Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing
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 c...
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-04-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/12/9/1095 |
| _version_ | 1797505928018264064 |
|---|---|
| author | Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Asim Faraz Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Nader Asadzadeh Mohammad Silawi Afsaneh Taghipour Sheshdeh Behrouz Mohammad Nazari Mohammad Ali Faghihi Zahra Roudbari |
| author_facet | Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Asim Faraz Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Nader Asadzadeh Mohammad Silawi Afsaneh Taghipour Sheshdeh Behrouz Mohammad Nazari Mohammad Ali Faghihi Zahra Roudbari |
| author_sort | Morteza Bitaraf Sani |
| collection | DOAJ |
| description | 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 <i>ANKRD26, GNB1, TSPYL4, TEKT5, DEXI, CIITA, TVP23B, CLEC16A, TMPRSS13, FXYD6, MPZL3, ANKRD26, HFM1, CDC7, TGFBR3</i>, and <i>HACE1</i> genes in neighboring flanking regions. The 13 significant SNPs associated with black color and the candidate genes were: <i>CAPN7, CHRM4, CIITA, CLEC16A, COL4A4, COL6A6, CREB3L1, DEXI, DGKZ, DGKZ, EAF1, HDLBP, INPP5F, MCMBP, MDK, SEC23IP, SNAI1, TBX15, TEKT5, TMEM189, trpS, TSPYL4, TVP23B,</i> and <i>UBE2V1</i>. 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. |
| first_indexed | 2024-03-10T04:25:19Z |
| format | Article |
| id | doaj.art-ecbe916668af4e478f0cd69dadaf8d40 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T04:25:19Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-ecbe916668af4e478f0cd69dadaf8d402023-11-23T07:42:19ZengMDPI AGAnimals2076-26152022-04-01129109510.3390/ani12091095Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-SequencingMorteza Bitaraf Sani0Javad Zare Harofte1Mohammad Hossein Banabazi2Asim Faraz3Saeid Esmaeilkhanian4Ali Shafei Naderi5Nader Salim6Abbas Teimoori7Ahmad Bitaraf8Mohammad Zadehrahmani9Pamela Anna Burger10Nader Asadzadeh11Mohammad Silawi12Afsaneh Taghipour Sheshdeh13Behrouz Mohammad Nazari14Mohammad Ali Faghihi15Zahra Roudbari16Animal 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, IranAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranDepartment of Livestock and Poultry Production, Bahauddin Zakariya University, Multan 60000, PakistanAnimal 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, IranOrganization of Agriculture—Jahad-Yazd, Ministry of Agriculture-Jahad, Yazd 8915813155, IranOrganization of Agriculture—Jahad-Yazd, Ministry of Agriculture-Jahad, Yazd 8915813155, IranAnimal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Yazd 8915813155, IranYazd Dar Al-Elm Higher Education Institute, Yazd 8915813155, IranResearch Institute of Wildlife Ecology, Vetmeduni Vienna, 1160 Vienna, AustriaAnimal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj 3146618361, IranPersian Bayan Gene Research and Training Center, Shiraz 7134767617, IranPersian Bayan Gene Research and Training Center, Shiraz 7134767617, IranAnimal Breeding Canter of Iran, Karaj 3173945591, IranPersian Bayan Gene Research and Training Center, Shiraz 7134767617, IranDepartment of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft 7867155311, IranThe 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 <i>ANKRD26, GNB1, TSPYL4, TEKT5, DEXI, CIITA, TVP23B, CLEC16A, TMPRSS13, FXYD6, MPZL3, ANKRD26, HFM1, CDC7, TGFBR3</i>, and <i>HACE1</i> genes in neighboring flanking regions. The 13 significant SNPs associated with black color and the candidate genes were: <i>CAPN7, CHRM4, CIITA, CLEC16A, COL4A4, COL6A6, CREB3L1, DEXI, DGKZ, DGKZ, EAF1, HDLBP, INPP5F, MCMBP, MDK, SEC23IP, SNAI1, TBX15, TEKT5, TMEM189, trpS, TSPYL4, TVP23B,</i> and <i>UBE2V1</i>. 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.https://www.mdpi.com/2076-2615/12/9/1095dromedarypigmentationcoat colorgenotyping-by-sequencing |
| spellingShingle | Morteza Bitaraf Sani Javad Zare Harofte Mohammad Hossein Banabazi Asim Faraz Saeid Esmaeilkhanian Ali Shafei Naderi Nader Salim Abbas Teimoori Ahmad Bitaraf Mohammad Zadehrahmani Pamela Anna Burger Nader Asadzadeh Mohammad Silawi Afsaneh Taghipour Sheshdeh Behrouz Mohammad Nazari Mohammad Ali Faghihi Zahra Roudbari Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing Animals dromedary pigmentation coat color genotyping-by-sequencing |
| title | Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing |
| title_full | Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing |
| title_fullStr | Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing |
| title_full_unstemmed | Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing |
| title_short | Identification of Candidate Genes for Pigmentation in Camels Using Genotyping-by-Sequencing |
| title_sort | identification of candidate genes for pigmentation in camels using genotyping by sequencing |
| topic | dromedary pigmentation coat color genotyping-by-sequencing |
| url | https://www.mdpi.com/2076-2615/12/9/1095 |
| work_keys_str_mv | AT mortezabitarafsani identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT javadzareharofte identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT mohammadhosseinbanabazi identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT asimfaraz identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT saeidesmaeilkhanian identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT alishafeinaderi identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT nadersalim identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT abbasteimoori identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT ahmadbitaraf identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT mohammadzadehrahmani identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT pamelaannaburger identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT naderasadzadeh identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT mohammadsilawi identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT afsanehtaghipoursheshdeh identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT behrouzmohammadnazari identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT mohammadalifaghihi identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing AT zahraroudbari identificationofcandidategenesforpigmentationincamelsusinggenotypingbysequencing |