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Su P, Wu H, Huang Y, Lu X, Yin J, Zhang Q, Lan X. The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene. Animals (Basel) 2023; 13:3218. [PMID: 37893942 PMCID: PMC10603658 DOI: 10.3390/ani13203218] [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: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.
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Affiliation(s)
- Peng Su
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hui Wu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yangming Huang
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaofang Lu
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Jing Yin
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Qingfeng Zhang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products. Genes (Basel) 2022; 13:genes13101825. [PMID: 36292710 PMCID: PMC9601671 DOI: 10.3390/genes13101825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/04/2022] Open
Abstract
The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products.
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Dong H, Dong Z, Wang F, Wang G, Luo X, Lei C, Chen J. Whole Genome Sequencing Provides New Insights Into the Genetic Diversity and Coat Color of Asiatic Wild Ass and Its Hybrids. Front Genet 2022; 13:818420. [PMID: 35646088 PMCID: PMC9135160 DOI: 10.3389/fgene.2022.818420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
The diversity of livestock coat color results from human positive selection and is an indispensable part of breed registration. As an important biodiversity resource, Asiatic wild ass has many special characteristics, including the most visualized feature, its yellowish-brown coat color, and excellent adaptation. To explore the genetic mechanisms of phenotypic characteristics in Asiatic wild ass and its hybrids, we resequenced the whole genome of one Mongolian Kulan (a subspecies of Asiatic wild ass) and 29 Kulan hybrids (Mongolian Kulan ♂×Xinjiang♀), and the ancestor composition indicated the true lineage of the hybrids. XP-EHH (Cross Population Extended Haplotype Homozygosity), θπ-ratio (Nucleotide Diversity Ratio), CLR (Composite Likelihood Ratio) and θπ (Nucleotide Diversity) methods were used to detect the candidate regions of positive selection in Asiatic wild ass and its hybrids. Several immune genes (DEFA1, DEFA5, DEFA7, GIMAP4, GIMAP1, IGLC1, IGLL5, GZMB and HLA) were observed by the CLR and θπ methods. XP-EHH and θπ-ratio revealed that these genes are potentially responsible for coat color (KITLG) and meat quality traits (PDE1B and MYLK2). Furthermore, the heatmap was able to show the clear difference in the haplotype of the KITLG gene between the Kulan hybrids and Asiatic wild ass group and the Guanzhong black donkey group, which is a powerful demonstration of the key role of KITLG in donkey color. Therefore, our study may provide new insights into the genetic basis of coat color, meat quality traits and immunity of Asiatic wild ass and its hybrids.
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Affiliation(s)
- Hong Dong
- College of Animal Science and Technology, SHIHEZI University, Shihezi, China
| | - Zheng Dong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jingbo Chen
- College of Animal Science and Technology, SHIHEZI University, Shihezi, China
- *Correspondence: Jingbo Chen,
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Gebreselassie G, Liang B, Berihulay H, Islam R, Abied A, Jiang L, Zhao Z, Ma Y. Genomic mapping identifies two genetic variants in the MC1R gene for coat colour variation in Chinese Tan sheep. PLoS One 2020; 15:e0235426. [PMID: 32817695 PMCID: PMC7444486 DOI: 10.1371/journal.pone.0235426] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Coat colour is one of the most important economic traits of sheep and is mainly used for breed identification and characterization. This trait is determined by the biochemical function, availability and distribution of phaeomelanin and eumelanin pigments. In our study, we conducted a genome-wide association study to identify candidate genes and genetic variants associated with coat colour in 75 Chinese Tan sheep using the ovine 600K SNP BeadChip. Accordingly, we identified two significant SNPs (rs409651063 at 14.232 Mb and rs408511664 at 14.228 Mb) associated with coat colour in the MC1R gene on chromosome 14 with −log10(P) = 2.47E-14 and 1.00E-13, respectively. The consequence of rs409651063 was a missense variant (g.14231948 G>A) that caused an amino acid change (Asp105Asn); however, the second SNP (rs408511664) was a synonymous substitution and is an upstream variant (g.14228343G>A). Moreover, our PCR analysis revealed that the genotype of white sheep was exclusively homozygous (GG), whereas the genotypes of black-head sheep were mainly heterozygous (GA). Interestingly, allele-specific expression analysis (using the missense variant for the skin cDNA samples from black-head sheep) revealed that only the G allele was expressed in the skin covered with white hair, while both the G and A alleles were expressed in the skin covered with black hair. This finding indicated that the missense mutation that we identified is probably responsible for white coat colour in Tan sheep. Furthermore, qPCR analysis of MC1R mRNA level in the skin samples was significantly higher in black-head than white sheep and very significantly higher in GA than GG individuals. Taken together, these results help to elucidate the genetic mechanism underlying coat colour variation in Chinese indigenous sheep.
