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

Sani, Morteza Bitaraf and Roudbari, Zahra and Karimi, Omid and Banabazi, Mohammad Hossein and Esmaeilkhanian, Saeid and Asadzadeh, Nader and Harofte, Javad Zare and Naderi, Ali Shafei and Burger, Pamela Anna (2022). Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries. Animals. 12 :2 , 184
[Research article]

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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.

Authors/Creators:Sani, Morteza Bitaraf and Roudbari, Zahra and Karimi, Omid and Banabazi, Mohammad Hossein and Esmaeilkhanian, Saeid and Asadzadeh, Nader and Harofte, Javad Zare and Naderi, Ali Shafei and Burger, Pamela Anna
Title:Gene-Set Enrichment Analysis for Identifying Genes and Biological Activities Associated with Growth Traits in Dromedaries
Series Name/Journal:Animals
Year of publishing :2022
Volume:12
Number:2
Article number:184
Number of Pages:8
Publisher:MDPI
ISSN:2076-2615
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
Keywords:growth, biological theme, gene ontology, dromedaries
URN:NBN:urn:nbn:se:slu:epsilon-p-116097
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-116097
Additional ID:
Type of IDID
DOI10.3390/ani12020184
Web of Science (WoS)000747832000001
ID Code:27194
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:23 Feb 2022 16:25
Metadata Last Modified:23 Feb 2022 16:31

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