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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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00569/full |
| _version_ | 1818205244519088128 |
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| author | Jie Cheng Xiukai Cao Quratulain Hanif Quratulain Hanif Quratulain Hanif Li Pi Linyong Hu Yongzhen Huang Xianyong Lan Chuzhao Lei Hong Chen |
| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-12T03:54:03Z |
| format | Article |
| id | doaj.art-8a7d941657e74865985aa78b0f14fba0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T03:54:03Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-8a7d941657e74865985aa78b0f14fba02022-12-22T00:39:18ZengFrontiers 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 |
| 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 |
| title | 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_short | 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 |
| 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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