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Twumasi G, Wang H, Xi Y, Qi J, Li L, Bai L, Liu H. Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks. Animals (Basel) 2023; 14:85. [PMID: 38200816 PMCID: PMC10778472 DOI: 10.3390/ani14010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
In modern advanced genetics and breeding programs, the study of genes related to pigmentation in ducks is gaining much attention and popularity. Genes and DNA mutation cause variations in the plumage color traits of ducks. Therefore, discovering related genes responsible for different color traits and pigment patterns on each side of the single feathers in Chinese ducks is important for genetic studies. In this study, we collected feather images from 340 ducks and transported them into Image Pro Plus (IPP) 6.0 software to quantify the melanin content in the feathers. Thereafter, a genome-wide association study was conducted to reveal the genes responsible for variations in the feather color trait. The results from this study revealed that the pigmented region was larger in the male ducks as compared to the female ducks. In addition, the pigmented region was larger on the right side of the feather vane than on the left side in both dorsal and ventral feathers, and a positive correlation was observed among the feather color traits. Further, among the annotated genes, WNT3A, DOCK1, RAB1A, and ALDH1A3 were identified to play important roles in the variation in pigmented regions of the various feathers. This study also revealed that five candidate genes, including DPP8, HACD3, INTS14, SLC24A1, and DENND4A, were associated with the color pigment on the dorsal feathers of the ducks. Genes such as PRKG1, SETD6, RALYL, and ZNF704 reportedly play important roles in ventral feather color traits. This study revealed that genes such as WNT3A, DOCK1, RAB1A, and ALDH1A3 were associated with different pigmentation patterns, thereby providing new insights into the genetic mechanisms of single-feather pigmentation patterns in ducks.
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Affiliation(s)
- Grace Twumasi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Huazhen Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Xi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingjing Qi
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hehe Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (G.T.); (H.W.); (Y.X.); (J.Q.); (L.L.); (L.B.)
- Farm Animal Genetic Resources Exploration and Innovation, Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Zhang X, Zhu T, Wang L, Lv X, Yang W, Qu C, Li H, Wang H, Ning Z, Qu L. Genome-Wide Association Study Reveals the Genetic Basis of Duck Plumage Colors. Genes (Basel) 2023; 14:genes14040856. [PMID: 37107611 PMCID: PMC10137861 DOI: 10.3390/genes14040856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/17/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Plumage color is an artificially and naturally selected trait in domestic ducks. Black, white, and spotty are the main feather colors in domestic ducks. Previous studies have shown that black plumage color is caused by MC1R, and white plumage color is caused by MITF. We performed a genome-wide association study (GWAS) to identify candidate genes associated with white, black, and spotty plumage in ducks. Two non-synonymous SNPs in MC1R (c.52G>A and c.376G>A) were significantly related to duck black plumage, and three SNPs in MITF (chr13:15411658A>G, chr13:15412570T>C and chr13:15412592C>G) were associated with white plumage. Additionally, we also identified the epistatic interactions between causing loci. Some ducks with white plumage carry the c.52G>A and c.376G>A in MC1R, which also compensated for black and spotty plumage color phenotypes, suggesting that MC1R and MITF have an epistatic effect. The MITF locus was supposed to be an upstream gene to MC1R underlying the white, black, and spotty colors. Although the specific mechanism remains to be further clarified, these findings support the importance of epistasis in plumage color variation in ducks.
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Affiliation(s)
- Xinye Zhang
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Tao Zhu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing 100107, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-Aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang 236037, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumchi 830052, China
| | - Huie Wang
- College of Animal Science, Tarim University, Alar 843300, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
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Jiang XX, Adeola AC, Sola-Ojo FE, Abubakar IA, Fatima IH, Olaoluwa OJ, Abodurin AB, Olasunkanmi OA, Abisola OH, Uthman O, Kehinde AE, Hamidat H, Nishola TE, Bello SF, Peng MS, Zhang YP. Association of MC1R variation and plumage color diversity of Nigerian domestic pigeon ( Columba livia domestica). J Adv Vet Anim Res 2022; 9:369-373. [PMID: 36382035 PMCID: PMC9597907 DOI: 10.5455/javar.2022.i604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 06/16/2023] Open
Abstract
OBJECTIVES Domestic pigeons (Columba livia domestica) have diverse plumage pigmentations. Melanocortin 1 receptor (MC1R) gene variation has been correlated with color traits. The association between MC1R and plumage coloration in African domestic pigeons is yet to be investigated. MATERIALS AND METHODS Herein, we report the relationships between single nucleotide polymorphisms (SNPs) in MC1R and plumage of 35 domestic pigeons from Nigeria with 4 different plumage phenotypes plus 37 published MC1R sequences from France (n = 14) and Russia (n = 11). RESULTS We obtained 14 SNP sites among 72 individuals. Missense mutations C206T (Ser69Leu) and G253A (Val85Met) were observed in 16 and 8 Nigerian pigeons, respectively. The chi-squared test (p < 0.05) for C206T, G253A, and A520G has the advantage of homozygous genotypes CC, GG, and AA, respectively. The association of C206T loci showed the advantage of CC genotype in ash-red, spread, and white pigeons, and TT in blue-bar, spread, and white feather pigeons. For G253A and A520G loci, GG and AA were dominant in all plumages except for genotype AA in G253A, which was prominent in ash-red, spread, and white plumages. The three SNPs were assigned to seven haplotypes. The median-joining network revealed 20 haplotypes, including 5 in Nigeria and 2 shared. CONCLUSION This study provides an insight into the association of MC1R variation and plumage diversity in Nigerian domestic pigeons. However, due to the limitation of the current data, we could not make further conclusions; this necessitates the need for more genomics studies on Nigerian pigeons.