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Affiliation(s)
- Gebremedhin Gebreselassie
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Agricultural Biotechnology, Biotechnology Center, Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Benmeng Liang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Haile Berihulay
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Rabul Islam
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Adam Abied
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lin Jiang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhengwei Zhao
- Institute of animal science, Ningxia Academy of Agriculture and Forestry Sciences, Ningxia, Yinchuan, China
- * E-mail: (YM); (ZZ)
| | - Yuehui Ma
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- * E-mail: (YM); (ZZ)
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7
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Nie C, Ban L, Ning Z, Qu L. Feather colour affects the aggressive behaviour of chickens with the same genotype on the dominant white (I) locus. PLoS One 2019; 14:e0215921. [PMID: 31048862 PMCID: PMC6497237 DOI: 10.1371/journal.pone.0215921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/10/2019] [Indexed: 11/18/2022] Open
Abstract
Aggression in chickens is a serious economic and animal welfare issue in poultry farming. Pigmentation traits have been documented to be associated with animal behaviour. Chicken pecking behaviour has been found to be related to feather colour, with premelanosome protein 17 (PMEL17) being one of the candidate genes. In the present study, we performed a genotypic and phenotypic association analysis between chicken plumage colour (red and white) and aggressive behaviour in an F1 hybrid group generated by crossing the autosomal dominant white-feathered breed White Leghorn (WL) and the red-feathered breed Rhode Island Red (RIR). In genetic theory, all the progeny should have white feathers because WL is homozygous autosomal dominant for white feathers. However, we found a few red-feathered female chickens. We compared the aggressiveness between the red and white females to determine whether the feather colour alone affected the behaviour, given that the genetic background should be the same except for feather colour. The aggressiveness was recorded 5 days after sexual maturity at 26 weeks. Generally, white plumage hens showed significantly higher aggressiveness compared to the red ones in chasing, attacking, pecking, and threatening behaviour traits. We assessed three candidate feather colour genes—PMEL17, solute carrier family 45 member 2 (SLC45A2), and SRY-box 10 (SOX10)—to determine the genetic basis for the red and white feather colour in our hybrid population; there was no association between the three loci and feather colour. The distinct behavioural findings observed herein provide clues to the mechanisms underlying the association between phenotype and behaviour in chickens. We suggest that mixing red and white chickens together might reduce the occurrence of aggressive behaviours.
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Affiliation(s)
- Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Liping Ban
- College of grassland science and technology, China Agricultural University, Beijing, China
| | - Zhonghua Ning
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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8
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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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Hamzaoui S, Burger C, Collier J, Collier R. Technical note: Method for isolation of the bovine sweat gland and conditions for in vitro culture. J Dairy Sci 2018; 101:4638-4642. [DOI: 10.3168/jds.2017-14056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/15/2018] [Indexed: 11/19/2022]
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10
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Amin M, Masoudi AA, Amirinia C, Emrani H. Molecular Study of the Extension Locus in Association with Coat Colour Variation of Iranian Indigenous Sheep Breeds. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Srikanth K, Kwon A, Lee E, Chung H. Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis. Cell Stress Chaperones 2017; 22:29-42. [PMID: 27848120 PMCID: PMC5225057 DOI: 10.1007/s12192-016-0739-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/21/2016] [Accepted: 10/06/2016] [Indexed: 12/20/2022] Open
Abstract
This study aimed to investigate the genes and pathways that respond to heat stress in Holstein bull calves exposed to severe ranges of temperature and humidity. A total of ten animals from 4 to 6 months of age were subjected to heat stress at 37 °C and 90 % humidity for 12 h. Skin and rectal temperatures were measured before and after heat stress; while no correlation was found between them before heat stress, a moderate correlation was detected after heat stress, confirming rectal temperature to be a better barometer for monitoring heat stress. RNAseq analysis identified 8567 genes to be differentially regulated, out of which 465 genes were significantly upregulated (≥2-fold, P < 0.05) and 49 genes were significantly downregulated (≤2-fold, P < 0.05) in response to heat stress. Significant terms and pathways enriched in response to heat stress included chaperones, cochaperones, cellular response to heat stress, phosphorylation, kinase activation, immune response, apoptosis, Toll-like receptor signaling pathway, Pi3K/AKT activation, protein processing in endoplasmic reticulum, interferon signaling, pathways in cancer, estrogen signaling pathway, and MAPK signaling pathway. The differentially expressed genes were validated by quantitative real-time PCR analysis, which confirmed the tendency of the expression. The genes and pathways identified in this analysis extend our understanding of transcriptional response to heat stress and their likely functioning in adapting the animal to hyperthermic stress. The identified genes could be used as candidate genes for association studies to select and breed animals with improved heat tolerance.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeollabuk-do, 565-851, Korea
| | - Anam Kwon
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeollabuk-do, 565-851, Korea
| | - Eunjin Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeollabuk-do, 565-851, Korea
| | - Hoyoung Chung
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Wanju, Jeollabuk-do, 565-851, Korea.
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12
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Jin S, Lee JH, Seo DW, Cahyadi M, Choi NR, Heo KN, Jo C, Park HB. A Major Locus for Quantitatively Measured Shank Skin Color Traits in Korean Native Chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1555-1561. [PMID: 27383802 PMCID: PMC5088374 DOI: 10.5713/ajas.16.0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/19/2016] [Accepted: 06/18/2016] [Indexed: 11/27/2022]
Abstract
Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [L*], redness [a*], and yellowness [b*]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects b* value (logarithm of odds [LOD] = 47.5, p = 1.60×10−49) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences a* value (LOD = 14.2, p = 6.14×10−16). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and a* (PMGA = 1.69×10−28; PQTDT = 2.40×10−25). The strongest associations were between BCDO2 g.9367 A>C and b* (PMGA = 3.56×10−66; PQTDT = 1.68×10−65). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.
