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Giuliotti L, Benvenuti MN, Preziuso G, Ventura E, Fresi P, Cecchi F. Demography and Genealogical Analysis of Massese Sheep, a Native Breed of Tuscany. Animals (Basel) 2024; 14:582. [PMID: 38396550 PMCID: PMC10886389 DOI: 10.3390/ani14040582] [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: 12/13/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population-WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007-2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average FPED of 13.56%, and 2713 in the RP, with an average FPED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates.
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Affiliation(s)
- Lorella Giuliotti
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Maria Novella Benvenuti
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Giovanna Preziuso
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
| | - Emilia Ventura
- Veterinarian Free lance, Via dell’alberaccio 15, 56017 San Giuliano Terme, Italy;
| | - Pancrazio Fresi
- Asso.Na.Pa (Associazione Nazionale della Pastorizia), Via XXIV Maggio 44, 00187 Roma, Italy;
| | - Francesca Cecchi
- Department of Veterinary Science, Università di Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.N.B.); (G.P.); (F.C.)
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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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Ji RL, Tao YX. Melanocortin-1 receptor mutations and pigmentation: Insights from large animals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:179-213. [PMID: 35595349 DOI: 10.1016/bs.pmbts.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The melanocortin-1 receptor (MC1R) is a G protein-coupled receptor expressed in cutaneous and hair follicle melanocytes, and plays a central role in coat color determination in vertebrates. Numerous MC1R variants have been identified in diverse species. Some of these variants have been associated with specific hair and skin color phenotypes in humans as well as coat color in animals. Gain-of-function mutations of the MC1R gene cause dominant or partially dominant black/dark coat color, and loss-of-function mutations of the MC1R gene cause recessive or partially recessive red/yellow/pale coat color phenotypes. These have been well documented in a large number of mammals, including human, dog, cattle, horse, sheep, pig, and fox. Higher similarities between large mammals and humans makes them better models to understand pathogenesis of human diseases caused by MC1R mutations. High identities in MC1Rs and similar variants identified in both humans and large mammals also provide an opportunity for receptor structure and function study. In this review, we aim to summarize the naturally occurring mutations of MC1R in humans and large animals.
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Affiliation(s)
- Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States.
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Giantsis IA, Antonopoulou D, Dekolis N, Zaralis K, Avdi M. Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep. Trop Anim Health Prod 2022; 54:73. [PMID: 35072809 DOI: 10.1007/s11250-022-03081-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
Abstract
Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.
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Affiliation(s)
- Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.
| | - Danai Antonopoulou
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.,Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Dekolis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Zaralis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece
| | - Melpomeni Avdi
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
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DHANDAPANI S, VOHRA VIKAS, MUKESH M, KUMAR SANJAY, MEHRARA KL, SINGH KP, KUMARI NAMITA, KATARIA RS. Revealing inheritance of white markings in Nili Ravi buffalo. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v91i3.114150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Among registered Indian buffalo breeds, Nili Ravi is well known for its production potential as well as unique typical five white markings, because of which it is also known as Panch-Kalyani. In this study an attempt was made to understand the inheritance pattern of white markings in 720 progenies sired by 21 bulls and belonging to 381 dams at an organized farm. Based on extent of white markings, animals were classified into typical, under and over white categories and significance of inheritance was tested by Chi- Square, Likelihood ratio and Mc-NemarBowker tests to confirm the results. The results showed distribution of inheritance pattern from sire to progeny, and dam to progeny was that the identical in white markings classes ratios and inheritance of skin/coat colour patterns could not be explained. Further, studies at genomic and epigenetic levels needed to reveal the genetic/methylation differentiation basis of white markings variation in Nili Ravi buffalo.
