Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs

In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yu Shen, Haiyan Wang, Jiahao Xie, Zixuan Wang, Yunlong Ma
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	selective sweeps phenotypic gradient differential population pairs population differentiation-based methods functional annotation meat quality Genetics QH426-470
Acceso en línea:	https://doaj.org/article/999d3db2ec7842c8bf9f6093c42a9128
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:999d3db2ec7842c8bf9f6093c42a9128
record_format	dspace
spelling	oai:doaj.org-article:999d3db2ec7842c8bf9f6093c42a91282021-11-16T05:15:56ZTrait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs1664-802110.3389/fgene.2021.761252https://doaj.org/article/999d3db2ec7842c8bf9f6093c42a91282021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.761252/fullhttps://doaj.org/toc/1664-8021In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of pigs. In this study, we focus on investigating the genetic basis of five meat quality traits, including intramuscular fat content (IMF), drip loss, water binding capacity, pH at 45 min (pH45min), and ultimate pH (pH24h). Through making phenotypic gradient differential population pairs, Wright’s fixation index (FST) and the cross-population extended haplotype homozogysity (XPEHH) were applied to detect selection signatures for these five traits. Finally, a total of 427 and 307 trait-specific selection signatures were revealed by FST and XPEHH, respectively. Further bioinformatics analysis indicates that some genes, such as USF1, NDUFS2, PIGM, IGSF8, CASQ1, and ACBD6, overlapping with the trait-specific selection signatures are responsible for the phenotypes including fat metabolism and muscle development. Among them, a series of promising trait-specific selection signatures that were detected in the high IMF subpopulation are located in the region of 93544042-95179724bp on SSC4, and the genes harboring in this region are all related to lipids and muscle development. Overall, these candidate genes of meat quality traits identified in this analysis may provide some fundamental information for further exploring the genetic basis of this complex trait.Yu ShenHaiyan WangJiahao XieZixuan WangYunlong MaFrontiers Media S.A.articleselective sweepsphenotypic gradient differential population pairspopulation differentiation-based methodsfunctional annotationmeat qualityGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	selective sweeps phenotypic gradient differential population pairs population differentiation-based methods functional annotation meat quality Genetics QH426-470
spellingShingle	selective sweeps phenotypic gradient differential population pairs population differentiation-based methods functional annotation meat quality Genetics QH426-470 Yu Shen Haiyan Wang Jiahao Xie Zixuan Wang Yunlong Ma Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
description	In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of pigs. In this study, we focus on investigating the genetic basis of five meat quality traits, including intramuscular fat content (IMF), drip loss, water binding capacity, pH at 45 min (pH45min), and ultimate pH (pH24h). Through making phenotypic gradient differential population pairs, Wright’s fixation index (FST) and the cross-population extended haplotype homozogysity (XPEHH) were applied to detect selection signatures for these five traits. Finally, a total of 427 and 307 trait-specific selection signatures were revealed by FST and XPEHH, respectively. Further bioinformatics analysis indicates that some genes, such as USF1, NDUFS2, PIGM, IGSF8, CASQ1, and ACBD6, overlapping with the trait-specific selection signatures are responsible for the phenotypes including fat metabolism and muscle development. Among them, a series of promising trait-specific selection signatures that were detected in the high IMF subpopulation are located in the region of 93544042-95179724bp on SSC4, and the genes harboring in this region are all related to lipids and muscle development. Overall, these candidate genes of meat quality traits identified in this analysis may provide some fundamental information for further exploring the genetic basis of this complex trait.
format	article
author	Yu Shen Haiyan Wang Jiahao Xie Zixuan Wang Yunlong Ma
author_facet	Yu Shen Haiyan Wang Jiahao Xie Zixuan Wang Yunlong Ma
author_sort	Yu Shen
title	Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
title_short	Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
title_full	Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
title_fullStr	Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
title_full_unstemmed	Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs
title_sort	trait-specific selection signature detection reveals novel loci of meat quality in large white pigs
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/999d3db2ec7842c8bf9f6093c42a9128
work_keys_str_mv	AT yushen traitspecificselectionsignaturedetectionrevealsnovellociofmeatqualityinlargewhitepigs AT haiyanwang traitspecificselectionsignaturedetectionrevealsnovellociofmeatqualityinlargewhitepigs AT jiahaoxie traitspecificselectionsignaturedetectionrevealsnovellociofmeatqualityinlargewhitepigs AT zixuanwang traitspecificselectionsignaturedetectionrevealsnovellociofmeatqualityinlargewhitepigs AT yunlongma traitspecificselectionsignaturedetectionrevealsnovellociofmeatqualityinlargewhitepigs
_version_	1718426683472609280

Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs

Ejemplares similares