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Affiliation(s)
- S Jin
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea
| | - J H Lee
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea
| | - D W Seo
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea
| | - M Cahyadi
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea.,Department of Animal Science, Faculty of Agriculture, Sebelas Maret University, Surakarta 57126, Indonesia
| | - N R Choi
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea
| | - K N Heo
- Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
| | - C Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Science, Seoul National University, Seoul 08826, Korea
| | - H B Park
- Division of Animal and Dairy Science, Chungnam National University, Deajeon 34134, Korea.,Subtropical Livestock Research Institute, National Institute of Animal Science, Jeju 63242, Korea
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13
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Nix MA, Kaelin CB, Palomino R, Miller JL, Barsh GS, Millhauser GL. Electrostatic Similarity Analysis of Human β-Defensin Binding in the Melanocortin System. Biophys J 2016; 109:1946-58. [PMID: 26536271 DOI: 10.1016/j.bpj.2015.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
The β-defensins are a class of small cationic proteins that serve as components of numerous systems in vertebrate biology, including the immune and melanocortin systems. Human β-defensin 3 (HBD3), which is produced in the skin, has been found to bind to melanocortin receptors 1 and 4 through complementary electrostatics, a unique mechanism of ligand-receptor interaction. This finding indicates that electrostatics alone, and not specific amino acid contact points, could be sufficient for function in this ligand-receptor system, and further suggests that other small peptide ligands could interact with these receptors in a similar fashion. Here, we conducted molecular-similarity analyses and functional studies of additional members of the human β-defensin family, examining their potential as ligands of melanocortin-1 receptor, through selection based on their electrostatic similarity to HBD3. Using Poisson-Boltzmann electrostatic calculations and molecular-similarity analysis, we identified members of the human β-defensin family that are both similar and dissimilar to HBD3 in terms of electrostatic potential. Synthesis and functional testing of a subset of these β-defensins showed that peptides with an HBD3-like electrostatic character bound to melanocortin receptors with high affinity, whereas those that were anticorrelated to HBD3 showed no binding affinity. These findings expand on the central role of electrostatics in the control of this ligand-receptor system and further demonstrate the utility of employing molecular-similarity analysis. Additionally, we identified several new potential ligands of melanocortin-1 receptor, which may have implications for our understanding of the role defensins play in melanocortin physiology.
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Affiliation(s)
- Matthew A Nix
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California
| | - Rafael Palomino
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jillian L Miller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; Department of Genetics, Stanford University, Stanford, California.
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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Mahmoud AH, Mashaly AM, Rady AM, Al-Anazi KM, Saleh AA. Allelic variation of melanocortin-1 receptor locus in Saudi indigenous sheep exhibiting different color coats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:154-159. [PMID: 27492350 PMCID: PMC5205600 DOI: 10.5713/ajas.16.0138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/21/2016] [Accepted: 08/01/2016] [Indexed: 11/27/2022]
Abstract
Objective This study was designed to characterize the DNA polymorphisms of the melanocortin-1 receptor (MC1R) gene in indigenous Saudi Arabian sheep breeds exhibiting different color coats, along with individuals of the Sawaknee breed, an exotic sheep imported from Sudan. Methods The complete coding region of MC1R gene including parts of 3′ and 5′ untranslated regions was amplified and sequenced from three the indigenous Saudi sheep; Najdi (generally black, n = 41), Naeimi (generally white with brown faces, n = 36) and Herri (generally white, n = 18), in addition to 13 Sawaknee sheep. Results Five single nucleotide polymorphisms (SNPs) were detected in the MC1R gene: two led to nonsynonymous mutations (c.218 T>A, p.73 Met>Lys and c.361 G>A, p.121 Asp>Asn) and three led to synonymous mutations (c.429 C>T, p.143 Tyr>Tyr; c.600 T>G, p.200 Leu>Leu, and c.735 C>T, p.245 Ile>Ile). Based on these five SNPs, eight haplotypes representing MC1R Ed and E+ alleles were identified among the studied sheep breeds. The most common haplotype (H3) of the dominant Ed allele was associated with either black or brown coat color in Najdi and Sawaknee sheep, respectively. Two other haplotypes (H6 and H7) of Ed allele, with only the nonsynonymous mutation A218T, were detected for the first time in Saudi indigenous sheep. Conclusion In addition to investigating the MC1R allelic variation in Saudi indigenous sheep populations, the present study supports the assumption that the two independent nonsynonymous Met73Lys and Asp121Asn mutations in MC1R gene are associated with black or red coat colors in sheep breeds.
