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Research article - Peer-reviewed, 2022

Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries

Sani, Morteza Bitaraf; Roudbari, Zahra; Karimi, Omid; Banabazi, Mohammad Hossein; Esmaeilkhanian, Saeid; Asadzadeh, Nader; Zare Harofte, Javad; Shafei Naderi, Ali; Burger, Pamela Anna

Abstract

Simple Summary This project aimed to find biological themes affecting growth in dromedaries. Candidate SNPs associated with growth were mapped to 22 genes, and 25 significant themes were identified related to growth. 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 JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs. 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 JAK-STAT, and cytokine activity. EFCAB5, MTIF2, MYO3A, TBX15, IFNL3, PREX1, and TMOD3 genes are candidates for improving growth in camel breeding programs.

Keywords

growth; biological theme; gene ontology; dromedaries

Published in

Animals
2022, volume: 12, number: 2, article number: 184
Publisher: MDPI

Authors' information

Sani, Morteza Bitaraf
Agricultural Research, Education & Extension Organization (AREEO)
Roudbari, Zahra
University of Jiroft
Karimi, Omid
Agricultural Research, Education and Extension Organization (ARREO)
Banabazi, Mohammad Hossein
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Banabazi, Mohammad Hossein
Agricultural Research, Education and Extension Organization (ARREO)
Esmaeilkhanian, Saeid
Agricultural Research, Education and Extension Organization (ARREO)
Asadzadeh, Nader
Agricultural Research, Education and Extension Organization (ARREO)
Harofte, Javad Zare
Agricultural Research, Education and Extension Organization (ARREO)
Naderi, Ali Shafei
Agricultural Research, Education and Extension Organization (ARREO)
Burger, Pamela Anna
University of Veterinary Medicine Vienna

UKÄ Subject classification

Animal and Dairy Science

Publication Identifiers

DOI: https://doi.org/10.3390/ani12020184

URI (permanent link to this page)

https://res.slu.se/id/publ/116097