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Affiliation(s)
| | - Adeniyi Charles Adeola
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Foluke Eunice Sola-Ojo
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | | | - Isiaka Hannah Fatima
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | | | | | | | - Oladejo Hafsat Abisola
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | - Oladipo Uthman
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | - Adeshina Esther Kehinde
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | - Hussein Hamidat
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | - Taiwo Eyitayo Nishola
- Department of Animal Production, Faculty of Agriculture, University of Ilorin, Ilorin, Nigeria
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Shen X, Wang Y, Cui C, Zhao X, Li D, Zhu Q, Jiang X, Yang C, Qiu M, Yu C, Li Q, Du H, Zhang Z, Yin H. Detection of Snps in the Melanocortin 1-Receptor (MC1R) and Its Association with Shank Color Trait in Hs Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- X Shen
- Sichuan Agricultural University, China
| | - Y Wang
- Sichuan Agricultural University, China
| | - C Cui
- Sichuan Agricultural University, China
| | - X Zhao
- Sichuan Agricultural University, China
| | - D Li
- Sichuan Agricultural University, China
| | - Q Zhu
- Sichuan Agricultural University, China
| | - X Jiang
- Sichuan Animal Science Academy, China
| | - C Yang
- Sichuan Animal Science Academy, China
| | - M Qiu
- Sichuan Animal Science Academy, China
| | - C Yu
- Sichuan Animal Science Academy, China
| | - Q Li
- Sichuan Animal Science Academy, China
| | - H Du
- Sichuan Animal Science Academy, China
| | - Z Zhang
- Sichuan Animal Science Academy, China
| | - H Yin
- Sichuan Agricultural University, China
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Sultana H, Seo D, Choi NR, Bhuiyan MSA, Lee SH, Heo KN, Lee JH. Identification of polymorphisms in MITF and DCT genes and their associations with plumage colors in Asian duck breeds. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:180-188. [PMID: 28823136 PMCID: PMC5767499 DOI: 10.5713/ajas.17.0298] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/30/2017] [Accepted: 07/28/2017] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) of the melanogenesis associated transcription factor (MITF) and dopachrome tautomerase (DCT) genes on plumage coloration in Asian native duck breeds. MITF encodes a protein for microphthalmia-associated transcription factor, which regulates the development and function of melanocytes for pigmentation of skin, hair, and eyes. Among the tyrosinase-related family genes, DCT is a pigment cell-specific gene that plays important roles in the melanin synthesis pathway and the expression of skin, feather, and retina color. METHODS Five Asian duck varieties (black Korean native, white Korean native, commercial Peking, Nageswari, and Bangladeshi Deshi white ducks) were investigated to examine the polymorphisms associated with plumage colors. Among previously identified SNPs, three synonymous SNPs and one indel of MITF and nine SNPs in exon regions of DCT were genotyped. The allele frequencies for SNPs of the black and white plumage color populations were estimated and Fisher's exact test was conducted to assess the association between the allele frequencies of these two populations. RESULTS Two synonymous SNPs (c.114T>G and c.147T>C) and a 14-bp indel (GCTGCAAAC AGATG) in intron 7 of MITF were significantly associated with the black- and white-colored breeds (p<0.001). One non-synonymous SNP [c.938A>G (p.His313Arg)] in DCT, was highly significantly associated (p<0.001) and a synonymous SNP (c.753A>G) was significantly associated (p<0.05) with black and white color plumage in the studied duck populations. CONCLUSION The results of this study provide a basis for further investigations of the associations between polymorphisms and plumage color phenotypes in Asian duck breeds.
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Affiliation(s)
- Hasina Sultana
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Nu-Ri Choi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Md. Shamsul Alam Bhuiyan
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Kang-Nyeong Heo
- Poultry Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
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