Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle
Abstract Background Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and...
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | BMC Genetics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12863-020-0837-6 |
| _version_ | 1817978290246254592 |
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| author | Bingxing An Lei Xu Jiangwei Xia Xiaoqiao Wang Jian Miao Tianpeng Chang Meihua Song Junqing Ni Lingyang Xu Lupei Zhang Junya Li Huijiang Gao |
| author_facet | Bingxing An Lei Xu Jiangwei Xia Xiaoqiao Wang Jian Miao Tianpeng Chang Meihua Song Junqing Ni Lingyang Xu Lupei Zhang Junya Li Huijiang Gao |
| author_sort | Bingxing An |
| collection | DOAJ |
| description | Abstract Background Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770 K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle. |
| first_indexed | 2024-04-13T22:28:16Z |
| format | Article |
| id | doaj.art-f147ffd56e074be4895bdf46f0667dae |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-13T22:28:16Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-f147ffd56e074be4895bdf46f0667dae2022-12-22T02:27:01ZengBMCBMC Genetics1471-21562020-03-0121111110.1186/s12863-020-0837-6Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattleBingxing AnLei XuJiangwei Xia0Xiaoqiao Wang1Jian Miao2Tianpeng Chang3Meihua Song4Junqing Ni5Lingyang Xu6Lupei Zhang7Junya Li8Huijiang Gao9Institute of Basic Medical Sciences, Westlake Institute for Advanced StudyInstitute of Animal Science, Chinese Academy of Agricultural ScienceInstitute of Animal Science, Chinese Academy of Agricultural ScienceInstitute of Animal Science, Chinese Academy of Agricultural ScienceZhuang Yuan Veterinary Station of Qixia cityHeibei Livestock Breeding WorkstationInstitute of Animal Science, Chinese Academy of Agricultural ScienceInstitute of Animal Science, Chinese Academy of Agricultural ScienceInstitute of Animal Science, Chinese Academy of Agricultural ScienceInstitute of Animal Science, Chinese Academy of Agricultural ScienceAbstract Background Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770 K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.http://link.springer.com/article/10.1186/s12863-020-0837-6Simmental beef cattleGenome-wide association studiesBody sizeCandidate genesBovine HD 770 K SNP |
| spellingShingle | Bingxing An Lei Xu Jiangwei Xia Xiaoqiao Wang Jian Miao Tianpeng Chang Meihua Song Junqing Ni Lingyang Xu Lupei Zhang Junya Li Huijiang Gao Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle BMC Genetics Simmental beef cattle Genome-wide association studies Body size Candidate genes Bovine HD 770 K SNP |
| title | Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle |
| title_full | Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle |
| title_fullStr | Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle |
| title_full_unstemmed | Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle |
| title_short | Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle |
| title_sort | multiple association analysis of loci and candidate genes that regulate body size at three growth stages in simmental beef cattle |
| topic | Simmental beef cattle Genome-wide association studies Body size Candidate genes Bovine HD 770 K SNP |
| url | http://link.springer.com/article/10.1186/s12863-020-0837-6 |
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