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Tsunoi T, Noju K, Eto T, Suzuki H. A 1-bp deletion in Mc1r in a Norway rat (Rattus norvegicus) from Sado Island, Japan gives rise to a yellowish color variant: an insight into mammalian MC1R variants. Genes Genet Syst 2021; 96:89-97. [PMID: 33994400 DOI: 10.1266/ggs.20-00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The melanocortin-1 receptor gene (MC1R) controls production of the pigments eumelanin and pheomelanin. Changes in MC1R lead to variation in coat color in mammals, which can range from entirely black (melanism) to yellowish. In this study, we report a case of a wild-caught Norway rat (Rattus norvegicus) from Sado Island, Japan with a yellowish coat color. Upon sequencing the whole coding region of the Mc1r gene (954 bp), we found a 1-bp deletion at site 337 (c.337del), indicative of a frameshift mutation, which was characterized as a severe loss-of-function or null mutation. A spectrophotometer was used to measure coat color, revealing that the rat had a distinctly lighter coat, based on lightness score, than mice with homozygous similar loss-of-function mutations. This implies that loss-of-function mutations can yield different phenotypes in murine rodents. The loss-of-function-mutant rat exhibited a contrasting coat pattern consisting of darker and lighter colors along its dorsal and ventral sides, respectively. Similar patterns have been observed in homozygous MC1R-deficient mutants in other mammals, implying that the countershading pattern can still be expressed despite the absence of MC1R in the melanocyte.
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Affiliation(s)
- Takeru Tsunoi
- Graduate School of Environmental Science, Hokkaido University
| | - Koki Noju
- Graduate School of Science, Hokkaido University
| | - Takeshi Eto
- Faculty of Agriculture, University of the Ryukyus
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University
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Shi X, Wu J, Lang X, Wang C, Bai Y, Riley DG, Liu L, Ma X. Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 2021; 9:e11122. [PMID: 33986980 PMCID: PMC8086576 DOI: 10.7717/peerj.11122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
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Affiliation(s)
- Xiaolei Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Xia Lang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Cailian Wang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China.,Key Laboratory for Sheep, Goat, and Cattle Germplasm and Straw Feed in Gansu Province, Lanzhou, Gansu Province, China
| | - Yan Bai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - David Greg Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Lishan Liu
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xiaoming Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
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8
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Nosrati M, Asadollahpour Nanaei H, Javanmard A, Esmailizadeh A. The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations. Genomics 2021; 113:1407-1415. [PMID: 33705888 DOI: 10.1016/j.ygeno.2021.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 02/21/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (FROH) was 0.09 ± 0.05. It was rising in a stepwise manner with distance from Southwest Asia and maximum values were detected in North European breeds. A total of 465 ROH hotspots were detected in 25 different autosomes which partially surrounding 257 Refseq genes across the genome. Most of the detected genes were related to growth, body weight, meat production and quality, wool production and pigmentation. In conclusion, our analysis showed that the sheep genome, compared with other livestock species such as cattle and pig, displays low levels of homozygosity and appropriate genetic diversity for selection response and genetic merit gain.
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Affiliation(s)
- Maryam Nosrati
- Department of Agriculture, Payame Noor University, PO BOX 19395-3697, Tehran, Iran.
| | - Hojjat Asadollahpour Nanaei
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Arash Javanmard
- Departement of Animal Sceince, Faculty of Agriculture, University of Tabriz, PB 5166616471,Tabriz, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran.
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Reiner G, Weber T, Nietfeld F, Fischer D, Wurmser C, Fries R, Willems H. A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama). BMC Genet 2020; 21:126. [PMID: 33213385 PMCID: PMC7678172 DOI: 10.1186/s12863-020-00950-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele. Conclusions A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00950-3.
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Affiliation(s)
- Gerald Reiner
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany. .,Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany.
| | - Tim Weber
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Florian Nietfeld
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Dominik Fischer
- Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany
| | - Christine Wurmser
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Ruedi Fries
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Hermann Willems
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
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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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11
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Gebreselassie G, Berihulay H, Jiang L, Ma Y. Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep ( Ovies aries). Animals (Basel) 2019; 10:E33. [PMID: 31877963 PMCID: PMC7022721 DOI: 10.3390/ani10010033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in 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 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Department of Agricultural Biotechnology, Biotechnology Center, Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa 1000, Ethiopia
| | - 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 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, 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 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - 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 100193, China; (G.G.); (H.B.); (L.J.)
