Volume 13, Issue 37 (11-2022)
rap 2022, 13(37): 139-147 |
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Department of Animal Sciences, Faculty of Agriculture and Environmental science, Arak University, Arak, Iran
Abstract: (1058 Views)
Extended Abstract
Introduction and Objective: Type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlate with other economically important traits in cattle including fertility, longevity and carcass traits. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the loci associated with conformation traits using the 50K arrays.
Material and Methods: Genome wide association study was performed with biometric traits using GEMMA software v. 0.98. Using the biomaRt2 R package R the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 25 kb up- and downstream of the gene. For the assignment of the genes to functional categories, the GO, KEGG, DAVID and PANTHER databases were used.
Results: In this research, 12 SNP markers on chromosomes 1, 3, 5, 7, 8, 10, 13, 16, 17, 22, 23 and 25 located in PLCB1, PTBP1, TMEM130, PLCB4 (BL), TGFBR3, SYN3, TRAK1 (WH), GLP1R, HMGA1 (CG) and CAPN3, MYOG and MYO18B (CD) genes were identified. Some of the genes that were found are consistent with some previous studies related biometric traits. According to pathway analysis, 17 pathways from gene ontology and biological pathways were associated with biometric traits (p˂0.05). Among these pathways, muscle structure development, anatomical structure formation involved in morphogenesis, anatomical structure homeostasis, Osteoclast differentiation, skeletal muscle cell differentiation and calcium signaling pathway have important functions in development of skeletal muscle, glucose homeostasis, osteogenesis process, regulation of ion calcium and activation.
Conclusion: The finding of this research confirms the results of previous studies from genomic scanning related to type traits, also revealed additional genomic regions, could be useful for genetic selection in the cattle breeding programs.
Introduction and Objective: Type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlate with other economically important traits in cattle including fertility, longevity and carcass traits. The present study aimed to conduct a genome wide association studies (GWAS) based on gene-set enrichment analysis for identifying the loci associated with conformation traits using the 50K arrays.
Material and Methods: Genome wide association study was performed with biometric traits using GEMMA software v. 0.98. Using the biomaRt2 R package R the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 25 kb up- and downstream of the gene. For the assignment of the genes to functional categories, the GO, KEGG, DAVID and PANTHER databases were used.
Results: In this research, 12 SNP markers on chromosomes 1, 3, 5, 7, 8, 10, 13, 16, 17, 22, 23 and 25 located in PLCB1, PTBP1, TMEM130, PLCB4 (BL), TGFBR3, SYN3, TRAK1 (WH), GLP1R, HMGA1 (CG) and CAPN3, MYOG and MYO18B (CD) genes were identified. Some of the genes that were found are consistent with some previous studies related biometric traits. According to pathway analysis, 17 pathways from gene ontology and biological pathways were associated with biometric traits (p˂0.05). Among these pathways, muscle structure development, anatomical structure formation involved in morphogenesis, anatomical structure homeostasis, Osteoclast differentiation, skeletal muscle cell differentiation and calcium signaling pathway have important functions in development of skeletal muscle, glucose homeostasis, osteogenesis process, regulation of ion calcium and activation.
Conclusion: The finding of this research confirms the results of previous studies from genomic scanning related to type traits, also revealed additional genomic regions, could be useful for genetic selection in the cattle breeding programs.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2021/11/28 | Revised: 2022/11/19 | Accepted: 2022/02/2 | Published: 2022/11/19
Received: 2021/11/28 | Revised: 2022/11/19 | Accepted: 2022/02/2 | Published: 2022/11/19
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