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Research article - Peer-reviewed, 2022

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

Sani, Morteza Bitaraf; Harofte, Javad Zare; Banabazi, Mohammad Hossein; Faraz, Asim; Esmaeilkhanian, Saeid; Naderi, Ali Shafei; Salim, Nader; Teimoori, Abbas; Bitaraf, Ahmad; Zadehrahmani, Mohammad; Burger, Pamela Anna; Asadzadeh, Nader; Silawi, Mohammad; Sheshdeh, Afsaneh Taghipour; Nazari, Behrouz Mohammad; Faghihi, Mohammad Ali; Roudbari, Zahra;

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.

Keywords

dromedary; pigmentation; coat color; genotyping-by-sequencing

Published in

Animals

2022, volume: 12, number: 9, article number: 1095
Publisher: MDPI

Authors' information

Sani, Morteza Bitaraf
Agr Res Educ and Extens Org AREEO
Harofte, Javad Zare
Agr Res Educ and Extens Org AREEO
Banabazi, Mohammad Hossein
Agricultural Research, Education and Extension Organization (ARREO)
Banabazi, Mohammad Hossein
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Faraz, Asim
Bahauddin Zakariya University
Esmaeilkhanian, Saeid
Agr Res Educ and Extens Org AREEO
Naderi, Ali Shafei
Agr Res Educ and Extens Org AREEO
Salim, Nader
Minist Agr Jahad
Teimoori, Abbas
Minist Agr Jahad
Bitaraf, Ahmad
Agr Res Educ and Extens Org AREEO
Zadehrahmani, Mohammad
Yazd Dar Al Elm Higher Educ Inst
Burger, Pamela Anna
University of Veterinary Medicine Vienna
Asadzadeh, Nader
Agr Res Educ and Extens Org AREEO
Silawi, Mohammad
Persian Bayan Gene Res and Training Ctr
Sheshdeh, Afsaneh Taghipour
Persian Bayan Gene Res and Training Ctr
Nazari, Behrouz Mohammad
Anim Breeding Canter Iran
Faghihi, Mohammad Ali
Persian Bayan Gene Res and Training Ctr
Roudbari, Zahra
Univ Jiroft

UKÄ Subject classification

Animal and Dairy Science

Publication Identifiers

DOI: https://doi.org/10.3390/ani12091095

URI (permanent link to this page)

https://res.slu.se/id/publ/117244