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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12
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Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Anim Genet 2019; 50:712-717. [PMID: 31475378 DOI: 10.1111/age.12837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 01/03/2023]
Abstract
By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.
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Affiliation(s)
- C M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden.,UFR Génétique, Élevage et Reproduction, Sciences de la Vie et Santé, AgroParisTech, Université Paris Saclay, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France.,Génétique Physiologie Systèmes d'Elevage, Animal Genetics Division, INRA, 24 chemin de Borde-Rouge-Auzeville Tolosane, F-31326 Castanet-Tolosan, France
| | - K Westberg Sunesson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - E Jonas
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
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13
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Ganbold O, Manjula P, Lee SH, Paek WK, Seo D, Munkhbayar M, Lee JH. Sequence characterization and polymorphism of melanocortin 1 receptor gene in some goat breeds with different coat color of Mongolia. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:939-948. [PMID: 30744336 PMCID: PMC6601070 DOI: 10.5713/ajas.18.0819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/08/2019] [Indexed: 11/27/2022]
Abstract
Objective Extension and Agouti loci play a key role for proportions of eumelanin and pheomelanin in determining coat color in several species, including goat. Mongolian goats exhibit diverse types of coat color phenotypes. In this study, investigation of the melanocortin 1 receptor (MC1R) coding region in different coat colors in Mongolian goats was performed to ascertain the presence of the extension allele. Methods A total of 105 goat samples representing three goat breeds were collected for this study from middle Mongolia. A 938 base pair (bp) long coding region of the MC1R gene was sequenced for three different breeds with different coat colors (Gobi Gurwan Saikhan: complete black, Zalaa Jinstiin Tsagaan: complete white, Mongolian native goat: admixture of different of coat colors). The genotypes of these goats were obtained from analyzing and comparing the sequencing results. Results A total of seven haplotypes defined by five substitution were identified. The five single nucleotide polymorphisms included two synonymous mutations (c.183C>T and c.489G>A) and three missense (non-synonymous) mutations (c.676A>G, c.748T>G, and c.770T>A). Comparison of genotypes frequencies of two common missense mutions using chi-sqaure (x2) test revealed significant differences between coat color groups (p<0.001). A logistic regression analysis additionally suggested highly significant association between genotypes and variation of black versus white uniform combination. Alternatively, most investigated goats (60.4%) belonged to H2 (TGAGT) haplotype. Conclusion According to the findings obtained in this study on the investigated coat colors, mutations in MC1R gene may have the crucial role for determining eumelanin and pheomelanin phenotypes. Due to the complication of coat color phenotype, more detailed investigation needed.
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Affiliation(s)
- Onolragchaa Ganbold
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea.,Department of Biological Science, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Prabuddha Manjula
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Seung-Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Woon Kee Paek
- Division of Research and Promotion, National Science Museum of Korea, Daejeon 34143, Korea
| | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Munkhbaatar Munkhbayar
- Department of Biological Science, Mongolian National University of Education, Ulaanbaatar 210685, Mongolia
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
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Koseniuk A, Ropka-Molik K, Rubiś D, Smołucha G. Genetic background of coat colour in sheep. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-173-2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The coat colour of animals is an extremely important trait that affects their
behaviour and is decisive for survival in the natural environment. In farm
animal breeding, as a result of the selection of a certain coat colour type,
animals are characterized by a much greater variety of coat types. This makes
them an appropriate model in research in this field. A very important aspect
of the coat colour types of farm animals is distinguishing between breeds and
varieties based on this trait. Furthermore, for the sheep breeds which are
kept for skins and wool, coat/skin colour is an important economic trait.
Until now the study of coat colour inheritance in sheep proved the dominance
of white colour over pigmented/black coat or skin and of black over brown.
