Volume 13, Issue 35 (3-2022)
Res Anim Prod 2022, 13(35): 168-175 |
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Mohammadi H, Najafi A, Javanmard A. (2022). Genome-wide Association Study Related to Semen Traits Based on Gene-set Enrichment Analysis in Holstein Bulls. Res Anim Prod. 13(35), 168-175. doi:10.52547/rap.13.35.168
URL: http://rap.sanru.ac.ir/article-1-1239-en.html
URL: http://rap.sanru.ac.ir/article-1-1239-en.html
1- Department of Animal Sciences, Faculty of Agriculture and Environmental science, Arak University, Arak, Iran
2- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran.
3- Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz., Tabriz, Iran.
2- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran.
3- Department of Animal Science, Faculty of Agricultural Sciences, University of Tabriz., Tabriz, Iran.
Abstract: (1764 Views)
Extended Abstract
Introduction and Objective: Unlike evaluation of male fertility which is done based on the phenotype records of females e.g., conception rate, semen traits are directly measured in bulls. The objective of this study was to identify genomic regions associated with sperm traits in Holstein bulls using the genome wide association based on gene set enrichment analysis.
Material and Methods: For this purpose, phenotype records included 1508 genotyped Holstein bulls were used for ejaculate volume, sperm concentration, number of motile sperm, progressive sperm motility, and number of progressive motile sperm in each ejaculation. The evaluation of genome-wide association was carried out PLINK software (v. 1.90). In the next step, using the biomaRt2 R package R the SNP was assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 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, 11 SNP markers on chromosomes 1, 2, 5, 7, 8, 15, 18, 20, 21, 25, and 27 associated with SPEF2, SEPT12, SLC24A, BSP3, ETNK1, ERBB4 (sperm motility and number of progressive motile sperm), DSCAML, MYH3, RPM1, RPM2, CAPSL (number of sperm and sperm concentration), DMRT1, and PPARγ genes (ejaculate volume) were identified. Some of these genes in the significant regions were consistent with some previous studies. In pathway analysis, 15 pathways from gene ontology were associated with the sperm traits. Among those pathways, the purine nucleotide metabolic process, cellular calcium ion homeostasis and regulation of fertilization biological pathway had an important role in the progressive sperm motility and number of progressive motile sperm. Also, the calcium channel regulator activity, PPAR signaling pathway, steroid hormone mediated signaling pathway and focal adhesion had significant association with ejaculate volume and sperm concentration.
Conclusion: The Identification of these candidate genes and selection bulls using genomic selection can considerable to improve male fertility and benefits of animal breeding centers and decrease production prices for consumers.
Introduction and Objective: Unlike evaluation of male fertility which is done based on the phenotype records of females e.g., conception rate, semen traits are directly measured in bulls. The objective of this study was to identify genomic regions associated with sperm traits in Holstein bulls using the genome wide association based on gene set enrichment analysis.
Material and Methods: For this purpose, phenotype records included 1508 genotyped Holstein bulls were used for ejaculate volume, sperm concentration, number of motile sperm, progressive sperm motility, and number of progressive motile sperm in each ejaculation. The evaluation of genome-wide association was carried out PLINK software (v. 1.90). In the next step, using the biomaRt2 R package R the SNP was assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 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, 11 SNP markers on chromosomes 1, 2, 5, 7, 8, 15, 18, 20, 21, 25, and 27 associated with SPEF2, SEPT12, SLC24A, BSP3, ETNK1, ERBB4 (sperm motility and number of progressive motile sperm), DSCAML, MYH3, RPM1, RPM2, CAPSL (number of sperm and sperm concentration), DMRT1, and PPARγ genes (ejaculate volume) were identified. Some of these genes in the significant regions were consistent with some previous studies. In pathway analysis, 15 pathways from gene ontology were associated with the sperm traits. Among those pathways, the purine nucleotide metabolic process, cellular calcium ion homeostasis and regulation of fertilization biological pathway had an important role in the progressive sperm motility and number of progressive motile sperm. Also, the calcium channel regulator activity, PPAR signaling pathway, steroid hormone mediated signaling pathway and focal adhesion had significant association with ejaculate volume and sperm concentration.
Conclusion: The Identification of these candidate genes and selection bulls using genomic selection can considerable to improve male fertility and benefits of animal breeding centers and decrease production prices for consumers.
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2021/09/28 | Accepted: 2021/11/7
Received: 2021/09/28 | Accepted: 2021/11/7
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