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Affiliation(s)
- Ahmed H Mahmoud
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashraf M Mashaly
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed M Rady
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid M Al-Anazi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Amgad A Saleh
- Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia.,Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza 12619, Egypt
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15
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Jakubczak A, Gryzinska M, Horecka B, Kowalczyk M, Kasperek K, Gajewska K, Jezewska-Witkowska G. Single-nucleotide polymorphism of MC1R, ASIP, and TYRP2 genes in wild and farmed foxes (Vulpes vulpes). CANADIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.1139/cjas-2015-0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA mutations within genes associated with melanogenesis can affect melanin production, leading to dyschromias. Genes that are involved in synthesis of melatonin and may affect the color of skin are melanocortin 1 receptor (MC1R), agouti locus (ASIP), and tyrosinase-related protein-2 (TYRP2). In this study, SNP identification within ASIP, MC1R, and TYRP2 gene fragments in wild and farmed foxes (Vulpes vulpes) was performed. Nine mutations in the ASIP gene which allowed us to distinguish seven SNP profiles, fourteen mutations and five SNP profiles in the MC1R gene, and seven SNP profiles based on four polymorphic nucleotides in the TYRP2 gene were detected. Analyses of obtained profiles indicate that ASIP did not undergo mutations in the wild, and significant variability of SNP profiles was found for TYRP2, with specific haplotypes noted for farm foxes and American and European wild foxes.
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Affiliation(s)
- Andrzej Jakubczak
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Magdalena Gryzinska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Beata Horecka
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Marek Kowalczyk
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Kornel Kasperek
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Katarzyna Gajewska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Grazyna Jezewska-Witkowska
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
- Department of Biological Basis of Animal Production, Faculty of Biology and Animal Breeding, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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Schneider A, Henegar C, Day K, Absher D, Napolitano C, Silveira L, David VA, O’Brien SJ, Menotti-Raymond M, Barsh GS, Eizirik E. Recurrent evolution of melanism in South American felids. PLoS Genet 2015; 11:e1004892. [PMID: 25695801 PMCID: PMC4335015 DOI: 10.1371/journal.pgen.1004892] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/13/2014] [Indexed: 12/04/2022] Open
Abstract
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus geoffroyi). To assess population level variation in the regions surrounding the causative mutations we apply genomic resources from the domestic cat to carry out clone-based capture and targeted resequencing of 299 kb and 251 kb segments that contain ASIP and MC1R, respectively, from 54 individuals (13–21 per species), achieving enrichment of ~500–2500-fold and ~150x coverage. Our analysis points to unique evolutionary histories for each of the three species, with a strong selective sweep in the pampas cat, a distinctive but short melanism-specific haplotype in the Geoffroy’s cat, and reduced nucleotide diversity for both ancestral and melanism-bearing chromosomes in the kodkod. These results reveal an important role for natural selection in a trait of longstanding interest to ecologists, geneticists, and the lay community, and provide a platform for comparative studies of morphological variation in other natural populations. Color polymorphism in closely related animal species provides an opportunity to study how the balance between natural selection and genetic drift shapes the evolution of appearance and form. The cat family, Felidae, is especially interesting; 13 of 37 extant species exhibit polymorphism for melanism, but evidence for any adaptive role is lacking, in part because the potential benefits of melanism to felid predators are not clear, and in part because the tools for genomic analysis of natural populations are limited. We identify the mutations responsible for melanism in three closely related South American wild felids, the pampas cat, the kodkod, and Geoffroy’s cat, then adapt a new approach for targeted genome sequencing to characterize molecular variation in the region surrounding each melanism mutation. We find that each mutation has developed independently, with strong evidence for natural selection in the black pampas cat, and reduced genetic variation in the entire population of kodkods. Our results demonstrate that some “black cats” are black not by chance, but by selection for a mutation that provides increased fitness.
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Affiliation(s)
- Alexsandra Schneider
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Corneliu Henegar
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Constanza Napolitano
- Laboratorio de Ecología Molecular & Instituto de Ecologia y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Leandro Silveira
- Jaguar Conservation Fund, Instituto Onça-Pintada, Mineiros, Goiás, Brazil
| | - Victor A. David
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Stephen J. O’Brien
- Theodosius Dobzhansky Center for Genome Informatics, St. Petersburg State University, St. Petersburg, Russia
| | - Marilyn Menotti-Raymond
- Basic Research Laboratory, Frederick National Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
- * E-mail: (GSB); (EE)
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, São Paulo, Brazil
- * E-mail: (GSB); (EE)
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17
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Jin S, Park H, Seo D, Cahyadi M, Choi N, Heo K, Jo C, Lee J. Association of MC1R genotypes with shank color traits in Korean native chicken. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.10.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Identification of differentially expressed miRNAs between white and black hair follicles by RNA-sequencing in the goat (Capra hircus). Int J Mol Sci 2014; 15:9531-45. [PMID: 24879525 PMCID: PMC4100108 DOI: 10.3390/ijms15069531] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/30/2023] Open
Abstract
MicroRNAs (miRNAs) play a key role in many biological processes by regulating gene expression at the post-transcriptional level. A number of miRNAs have been identified from livestock species. However, compared with other animals, such as pigs and cows, the number of miRNAs identified in goats is quite low, particularly in hair follicles. In this study, to investigate the functional roles of miRNAs in goat hair follicles of goats with different coat colors, we sequenced miRNAs from two hair follicles samples (white and black) using Solexa sequencing. A total of 35,604,016 reads were obtained, which included 30,878,637 clean reads (86.73%). MiRDeep2 software identified 214 miRNAs. Among them, 205 were conserved among species and nine were novel miRNAs. Furthermore, DESeq software identified six differentially expressed miRNAs. Quantitative PCR confirmed differential expression of two miRNAs, miR-10b and miR-211. KEGG pathways were analyzed using the DAVID website for the predicted target genes of the differentially expressed miRNAs. Several signaling pathways including Notch and MAPK pathways may affect the process of coat color formation. Our study showed that the identified miRNAs might play an essential role in black and white follicle formation in goats.
