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Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing

Sani, Morteza Bitaraf and Harofte, Javad Zare and Banabazi, Mohammad Hossein and Faraz, Asim and Esmaeilkhanian, Saeid and Naderi, Ali Shafei and Salim, Nader and Teimoori, Abbas and Bitaraf, Ahmad and Zadehrahmani, Mohammad and Burger, Pamela Anna and Asadzadeh, Nader and Silawi, Mohammad and Sheshdeh, Afsaneh Taghipour and Nazari, Behrouz Mohammad and Faghihi, Mohammad Ali and Roudbari, Zahra (2022). Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing. Animals. 12 :9 , 1095
[Research article]

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Abstract

Simple Summary The coat color of dromedary is usually uniform and varies from black to white. We identified 9 significant SNPs associated with white color, and the 13 significant SNPs associated with black color using genotyping-by-sequencing (GBS). Among candidate genes, SNAI1 that interacts with MCIR, ASIP and KIT genes plays a key role in the melanin biosynthetic and pigmentation biological process and melanogenesis biological pathway. The coat color of dromedary is usually uniform and varies from black to white, although dark- to light-brown colors are the most common phenotypes. This project was designed to gain knowledge on novel color-related variants using genotyping-by-sequencing (GBS). The association between the SNPs and coat color was tested using MLM (mixed linear models) with kinship matrix. Three GWAS models including white color vs. non-white color, black vs. non-black color, and light-brown vs. dark-brown color were performed. There were no distinct genetic clusters detected based on the color phenotypes. However, admixture occurred among all individuals of the four different coat color groups. We identified nine significant SNPs associated with white color after Bonferroni correction, located close to ANKRD26, GNB1, TSPYL4, TEKT5, DEXI, CIITA, TVP23B, CLEC16A, TMPRSS13, FXYD6, MPZL3, ANKRD26, HFM1, CDC7, TGFBR3, and HACE1 genes in neighboring flanking regions. The 13 significant SNPs associated with black color and the candidate genes were: CAPN7, CHRM4, CIITA, CLEC16A, COL4A4, COL6A6, CREB3L1, DEXI, DGKZ, DGKZ, EAF1, HDLBP, INPP5F, MCMBP, MDK, SEC23IP, SNAI1, TBX15, TEKT5, TMEM189, trpS, TSPYL4, TVP23B, and UBE2V1. The SNAI1 gene interacted with MCIR, ASIP and KIT genes. These genes play a key role in the melanin biosynthetic and pigmentation biological process and melanogenesis biological pathway. Further research using a larger sample size and pedigree data will allow confirmation of associated SNPs and the identified candidate genes.

Authors/Creators:Sani, Morteza Bitaraf and Harofte, Javad Zare and Banabazi, Mohammad Hossein and Faraz, Asim and Esmaeilkhanian, Saeid and Naderi, Ali Shafei and Salim, Nader and Teimoori, Abbas and Bitaraf, Ahmad and Zadehrahmani, Mohammad and Burger, Pamela Anna and Asadzadeh, Nader and Silawi, Mohammad and Sheshdeh, Afsaneh Taghipour and Nazari, Behrouz Mohammad and Faghihi, Mohammad Ali and Roudbari, Zahra
Title:Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing
Series Name/Journal:Animals
Year of publishing :2022
Volume:12
Number:9
Article number:1095
Number of Pages:9
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:dromedary, pigmentation, coat color, genotyping-by-sequencing
URN:NBN:urn:nbn:se:slu:epsilon-p-117244
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-117244
Additional ID:
Type of IDID
DOI10.3390/ani12091095
Web of Science (WoS)000794430600001
ID Code:28181
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:02 Jun 2022 07:29
Metadata Last Modified:02 Jun 2022 07:31

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