Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs
Abstract Background The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-04-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07570-w |
| _version_ | 1818972133469978624 |
|---|---|
| author | Yuanxin Miao Quanshun Mei Chuanke Fu Mingxing Liao Yan Liu Xuewen Xu Xinyun Li Shuhong Zhao Tao Xiang |
| author_facet | Yuanxin Miao Quanshun Mei Chuanke Fu Mingxing Liao Yan Liu Xuewen Xu Xinyun Li Shuhong Zhao Tao Xiang |
| author_sort | Yuanxin Miao |
| collection | DOAJ |
| description | Abstract Background The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR. Results A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2, and TRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway. Conclusions Based on the results from GWAS and transcriptome analyses, the TPH2, GRIP1, FRS2, TRHDE, and CNOT2 genes were considered candidate genes for regulating FCR in Yorkshire pigs. These findings improve the understanding of the genetic mechanisms of FCR and may help optimize the design of breeding schemes. |
| first_indexed | 2024-12-20T15:03:25Z |
| format | Article |
| id | doaj.art-670059e0e8694a6482f587178024e5f9 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T15:03:25Z |
| publishDate | 2021-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-670059e0e8694a6482f587178024e5f92022-12-21T19:36:35ZengBMCBMC Genomics1471-21642021-04-0122111110.1186/s12864-021-07570-wGenome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigsYuanxin Miao0Quanshun Mei1Chuanke Fu2Mingxing Liao3Yan Liu4Xuewen Xu5Xinyun Li6Shuhong Zhao7Tao Xiang8Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityKey Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural UniversityAbstract Background The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR. Results A total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2, and TRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway. Conclusions Based on the results from GWAS and transcriptome analyses, the TPH2, GRIP1, FRS2, TRHDE, and CNOT2 genes were considered candidate genes for regulating FCR in Yorkshire pigs. These findings improve the understanding of the genetic mechanisms of FCR and may help optimize the design of breeding schemes.https://doi.org/10.1186/s12864-021-07570-wGWASTranscriptomicsFeed conversion ratioPigsPathwaysHypothalamus |
| spellingShingle | Yuanxin Miao Quanshun Mei Chuanke Fu Mingxing Liao Yan Liu Xuewen Xu Xinyun Li Shuhong Zhao Tao Xiang Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs BMC Genomics GWAS Transcriptomics Feed conversion ratio Pigs Pathways Hypothalamus |
| title | Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| title_full | Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| title_fullStr | Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| title_full_unstemmed | Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| title_short | Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| title_sort | genome wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs |
| topic | GWAS Transcriptomics Feed conversion ratio Pigs Pathways Hypothalamus |
| url | https://doi.org/10.1186/s12864-021-07570-w |
| work_keys_str_mv | AT yuanxinmiao genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT quanshunmei genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT chuankefu genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT mingxingliao genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT yanliu genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT xuewenxu genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT xinyunli genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT shuhongzhao genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs AT taoxiang genomewideassociationandtranscriptomestudiesidentifycandidategenesandpathwaysforfeedconversionratioinpigs |