Due to the current knowledge of the molecular basis of ovine coat colour
inheritance, there is no molecular test to distinguish coat colour types in
sheep although some are available for other species, such as cattle, dogs,
and horses. Understanding the genetic background of variation in one of the
most important phenotypic traits in livestock would help to identify new
genes which have a great effect on the coat colour type. Considering that
coat colour variation is a crucial trait for discriminating between breeds
(including sheep), it is important to broaden our knowledge of the genetic
background of pigmentation. The results may be used in the future to
determine the genetic pattern of a breed. Until now, identified candidate
genes that have a significant impact on colour type in mammals mainly code
for factors located in melanocytes. The proposed candidate genes code for the
melanocortin 1 receptor (MC1R), agouti signaling
protein (ASIP), tyrosinase-related protein 1 (TYRP1),
microphthalmia-associated transcription factor MITF, and v-kit
Hardy–Zuckerman 4 feline sarcoma viral oncogene homologue (KIT).
However, there is still no conclusive evidence of established polymorphisms
for specific coat colour types in sheep.
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15
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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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16
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Rochus CM, Tortereau F, Plisson-Petit F, Restoux G, Moreno-Romieux C, Tosser-Klopp G, Servin B. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep. BMC Genomics 2018; 19:71. [PMID: 29357834 PMCID: PMC5778797 DOI: 10.1186/s12864-018-4447-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/11/2018] [Indexed: 01/11/2023] Open
Abstract
Background One of the approaches to detect genetics variants affecting fitness traits is to identify their surrounding genomic signatures of past selection. With established methods for detecting selection signatures and the current and future availability of large datasets, such studies should have the power to not only detect these signatures but also to infer their selective histories. Domesticated animals offer a powerful model for these approaches as they adapted rapidly to environmental and human-mediated constraints in a relatively short time. We investigated this question by studying a large dataset of 542 individuals from 27 domestic sheep populations raised in France, genotyped for more than 500,000 SNPs. Results Population structure analysis revealed that this set of populations harbour a large part of European sheep diversity in a small geographical area, offering a powerful model for the study of adaptation. Identification of extreme SNP and haplotype frequency differences between populations listed 126 genomic regions likely affected by selection. These signatures revealed selection at loci commonly identified as selection targets in many species (“selection hotspots”) including ABCG2, LCORL/NCAPG, MSTN, and coat colour genes such as ASIP, MC1R, MITF, and TYRP1. For one of these regions (ABCG2, LCORL/NCAPG), we could propose a historical scenario leading to the introgression of an adaptive allele into a new genetic background. Among selection signatures, we found clear evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. We confirmed this allelic heterogeneity in one case by resequencing the MC1R gene in three black-faced breeds. Conclusions Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4447-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina Marie Rochus
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France. .,UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France. .,Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Flavie Tortereau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | | | - Gwendal Restoux
- UFR Génétique, Élevage et Reproduction, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France.,Génétique Animale et Biologie Intégrative, INRA, AgroParisTech, Université Paris-Saclay, 752 31, Paris, France
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 313 26, Castanet Tolosan, France
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Stamatis C, Giannoulis T, Galliopoulou E, Billinis C, Mamuris Z. Genetic analysis of melanocortin 1 receptor gene in endangered Greek sheep breeds. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Polymorphisms in MC1R and ASIP genes and their association with coat color phenotypes in llamas (Lama glama). Small Rumin Res 2016. [DOI: 10.1016/j.smallrumres.2016.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Ducret V, Gaigher A, Simon C, Goudet J, Roulin A. Sex-specific allelic transmission bias suggests sexual conflict at MC1R. Mol Ecol 2016; 25:4551-63. [PMID: 27480981 DOI: 10.1111/mec.13781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 02/03/2023]
Abstract
Sexual conflict arises when selection in one sex causes the displacement of the other sex from its phenotypic optimum, leading to an inevitable tension within the genome - called intralocus sexual conflict. Although the autosomal melanocortin-1-receptor gene (MC1R) can generate colour variation in sexually dichromatic species, most previous studies have not considered the possibility that MC1R may be subject to sexual conflict. In the barn owl (Tyto alba), the allele MC1RWHITE is associated with whitish plumage coloration, typical of males, and the allele MC1RRUFOUS is associated with dark rufous coloration, typical of females, although each sex can express any phenotype. Because each colour variant is adapted to specific environmental conditions, the allele MC1RWHITE may be more strongly selected in males and the allele MC1RRUFOUS in females. We therefore investigated whether MC1R genotypes are in excess or deficit in male and female fledglings compared with the expected Hardy-Weinberg proportions. Our results show an overall deficit of 7.5% in the proportion of heterozygotes in males and of 12.9% in females. In males, interannual variation in assortative pairing with respect to MC1R explained the year-specific deviations from Hardy-Weinberg proportions, whereas in females, the deficit was better explained by the interannual variation in the probability of inheriting the MC1RWHITE or MC1RRUFOUS allele. Additionally, we observed that sons inherit the MC1RRUFOUS allele from their fathers on average slightly less often than expected under the first Mendelian law. Transmission ratio distortion may be adaptive in this sexually dichromatic species if males and females are, respectively, selected to display white and rufous plumages.