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19
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Nunome M, Kinoshita G, Tomozawa M, Torii H, Matsuki R, Yamada F, Matsuda Y, Suzuki H. Lack of association between winter coat colour and genetic population structure in the Japanese hare,Lepus brachyurus(Lagomorpha: Leporidae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mitsuo Nunome
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Gohta Kinoshita
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
| | | | - Harumi Torii
- Center for Natural Environment Education; Nara University of Education; Takabatake-cho Nara 630-8528 Japan
| | - Rikyu Matsuki
- Environmental Science Research Laboratory; Central Research Institute of Electric Power Industry; 1646 Abiko Chiba 270-1194 Japan
| | - Fumio Yamada
- Forestry and Forest Products Research Institute; PO Box 16 Tsukuba Norin Ibaraki 305-8687 Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics; Department of Applied Molecular Biosciences; Graduate School of Bioagricultural Sciences; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics; Faculty of Environmental Earth Science; Hokkaido University; Kita-ku Sapporo 060-0810 Japan
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20
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Linderholm A, Larson G. The role of humans in facilitating and sustaining coat colour variation in domestic animals. Semin Cell Dev Biol 2013; 24:587-93. [PMID: 23567209 DOI: 10.1016/j.semcdb.2013.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 03/28/2013] [Indexed: 11/27/2022]
Abstract
Though the process of domestication results in a wide variety of novel phenotypic and behavioural traits, coat colour variation is one of the few characteristics that distinguishes all domestic animals from their wild progenitors. A number of recent reviews have discussed and synthesised the hundreds of genes known to underlie specific coat colour patterns in a wide range of domestic animals. This review expands upon those studies by asking how what is known about the causative mutations associated with variable coat colours, can be used to address three specific questions related to the appearance of non wild-type coat colours in domestic animals. Firstly, is it possible that coat colour variation resulted as a by-product of an initial selection for tameness during the early phases of domestication? Secondly, how soon after the process began did domestic animals display coat colour variation? Lastly, what evidence is there that intentional human selection, rather than drift, is primarily responsible for the wide range of modern coat colours? By considering the presence and absence of coat colour genes within the context of the different pathways animals travelled from wild to captive populations, we conclude that coat colour variability was probably not a pleiotropic effect of the selection for tameness, that coat colours most likely appeared very soon after the domestication process began, and that humans have been actively selecting for colour novelty and thus allowing for the proliferation of new mutations in coat colour genes.
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Affiliation(s)
- Anna Linderholm
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham, United Kingdom
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21
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Signature of balancing selection at the MC1R gene in Kunming dog populations. PLoS One 2013; 8:e55469. [PMID: 23424634 PMCID: PMC3570536 DOI: 10.1371/journal.pone.0055469] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/23/2012] [Indexed: 12/21/2022] Open
Abstract
Coat color in dog breeds is an excellent character for revealing the power of artificial selection, as it is extremely diverse and likely the result of recent domestication. Coat color is generated by melanocytes, which synthesize pheomelanin (a red or yellow pigment) or eumelanin (a black or brown pigment) through the pigment type-switching pathway, and is regulated by three genes in dogs: MC1R (melanocortin receptor 1), CBD103 (β-defensin 103), and ASIP (agouti-signaling protein precursor). The genotypes of these three gene loci in dog breeds are associated with coat color pattern. Here, we resequenced these three gene loci in two Kunming dog populations and analyzed these sequences using population genetic approaches to identify evolutionary patterns that have occurred at these loci during the recent domestication and breeding of the Kunming dog. The analysis showed that MC1R undergoes balancing selection in both Kunming dog populations, and that the Fst value for MC1R indicates significant genetic differentiation across the two populations. In contrast, similar results were not observed for CBD103 or ASIP. These results suggest that high heterozygosity and allelic differences at the MC1R locus may explain both the mixed color coat, of yellow and black, and the difference in coat colors in both Kunming dog populations.
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22
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Zhang H, An T, He J, Luo Y, Han J. Conserved Exon 2 but a Highly Polymorphic 5’-UTR of Tyrosinase Gene in Tianzhu White Yak (Bos grunniens). ACTA ACUST UNITED AC 2012. [DOI: 10.3923/ajava.2012.1090.1099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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23
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Nowacka-Woszuk J, Salamon S, Gorna A, Switonski M. Missense polymorphisms in the MC1R
gene of the dog, red fox, arctic fox and Chinese raccoon dog. J Anim Breed Genet 2012; 130:136-41. [DOI: 10.1111/jbg.12005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/25/2012] [Indexed: 12/13/2022]
Affiliation(s)
- J. Nowacka-Woszuk
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
| | - S. Salamon
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
| | - A. Gorna
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
| | - M. Switonski
- Department of Genetics and Animal Breeding; Poznan University of Life Sciences; Poznan Poland
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24
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Abstract
During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat-colour-associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat-colour variants. Recent studies demonstrate that this selection for coat-colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat-colour-associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat-colour-associated genes act.
