.3389/fgene.2021.650370/fullgenome-wide association studybody lengthbody heighttotal teat numberLarge white pigs |