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Affiliation(s)
- Valérie Ducret
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland.
| | - Arnaud Gaigher
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Céline Simon
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
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Muniz MMM, Caetano AR, McManus C, Cavalcanti LCG, Façanha DAE, Leite JHGM, Facó O, Paiva SR. Application of genomic data to assist a community-based breeding program: A preliminary study of coat color genetics in Morada Nova sheep. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Hepp D, Gonçalves GL, Moreira GRP, de Freitas TRO. Epistatic Interaction of the Melanocortin 1 Receptor and Agouti Signaling Protein Genes Modulates Wool Color in the Brazilian Creole Sheep. J Hered 2016; 107:544-52. [PMID: 27288530 DOI: 10.1093/jhered/esw037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/29/2016] [Indexed: 02/01/2023] Open
Abstract
Different pigmentation genes have been associated with color diversity in domestic animal species. The melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are candidate genes responsible for variation in wool color among breeds of sheep. Although the influence of these genes has been described in some breeds, in many others the effect of interactions among genes underlying wool color has not been investigated. The Brazilian Creole sheep is a local breed with a wide variety of wool color, ranging from black to white with several intermediate hues. We analyzed in this study the influence of the genes MC1R, ASIP, TYRP1, and KIT on the control of wool color in this breed. A total of 410 samples were analyzed, including 148 white and 262 colored individuals. The MC1R and ASIP polymorphisms were significantly associated with the segregation of either white or colored wool. The dominant MC1R allele (E(D) p.M73K and p.D121N) was present only in colored animals. All white individuals were homozygous for the MC1R recessive allele (E(+)) and carriers of the duplicated copy of ASIP A gene expression assay showed that only the carrier of the duplicated copy of ASIP produces increased levels in skin, not detectable in the single homozygous copy. These results demonstrate that the epistatic interaction of the genotypes in the MC1R and ASIP gene is responsible for the striking color variation in the Creole breed.
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Affiliation(s)
- Diego Hepp
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp).
| | - Gislene Lopes Gonçalves
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Gilson Rudinei Pires Moreira
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Thales Renato Ochotorena de Freitas
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
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Yang GL, Fu DL, Lang X, Yan YF, Luo YZ. Genetic variation of 5 SNPs of MC1R gene in Chinese indigenous sheep breeds. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414100159] [Citation(s) in RCA: 2] [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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23
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Fontanesi L, Scotti E, Cisarova K, Battista PD, Dall'Olio S, Fornasini D, Frabetti A. A Missense Mutation in the Rabbit Melanocortin 4 Receptor (MC4R) Gene is Associated with Finisching Weight in a Meat Rabbit Line. Anim Biotechnol 2013; 24:268-77. [DOI: 10.1080/10495398.2013.781034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Mutations in MC1R gene determine black coat color phenotype in Chinese sheep. ScientificWorldJournal 2013; 2013:675382. [PMID: 24082855 PMCID: PMC3776380 DOI: 10.1155/2013/675382] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 07/26/2013] [Indexed: 11/24/2022] Open
Abstract
The melanocortin receptor 1 (MC1R) plays a central role in regulation of animal coat color formation. In this study, we sequenced the complete coding region
and parts of the 5′- and 3′-untranslated regions of the MC1R gene in Chinese sheep with completely
white (Large-tailed Han sheep), black (Minxian Black-fur sheep), and brown coat colors (Kazakh Fat-Rumped sheep). The results showed five single nucleotide
polymorphisms (SNPs): two non-synonymous mutations previously associated with coat color (c.218 T>A, p.73 Met>Lys. c.361 G>A, p.121 Asp>Asn)
and three synonymous mutations (c.429 C>T, p.143 Tyr>Tyr; c.600 T>G, p.200 Leu>Leu. c.735 C>T, p.245 Ile>Ile). Meanwhile, all mutations
were detected in Minxian Black-fur sheep. However, the two nonsynonymous mutation sites were not in all studied breeds (Large-tailed Han, Small-tailed Han, Gansu Alpine Merino,
and China Merino breeds), all of which are in white coat. A single haplotype AATGT (haplotype3) was uniquely associated with black coat color in Minxian Black-fur breed (P = 9.72E − 72, chi-square test). The first and second A alleles in this haplotype 3 represent location at 218 and 361 positions, respectively. Our results suggest that the mutations
of MC1R gene are associated with black coat color phenotype in Chinese sheep.