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Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Research Group of Evolutionary Genetics, Berlin, Germany
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25
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Tixier-Boichard M, Bed’hom B, Rognon X. Chicken domestication: From archeology to genomics. C R Biol 2011; 334:197-204. [DOI: 10.1016/j.crvi.2010.12.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Dybvig T, Facci M, Gerdts V, Wilson HL. Biological roles of host defense peptides: lessons from transgenic animals and bioengineered tissues. Cell Tissue Res 2010; 343:213-25. [PMID: 21088855 DOI: 10.1007/s00441-010-1075-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 10/08/2010] [Indexed: 12/18/2022]
Abstract
Host defense peptides (HDPs) have long been recognized as microbicidal agents, but their roles as modulators of innate and adaptive immunity have only more recently been appreciated. The study of transgenic animal and tissue models has provided platforms to improve our understanding of the immune modulatory functions of HDPs. Here, the characterization of transgenic animals or tissue models that over-express and/or are deficient for specific HDPs is reviewed. We also attempt to reconcile this data with evidence from human studies monitoring HDP expression at constitutive levels and/or in conjunction with inflammation, infection models, or disease states. We have excluded activities ascribed to HDPs derived exclusively from in vitro experiments. An appreciation of the way that HDPs promote innate immunity or influence the adaptive immune response is necessary in order to exploit their therapeutic or adjuvant potential and to open new perspectives in understanding the basis of immunity. The potential applications for HDPs are discussed.
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Affiliation(s)
- Tova Dybvig
- Vaccine & Infectious Disease Organization (VIDO), University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, S7N 5E3, Canada
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27
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Walker WP, Gunn TM. Shades of meaning: the pigment-type switching system as a tool for discovery. Pigment Cell Melanoma Res 2010; 23:485-95. [PMID: 20465596 DOI: 10.1111/j.1755-148x.2010.00721.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The pigment-type switching system, which controls whether melanocytes produce black/brown eumelanin or yellow/red pheomelanin, is responsible for many familiar coat coloration patterns in both domestic and wild mammals. In conjunction with the accessory proteins attractin and mahogunin ring finger 1, endogenous agonists and antagonists modulate signaling by the melanocortin 1 receptor to determine pigment type. Mutations in pigment-type switching genes can cause a variety of pleiotropic phenotypes, and these are often similar between mutants at different loci because the proteins encoded by these genes act together as part of conserved molecular pathways that are deployed in multiple biological contexts. When this is the case, pigment-type switching provides a powerful model system for elucidating the shared molecular mechanisms underlying the pigmentary and non-pigmentary phenotypes. This review outlines the current understanding of the pigment-type switching pathway and discusses the opportunities that exist for exploring the molecular basis of pleiotropic phenotypes using this model system.
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28
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Okumura N, Hayashi T, Uenishi H, Fukudome N, Komatsuda A, Suzuki A, Shibata M, Nii M, Yamaguchi T, Kojima-Shibata C, Hamasima N, Awata T. Sequence polymorphisms in porcine homologs of murine coat colour-related genes. Anim Genet 2010; 41:113-21. [DOI: 10.1111/j.1365-2052.2009.01968.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Peterschmitt M, Grain F, Arnaud B, Deléage G, Lambert V. Mutation in the melanocortin 1 receptor is associated with amber colour in the Norwegian Forest Cat. Anim Genet 2009; 40:547-52. [PMID: 19422360 DOI: 10.1111/j.1365-2052.2009.01864.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amber (previously called X-Colour) is a yellow recessive coat colour observed in the Norwegian Forest Cat (NFC) population and apparently absent in other cat breeds. Until now, there has never been any scientific evidence of yellow recessive mutation (e) reported in the extension gene in Felidae. We sequenced the complete coding sequence region for the melanocortin 1 receptor in 12 amber, three carriers, two wild-type NFCs, one wild-type European Shorthair and two 'golden' Siberian cats and identified two single nucleotide polymorphisms (SNPs): a non-synonymous (FM180571: c.250G>A) and a synonymous (FM180571: c.840T>C) mutation. The c.250G>A SNP, further genotyped on 56 cats using PCR-RFLP, is associated with amber colour and only present in the amber cat lineages. It replaced an aspartic acid with a neutral polar asparagine in the second transmembrane helix (p.Asp84Asn), a position where e mutations have already been described. Three-dimensional models were built and showed electrostatic potential modification in the mutant receptor. With these results and together with those in the scientific literature, we can conclude that amber colour in NFCs is caused by a single MC1R allele called e, which has never been documented.
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Affiliation(s)
- M Peterschmitt
- Université de Lyon, Ecole Nationale Vétérinaire de Lyon, Unité Génétique & Biologie Moléculaire et Laboratoire Vétérinaire Départemental du Rhône, F-69280 Marcy l'Etoile, France
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30
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Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, Stahler DR, Smith DW, Padhukasahasram B, Randi E, Leonard JA, Bustamante CD, Ostrander EA, Tang H, Wayne RK, Barsh GS. Molecular and evolutionary history of melanism in North American gray wolves. Science 2009; 323:1339-43. [PMID: 19197024 DOI: 10.1126/science.1165448] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the Melanocortin 1 receptor (Mc1r) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the gray wolf, Canis lupus, is caused by a different melanocortin pathway component, the K locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic K locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the coyote, Canis latrans, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence the morphological diversity of their wild relatives.
