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Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle

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Title: Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle
Authors: Mang Liang, Bingxing An, Tianyu Deng, Lili Du, Keanning Li, Sheng Cao, Yueying Du, Lingyang Xu, Lupei Zhang, Xue Gao, Yang Cao, Yuming Zhao, Junya Li, Huijiang Gao
Source: Frontiers in Genetics, Vol 13 (2023)
Publisher Information: Frontiers Media S.A., 2023.
Publication Year: 2023
Collection: LCC:Genetics
Subject Terms: longissimus dorsi muscle, GWAS, TWAS, FCT, Huaxi cattle, Genetics, QH426-470
More Details: Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher’s combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: PENK was located by GWAS and FCT, PPAT was located by TWAS and FCT, and XKR4, MTMR3, FGFRL1, DHRS4, and LAP3 were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 1664-8021
Relation: https://www.frontiersin.org/articles/10.3389/fgene.2022.982433/full; https://doaj.org/toc/1664-8021
DOI: 10.3389/fgene.2022.982433
Access URL: https://doaj.org/article/66d58d4f45264bdf89739bf97f6acf54
Accession Number: edsdoj.66d58d4f45264bdf89739bf97f6acf54
Database: Directory of Open Access Journals
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  Data: Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle
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  Data: <searchLink fieldCode="AR" term="%22Mang+Liang%22">Mang Liang</searchLink><br /><searchLink fieldCode="AR" term="%22Bingxing+An%22">Bingxing An</searchLink><br /><searchLink fieldCode="AR" term="%22Tianyu+Deng%22">Tianyu Deng</searchLink><br /><searchLink fieldCode="AR" term="%22Lili+Du%22">Lili Du</searchLink><br /><searchLink fieldCode="AR" term="%22Keanning+Li%22">Keanning Li</searchLink><br /><searchLink fieldCode="AR" term="%22Sheng+Cao%22">Sheng Cao</searchLink><br /><searchLink fieldCode="AR" term="%22Yueying+Du%22">Yueying Du</searchLink><br /><searchLink fieldCode="AR" term="%22Lingyang+Xu%22">Lingyang Xu</searchLink><br /><searchLink fieldCode="AR" term="%22Lupei+Zhang%22">Lupei Zhang</searchLink><br /><searchLink fieldCode="AR" term="%22Xue+Gao%22">Xue Gao</searchLink><br /><searchLink fieldCode="AR" term="%22Yang+Cao%22">Yang Cao</searchLink><br /><searchLink fieldCode="AR" term="%22Yuming+Zhao%22">Yuming Zhao</searchLink><br /><searchLink fieldCode="AR" term="%22Junya+Li%22">Junya Li</searchLink><br /><searchLink fieldCode="AR" term="%22Huijiang+Gao%22">Huijiang Gao</searchLink>
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  Data: Frontiers in Genetics, Vol 13 (2023)
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  Data: <searchLink fieldCode="DE" term="%22longissimus+dorsi+muscle%22">longissimus dorsi muscle</searchLink><br /><searchLink fieldCode="DE" term="%22GWAS%22">GWAS</searchLink><br /><searchLink fieldCode="DE" term="%22TWAS%22">TWAS</searchLink><br /><searchLink fieldCode="DE" term="%22FCT%22">FCT</searchLink><br /><searchLink fieldCode="DE" term="%22Huaxi+cattle%22">Huaxi cattle</searchLink><br /><searchLink fieldCode="DE" term="%22Genetics%22">Genetics</searchLink><br /><searchLink fieldCode="DE" term="%22QH426-470%22">QH426-470</searchLink>
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  Data: Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher’s combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: PENK was located by GWAS and FCT, PPAT was located by TWAS and FCT, and XKR4, MTMR3, FGFRL1, DHRS4, and LAP3 were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.
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        Value: 10.3389/fgene.2022.982433
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    Subjects:
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      – SubjectFull: GWAS
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      – SubjectFull: TWAS
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