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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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Expression levels of Slc7a11 in the skin of Kazakh sheep with different coat colors. YI CHUAN = HEREDITAS 2012; 34:1314-9. [DOI: 10.3724/sp.j.1005.2012.01314] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hepp D, Gonçalves GL, Moreira GRP, Freitas TRO, Martins CTDC, Weimer TA, Passos DT. Identification of the e allele at the Extension locus (MC1R) in Brazilian Creole sheep and its role in wool color variation. GENETICS AND MOLECULAR RESEARCH 2012; 11:2997-3006. [PMID: 22653672 DOI: 10.4238/2012.may.22.5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The melanocortin 1 receptor (MC1R) gene has been described as responsible for the black color in some breeds of sheep, but little is known about its function in many colored breeds, particularly those with a wide range of pigmentation phenotypes. The Brazilian Creole is a local breed of sheep from southern Brazil that has a wide variety of wool colors. We examined the MC1R gene (Extension locus) to search for the e allele and determine its role in controlling wool color variation in this breed. One hundred and twenty-five animals, covering the most common Creole sheep phenotypes (black, brown, dark gray, light gray, and white), were sequenced to detect the mutations p.M73K and p.D121N. Besides these two mutations, three other synonymous sites (429, 600, and 725) were found. The dominant allele (E(D): p.73K, and p.121N) was found only in colored animals, whereas the recessive allele (E⁺: p.73M, and p.121D) was homozygous only in white individuals. We concluded that MC1R is involved in the control of wool color in Brazilian Creole sheep, particularly the dark phenotypes, although a second gene may be involved in the expression of the white phenotype in this breed.
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Affiliation(s)
- D Hepp
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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Analysis of polymorphisms in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes and association with coat colours in two Pramenka sheep types. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2012.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes. Animal 2012; 5:8-17. [PMID: 22440696 DOI: 10.1017/s1751731110001382] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Massese is an Italian dairy sheep breed characterized by animals with black skin and horns and black or apparent grey hairs. Owing to the presence of these two coat colour types, this breed can be considered an interesting model to evaluate the effects of coat colour gene polymorphisms on this phenotypic trait. Two main loci have been already shown to affect coat colour in sheep: Agouti and Extension coding for the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes, respectively. The Agouti locus is affected by a large duplication including the ASIP gene that may determine the Agouti white and tan allele (A(Wt)). Other disrupting or partially inactivating mutations have been identified in exon 2 (a deletion of 5 bp, D(5); and a deletion of 9 bp, D(9)) and in exon 4 (g.5172T>A, p.C126S) of the ASIP gene. Three missense mutations in the sheep MC1R gene cause the dominant black E(D) allele (p.M73K and p.D121N) and the putative recessive e allele (p.R67C). Here, we analysed these ASIP and MC1R mutations in 161 Massese sheep collected from four flocks. The presence of one duplicated copy allele including the ASIP gene was associated with grey coat colour (P = 9.4E-30). Almost all animals with a duplicated copy allele (37 out of 41) showed uniform apparent grey hair and almost all animals without a duplicated allele (117 out of 120) were completely black. Different forms of duplicated alleles were identified in Massese sheep including, in almost all cases, copies with exon 2 disrupting or partially inactivating mutations making these alleles different from the A(Wt) allele. A few exceptions were observed in the association between ASIP polymorphisms and coat colour: three grey sheep did not carry any duplicated copy allele and four black animals carried a duplicated copy allele. Of the latter four sheep, two carried the E(D) allele of the MC1R gene that may be the cause of their black coat colour. The coat colour of all other black animals may be determined by non-functional ASIP alleles (non-agouti alleles, A(a)) and in a few cases by the E(D) Extension allele. At least three frequent ASIP haplotypes ([D(5):g.5172T], [N:g.5172A] and [D(5):g.5172A]) were detected (organized into six different diplotypes). In conclusion, the results indicated that coat colours in the Massese sheep breed are mainly derived by combining ASIP and MC1R mutations.