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Affiliation(s)
- Tovi M Anderson
- Departments of Genetics and Pediatrics, Stanford University, Stanford, CA 94305, USA
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Abstract
Alternating patches of black and yellow pigment are a ubiquitous feature of mammalian color variation that contributes to camouflage, species recognition, and morphologic diversity. X-linked determinants of this pattern--recognized by variegation in females but not in males--have been described in the domestic cat as Orange, and in the Syrian hamster as Sex-linked yellow (Sly), but are curiously absent from other vertebrate species. Using a comparative genomic approach, we develop molecular markers and a linkage map for the euchromatic region of the Syrian hamster X chromosome that places Sly in a region homologous to the centromere-proximal region of human Xp. Comparison to analogous work carried out for Orange in domestic cats indicates, surprisingly, that the cat and hamster mutations lie in nonhomologous regions of the X chromosome. We also identify the molecular cause of recessively inherited black coat color in hamsters (historically referred to as nonagouti) as a Cys115Tyr mutation in the Agouti gene. Animals doubly mutant for Sly and nonagouti exhibit a Sly phenotype. Our results indicate that Sly represents a melanocortin pathway component that acts similarly to, but is genetically distinct from, Mc1r and that has implications for understanding both the evolutionary history and the mutational mechanisms of pigment-type switching.
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Characterization of the effect of Melanocortin 1 Receptor, a member of the hair color genetic locus, in alpaca (Lama pacos) fleece color differentiation. Small Rumin Res 2008. [DOI: 10.1016/j.smallrumres.2008.07.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Collier RJ, Collier JL, Rhoads RP, Baumgard LH. Invited review: genes involved in the bovine heat stress response. J Dairy Sci 2008; 91:445-54. [PMID: 18218730 DOI: 10.3168/jds.2007-0540] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The cellular heat stress (HS) response is one component of the acute systemic response to HS. Gene networks within and across cells and tissues respond to environmental heat loads above the thermoneutral zone with both intra- and extracellular signals that coordinate cellular and whole-animal metabolism. Activation of these systems appears to be initiated at skin surface temperatures exceeding 35 degrees C as animals begin to store heat and rapidly increase evaporative heat loss (EVHL) mechanisms. Gene expression changes include 1) activation of heat shock transcription factor 1 (HSF1); 2) increased expression of heat shock proteins (HSP) and decreased expression and synthesis of other proteins; 3) increased glucose and amino acid oxidation and reduced fatty acid metabolism; 4) endocrine system activation of the stress response; and 5) immune system activation via extracellular secretion of HSP. If the stress persists, these gene expression changes lead to an altered physiological state referred to as "acclimation," a process largely controlled by the endocrine system. In the acclimated state, metabolism is adjusted to minimize detrimental effects of increased thermal heat load. The role of secreted HSP in feedback regulation of the immune and endocrine system has not yet been investigated. The variation in EVHL among animals and the central role that HSF1 has in coordinating thermal tolerance suggest that there is opportunity to improve thermal tolerance via gene manipulation. Determining the basis for altered energy metabolism during thermal stress will lead to opportunities for improved animal performance via altered nutritional management.
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Affiliation(s)
- R J Collier
- Department of Animal Sciences, University of Arizona, Tucson, AZ 85721, USA.
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Chapter 6 New Insights into Melanosome Transport in Vertebrate Pigment Cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 272:245-302. [DOI: 10.1016/s1937-6448(08)01606-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Candille SI, Kaelin CB, Cattanach BM, Yu B, Thompson DA, Nix MA, Kerns JA, Schmutz SM, Millhauser GL, Barsh GS. A -defensin mutation causes black coat color in domestic dogs. Science 2007; 318:1418-23. [PMID: 17947548 PMCID: PMC2906624 DOI: 10.1126/science.1147880] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Genetic analysis of mammalian color variation has provided fundamental insight into human biology and disease. In most vertebrates, two key genes, Agouti and Melanocortin 1 receptor (Mc1r), encode a ligand-receptor system that controls pigment type-switching, but in domestic dogs, a third gene is implicated, the K locus, whose genetic characteristics predict a previously unrecognized component of the melanocortin pathway. We identify the K locus as beta-defensin 103 (CBD103) and show that its protein product binds with high affinity to the Mc1r and has a simple and strong effect on pigment type-switching in domestic dogs and transgenic mice. These results expand the functional role of beta-defensins, a protein family previously implicated in innate immunity, and identify an additional class of ligands for signaling through melanocortin receptors.
