Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries
Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, b...
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| Format: | Article |
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MDPI AG
2022-01-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/2/184 |
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| author | Morteza Bitaraf Sani Zahra Roudbari Omid Karimi Mohammad Hossein Banabazi Saeid Esmaeilkhanian Nader Asadzadeh Javad Zare Harofte Ali Shafei Naderi Pamela Anna Burger |
| author_facet | Morteza Bitaraf Sani Zahra Roudbari Omid Karimi Mohammad Hossein Banabazi Saeid Esmaeilkhanian Nader Asadzadeh Javad Zare Harofte Ali Shafei Naderi Pamela Anna Burger |
| author_sort | Morteza Bitaraf Sani |
| collection | DOAJ |
| description | Growth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via <i>JAK-STAT</i>, and cytokine activity. <i>EFCAB5</i>, <i>MTIF2</i>, <i>MYO3A</i>, <i>TBX15</i>, <i>IFNL3</i>, <i>PREX1</i>, and <i>TMOD3</i> genes are candidates for improving growth in camel breeding programs. |
| first_indexed | 2024-03-10T03:04:08Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T03:04:08Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-e31465b200b64f4abf9ab5ce3eb9c72d2023-11-23T12:41:52ZengMDPI AGAnimals2076-26152022-01-0112218410.3390/ani12020184Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in DromedariesMorteza Bitaraf Sani0Zahra Roudbari1Omid Karimi2Mohammad Hossein Banabazi3Saeid Esmaeilkhanian4Nader Asadzadeh5Javad Zare Harofte6Ali Shafei Naderi7Pamela Anna Burger8Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranDepartment of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft 7867155311, IranDepartment of Animal Viral Diseases Research, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj 3146618361, IranAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranResearch Institute of Wildlife Ecology, Vetmeduni Vienna, 1160 Vienna, AustriaGrowth is an important heritable economic trait for dromedaries and necessary for planning a successful breeding program. Until now, genome-wide association studies (GWAS) and QTL-mapping have identified significant single nucleotide polymorphisms (SNPs) associated with growth in domestic animals, but in dromedaries, the number of studies is very low. This project aimed to find biological themes affecting growth in dromedaries. In the first step, 99 candidate SNPs were chosen from a previously established set of SNPs associated with body weight, gain, and birth weight in Iranian dromedaries. Next, 0.5 kb upstream and downstream of each candidate SNP were selected from NCBI (assembly accession: GCA_000803125.3). The annotation of fragments with candidate SNPs regarding the reference genome was retrieved using the Blast2GO tool. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant biological themes were identified to be related to growth in dromedaries. The main biological functions included calcium ion binding, protein binding, DNA-binding transcription factor activity, protein kinase activity, tropomyosin binding, myosin complex, actin-binding, ATP binding, receptor signaling pathway via <i>JAK-STAT</i>, and cytokine activity. <i>EFCAB5</i>, <i>MTIF2</i>, <i>MYO3A</i>, <i>TBX15</i>, <i>IFNL3</i>, <i>PREX1</i>, and <i>TMOD3</i> genes are candidates for improving growth in camel breeding programs.https://www.mdpi.com/2076-2615/12/2/184growthbiological themegene ontologydromedaries |
| spellingShingle | Morteza Bitaraf Sani Zahra Roudbari Omid Karimi Mohammad Hossein Banabazi Saeid Esmaeilkhanian Nader Asadzadeh Javad Zare Harofte Ali Shafei Naderi Pamela Anna Burger Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries Animals growth biological theme gene ontology dromedaries |
| title | Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries |
| title_full | Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries |
| title_fullStr | Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries |
| title_full_unstemmed | Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries |
| title_short | Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries |
| title_sort | gene set enrichment analysis for identifying genes and biological activities associated with growth traits in dromedaries |
| topic | growth biological theme gene ontology dromedaries |
| url | https://www.mdpi.com/2076-2615/12/2/184 |
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