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Xi D, Liu Q, Huo Y, Sun Y, Leng J, Gou X, Mao H, Deng W. Nucleotide diversity of the melanocortin 1 receptor gene (MC1R) in the gayal (Bos frontalis). Mol Biol Rep 2012; 39:7293-301. [PMID: 22307797 DOI: 10.1007/s11033-012-1559-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 01/24/2012] [Indexed: 02/02/2023]
Abstract
The melanocortin 1 receptor gene (MC1R) plays a crucial role in determining coat colour of mammals. To investigate the relationship of polymorphism of the MC1R with coat colour in gayal, the coding sequence (CDS), and the 5'- and 3'-untranslated regions (UTR) of the MC1R were sequenced from 63 samples from the gayal and compared with the sequences of the MC1R from other ruminant species. A sequence of 1,136 bp including the whole CDS (954 bp) and parts of the 5'- and 3'-UTR (164 and 18 bp, respectively) of the gayal MC1R was obtained. A total of nine single nucleotide polymorphisms (SNPs) including four SNPs (c.-129T>C, c.-127A>C, c.-106C>T, c.-1G>A) in the 5'-UTR and five SNPs (c.201C>T, c.583C>T, c.663T>C, c.871A>G and c.876T>C) in the CDS were detected, revealing high genetic diversity. Three novel coding SNPs including c.201C>T, c.583C>T and c.876T>C, which have not been reported previously in bovid species, were retrieved. Within five coding SNPs, c.201C>T, c.663T>C and c.876T>C were silent mutations, while c.583C>T and c.871A>G were mis-sense mutations, resulting in changes in the amino acids located in the fifth (p.L195F) and seventh (p.T291A) transmembrane regions, respectively. The alignment of amino acid sequences was found to be very similar to those for other bovid species. It was demonstrated, using the functional effect prediction, that the p.T291A amino acid replacement could have an effect on MC1R protein function but not for the p.L195F substitution. Using phylogenetic analyses it was revealed that the gayal has a close genetic relationship with the yak. However, three classical bovine MC1R loci the E (D), E (+) and e were not retrieved in the gayal, indicating other genes or factors could affect coat colour in this species.
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Affiliation(s)
- Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products. J DAIRY RES 2011; 78:122-8. [DOI: 10.1017/s0022029910000890] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set up a DNA based protocol for authentication of Massese dairy products, we further investigated the presence and distribution of one of these SNPs (c.-31G>A) in 143 Massese sheep and in another 13 sheep breeds (for a total of 351 animals). The Massese breed was fixed for allele c.-31A, whereas in all other breeds allele c.-31 G was the most frequent or with frequency of 0·50. At the same nucleotide position the cattleMC1Rgene carries the G nucleotide. Using these data we developed a method to detect adulterating milk (from other sheep breeds or from cow) in Massese dairy products based on the analysis of the c.-31G>A SNP. We first tested the sensitivity of the protocol and then applied it to analyse DNA extracted from ricotta and Pecorino cheese obtained with only Massese milk or obtained with unrestricted sheep and cattle milk. To our knowledge, this system represents the first one that can be used for breed authentication of a sheep production and that, at the same time, can reveal frauds derived from the admixture of milk of an unreported species.
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