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Affiliation(s)
- Sophie I. Candille
- Departments of Genetics and Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Bruce M. Cattanach
- Medical Research Council (MRC) Mammalian Genetics Unit, Harwell, Oxfordshire, OX11 ORD, UK
| | - Bin Yu
- Departments of Chemistry and Biochemistry, University of California at Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Darren A. Thompson
- Departments of Chemistry and Biochemistry, University of California at Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Matthew A. Nix
- Departments of Chemistry and Biochemistry, University of California at Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Julie A. Kerns
- Departments of Genetics and Pediatrics, Stanford University, Stanford, CA, USA
| | - Sheila M. Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon S7N 5A8, Canada
| | - Glenn L. Millhauser
- Departments of Chemistry and Biochemistry, University of California at Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Gregory S. Barsh
- Departments of Genetics and Pediatrics, Stanford University, Stanford, CA, USA
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GAN HY, LI JB, WANG HM, GAO YD, LIU WH, LI JP, ZHONG JF. Allele frequencies of TYR and MC1R in Chinese native cattle. Anim Sci J 2007. [DOI: 10.1111/j.1740-0929.2007.00466.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kerns JA, Cargill EJ, Clark LA, Candille SI, Berryere TG, Olivier M, Lust G, Todhunter RJ, Schmutz SM, Murphy KE, Barsh GS. Linkage and segregation analysis of black and brindle coat color in domestic dogs. Genetics 2007; 176:1679-89. [PMID: 17483404 PMCID: PMC1931550 DOI: 10.1534/genetics.107.074237] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutations of pigment type switching have provided basic insight into melanocortin physiology and evolutionary adaptation. In all vertebrates that have been studied to date, two key genes, Agouti and Melanocortin 1 receptor (Mc1r), encode a ligand-receptor system that controls the switch between synthesis of red-yellow pheomelanin vs. black-brown eumelanin. However, in domestic dogs, historical studies based on pedigree and segregation analysis have suggested that the pigment type-switching system is more complicated and fundamentally different from other mammals. Using a genomewide linkage scan on a Labrador x greyhound cross segregating for black, yellow, and brindle coat colors, we demonstrate that pigment type switching is controlled by an additional gene, the K locus. Our results reveal three alleles with a dominance order of black (K(B)) > brindle (k(br)) > yellow (k(y)), whose genetic map position on dog chromosome 16 is distinct from the predicted location of other pigmentation genes. Interaction studies reveal that Mc1r is epistatic to variation at Agouti or K and that the epistatic relationship between Agouti and K depends on the alleles being tested. These findings suggest a molecular model for a new component of the melanocortin signaling pathway and reveal how coat-color patterns and pigmentary diversity have been shaped by recent selection.
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Affiliation(s)
- Julie A Kerns
- Department of Genetics, Stanford University, Stanford, California 94035, USA
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Fontanesi L, Tazzoli M, Beretti F, Russo V. Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domestic rabbit (Oryctolagus cuniculus). Anim Genet 2006; 37:489-93. [PMID: 16978179 DOI: 10.1111/j.1365-2052.2006.01494.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We sequenced almost the complete coding region of the MC1R gene in several domestic rabbits (Oryctolagus cuniculus) and identified four alleles: two wild-type alleles differing by two synonymous single nucleotide polymorphisms (c.333A>G;c.555T>C), one allele with a 30-nucleotide in-frame deletion (c.304_333del30) and one allele with a 6-nucleotide in-frame deletion (c.280_285del6). A polymerase chain reaction-based protocol was used to distinguish the wild-type alleles from the other two alleles in 263 rabbits belonging to 37 breeds or strains. All red/fawn/yellow rabbits were homozygous for the c.304_333del30 allele. This allele represents the recessive e allele at the extension locus identified through pioneering genetic studies in this species. All Californian, Checkered, Giant White and New Zealand White rabbits were homozygous for allele c.280_285del6, which was also observed in the heterozygous condition in a few other breeds. Black coat colour is part of the standard colour in Californian and Checkered breeds, in contrast to the two albino breeds, Giant White and New Zealand White. Following the nomenclature established for the rabbit extension locus, the c.280_285del6 allele, which is dominant over c.304_333del30, may be allele E(D) or allele E(S).
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Affiliation(s)
- L Fontanesi
- DIPROVAL, Sezione di Allevamenti Zootecnici, Faculty of Agriculture, University of Bologna, Via F.lli Rosselli 107, Villa Levi - Coviolo, 42100 Reggio Emilia, Italy.
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Berryere TG, Kerns JA, Barsh GS, Schmutz SM. Association of an Agouti allele with fawn or sable coat color in domestic dogs. Mamm Genome 2005; 16:262-72. [PMID: 15965787 DOI: 10.1007/s00335-004-2445-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Accepted: 01/12/2005] [Indexed: 10/25/2022]
Abstract
The type of pigment synthesized in mammalian hair, yellow-red pheomelanin or black-brown eumelanin, depends on the interaction between Agouti protein and the Melanocortin 1 receptor. Although the genetics of pigmentation is broadly conserved across most mammalian species, pigment type-switching in domestic dogs is unusual because a yellow-tan coat with variable amounts of dark hair is thought to be caused by an allele of the Agouti locus referred to as fawn or sable (a(y)). In a large survey covering thirty seven breeds, we identified an Agouti allele with two missense alterations, A82S and R83H, which was present (heterozygous or homozygous) in 41 dogs (22 breeds) with a fawn or sable coat, but was absent from 16 dogs (8 breeds) with a black-and-tan or tricolor phenotype. In an additional 33 dogs (14 breeds) with a eumelanic coat, 8 (German Shepherd Dogs, Groenendaels, Schipperkes, or Shetland Sheepdogs) were homozygous for a previously reported mutation, non-agouti R96C; the remainder are likely to have carried dominant black, which is independent of and epistatic to Agouti. This work resolves some of the complexity in dog coat color genetics and provides diagnostic opportunities and practical guidelines for breeders.
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Affiliation(s)
- Tom G Berryere
- Department of Animal and Poultry Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, Saskatchewan, Canada S7N 5A8
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