Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotyp...

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Autores principales:	Young-Sup Lee, Seungwoo Son, Jaeyoung Heo, Donghyun Shin
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	cross-population phenotype associated variant (xp-pav) differential genomic variant t-test back fat thickness daily weight gain Medicine (General) R5-920 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/8023e43a17284b79ac2dd22c5844c259
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spelling	oai:doaj.org-article:8023e43a17284b79ac2dd22c5844c2592021-12-01T14:40:59ZDetecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea1976-83542151-248510.1080/19768354.2021.2006310https://doaj.org/article/8023e43a17284b79ac2dd22c5844c2592021-11-01T00:00:00Zhttp://dx.doi.org/10.1080/19768354.2021.2006310https://doaj.org/toc/1976-8354https://doaj.org/toc/2151-2485Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.Young-Sup LeeSeungwoo SonJaeyoung HeoDonghyun ShinTaylor & Francis Grouparticlecross-population phenotype associated variant (xp-pav)differential genomic variantt-testback fat thicknessdaily weight gainMedicine (General)R5-920Biology (General)QH301-705.5ENAnimal Cells and Systems, Vol 0, Iss 0, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cross-population phenotype associated variant (xp-pav) differential genomic variant t-test back fat thickness daily weight gain Medicine (General) R5-920 Biology (General) QH301-705.5
spellingShingle	cross-population phenotype associated variant (xp-pav) differential genomic variant t-test back fat thickness daily weight gain Medicine (General) R5-920 Biology (General) QH301-705.5 Young-Sup Lee Seungwoo Son Jaeyoung Heo Donghyun Shin Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
description	Although there have been many genome-wide association studies (GWAS) and selective sweep analyses to understand pig genomic regions related to growth performance, these methods considered only the gene effect and selection signal, respectively. In this study, we suggest the cross-population phenotype associated variant (XP-PAV) analysis as a novel method to determine the genomic variants with different effects between the two populations. XP-PAV analysis could reveal the differential genetic variants between the two populations by considering the gene effect and selection signal simultaneously. In this study, we used daily weight gain (DWG) and back fat thickness (BF) as phenotypes and the Landrace and Yorkshire populations were used for XP-PAV analysis. The main aim was to reveal the differential selection by considering the gene effect between Landrace and Yorkshire pigs. In the gene ontology analysis of XP-PAV results, differential selective genes in DWG analysis were involved in the regulation of interleukin-2 production and cell cycle G2/M transition. The protein modification and glycerophospholipid biosynthetic processes were the most enriched terms in the BF analysis. Therefore, we could identify genetic differences for immune and several metabolic pathways between Landrace and Yorkshire breeds using the XP-PAV analysis. In this study, we expect that XP-PAV analysis will play a role in determining useful selective variants with gene effects and provide a new interpretation of the genetic differences between the two populations.
format	article
author	Young-Sup Lee Seungwoo Son Jaeyoung Heo Donghyun Shin
author_facet	Young-Sup Lee Seungwoo Son Jaeyoung Heo Donghyun Shin
author_sort	Young-Sup Lee
title	Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
title_short	Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
title_full	Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
title_fullStr	Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
title_full_unstemmed	Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea
title_sort	detecting the differential genomic variants using cross-population phenotype-associated variant (xp-pav) of the landrace and yorkshire pigs in korea
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/8023e43a17284b79ac2dd22c5844c259
work_keys_str_mv	AT youngsuplee detectingthedifferentialgenomicvariantsusingcrosspopulationphenotypeassociatedvariantxppavofthelandraceandyorkshirepigsinkorea AT seungwooson detectingthedifferentialgenomicvariantsusingcrosspopulationphenotypeassociatedvariantxppavofthelandraceandyorkshirepigsinkorea AT jaeyoungheo detectingthedifferentialgenomicvariantsusingcrosspopulationphenotypeassociatedvariantxppavofthelandraceandyorkshirepigsinkorea AT donghyunshin detectingthedifferentialgenomicvariantsusingcrosspopulationphenotypeassociatedvariantxppavofthelandraceandyorkshirepigsinkorea
_version_	1718405002379132928

Detecting the differential genomic variants using cross-population phenotype-associated variant (XP-PAV) of the Landrace and Yorkshire pigs in Korea

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