Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits

Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits

Copy number variations (CNVs) are important source of genetic variation, which can affect diverse economic traits through a variety of mechanisms. In addition, genome scan can identify many quantitative trait loci (QTLs) for the economic traits, while genome-wide association studies (GWAS) can local...

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Main Authors: Jie Cheng, Xiukai Cao, Quratulain Hanif, Li Pi, Linyong Hu, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Hong Chen
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-06-01
Series:Frontiers in Genetics
Subjects:
copy number variations
QTL
GWAS
GWAScore
sheep economic traits
Online Access:https://www.frontiersin.org/article/10.3389/fgene.2020.00569/full
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spelling doaj-8a7d941657e74865985aa78b0f14fba02020-11-25T03:13:14ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-06-011110.3389/fgene.2020.00569527424Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic TraitsJie Cheng0Xiukai Cao1Quratulain Hanif2Quratulain Hanif3Quratulain Hanif4Li Pi5Linyong Hu6Yongzhen Huang7Xianyong Lan8Chuzhao Lei9Hong Chen10Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaComputational Biology Lab, National Institute for Biotechnology and Genetic Engineering, Faisalabad, PakistanPakistan Institute of Engineering and Applied Sciences, Islamabad, PakistanKey Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, ChinaKey Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, ChinaCopy number variations (CNVs) are important source of genetic variation, which can affect diverse economic traits through a variety of mechanisms. In addition, genome scan can identify many quantitative trait loci (QTLs) for the economic traits, while genome-wide association studies (GWAS) can localize genetic variants associated with the phenotypic variations. Here, we developed a method called GWAScore which collected GWAS summary data to identify potential candidates, and integrated CNVs into QTLs and high confidence GWAScore regions to detect crucial CNV markers for sheep growth traits. We got 197 candidate genes which were overlapping with the candidate CNVs. Some crucial genes (MYLK3, TTC29, HERC6, ABCG2, RUNX1, etc.) showed significantly elevated GWAScore peaks than other candidate genes. In this study, we developed the GWAScore method to excavate the potential value of candidate genes as markers for the sheep molecular breeding.https://www.frontiersin.org/article/10.3389/fgene.2020.00569/fullcopy number variationsQTLGWASGWAScoresheep economic traits
collection DOAJ
language English
format Article
sources DOAJ
author Jie Cheng
Xiukai Cao
Quratulain Hanif
Quratulain Hanif
Quratulain Hanif
Li Pi
Linyong Hu
Yongzhen Huang
Xianyong Lan
Chuzhao Lei
Hong Chen
spellingShingle Jie Cheng
Xiukai Cao
Quratulain Hanif
Quratulain Hanif
Quratulain Hanif
Li Pi
Linyong Hu
Yongzhen Huang
Xianyong Lan
Chuzhao Lei
Hong Chen
Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
Frontiers in Genetics
copy number variations
QTL
GWAS
GWAScore
sheep economic traits
author_facet Jie Cheng
Xiukai Cao
Quratulain Hanif
Quratulain Hanif
Quratulain Hanif
Li Pi
Linyong Hu
Yongzhen Huang
Xianyong Lan
Chuzhao Lei
Hong Chen
author_sort Jie Cheng
title Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
title_short Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
title_full Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
title_fullStr Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
title_full_unstemmed Integrating Genome-Wide CNVs Into QTLs and High Confidence GWAScore Regions Identified Positional Candidates for Sheep Economic Traits
title_sort integrating genome-wide cnvs into qtls and high confidence gwascore regions identified positional candidates for sheep economic traits
publisher Frontiers Media S.A.
series Frontiers in Genetics
issn 1664-8021
publishDate 2020-06-01
description Copy number variations (CNVs) are important source of genetic variation, which can affect diverse economic traits through a variety of mechanisms. In addition, genome scan can identify many quantitative trait loci (QTLs) for the economic traits, while genome-wide association studies (GWAS) can localize genetic variants associated with the phenotypic variations. Here, we developed a method called GWAScore which collected GWAS summary data to identify potential candidates, and integrated CNVs into QTLs and high confidence GWAScore regions to detect crucial CNV markers for sheep growth traits. We got 197 candidate genes which were overlapping with the candidate CNVs. Some crucial genes (MYLK3, TTC29, HERC6, ABCG2, RUNX1, etc.) showed significantly elevated GWAScore peaks than other candidate genes. In this study, we developed the GWAScore method to excavate the potential value of candidate genes as markers for the sheep molecular breeding.
topic copy number variations
QTL
GWAS
GWAScore
sheep economic traits
url https://www.frontiersin.org/article/10.3389/fgene.2020.00569/full
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