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Otte PJ, Cromsigt JPGM, Smit C, Hofmeester TR. Snow cover-related camouflage mismatch increases detection by predators. J Exp Zool A Ecol Integr Physiol 2024; 341:327-337. [PMID: 38247310 DOI: 10.1002/jez.2784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Camouflage expressed by animals is an adaptation to local environments that certain animals express to maximize survival and fitness. Animals at higher latitudes change their coat color according to a seasonally changing environment, expressing a white coat in winter and a darker coat in summer. The timing of molting is tightly linked to the appearance and disappearance of snow and is mainly regulated by photoperiod. However, due to climate change, an increasing mismatch is observed between the coat color of these species and their environment. Here, we conducted an experiment in northern Sweden, with white and brown decoys to study how camouflage (mis)-match influenced (1) predator attraction to decoys, and (2) predation events. Using camera trap data, we showed that mismatching decoys attracted more predators and experienced a higher likelihood of predation events in comparison to matching decoys, suggesting that camouflage mismatched animals experience increased detection by predators. These results provide insight into the function of a seasonal color coat and the need for this adaptation to maximize fitness in an environment that is exposed to high seasonality. Thus, our results suggest that, with increasing climate change and reduced snow cover, animals expressing a seasonal color coat will experience a decrease in survival.
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Affiliation(s)
- Pieter J Otte
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joris P G M Cromsigt
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Zoology, Centre for African Conservation Ecology, Nelson Mandela University, Gqeberha, South Africa
| | - Christian Smit
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Tim R Hofmeester
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
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2
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Hempel E, Faith JT, Preick M, de Jager D, Barish S, Hartmann S, Grau JH, Moodley Y, Gedman G, Pirovich KM, Bibi F, Kalthoff DC, Bocklandt S, Lamm B, Dalén L, Westbury MV, Hofreiter M. Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size. Curr Biol 2024:S0960-9822(24)00391-9. [PMID: 38614080 DOI: 10.1016/j.cub.2024.03.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/09/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.1,2,3,4,5,6 Moreover, small population size may promote gene flow with congeners and outbreeding depression.7,8,9,10,11,12,13 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,14,15 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.16,17,18 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species' unique traits.
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Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany.
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, 301 Wakara Way, Salt Lake City, UT 84108, USA; Department of Anthropology, University of Utah, 260 South Central Campus Drive, Salt Lake City, UT 84112, USA; Origins Centre, University of the Witwatersrand, 2000 Johannesburg, Republic of South Africa
| | - Michaela Preick
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Deon de Jager
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - José H Grau
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA; Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | | | - Faysal Bibi
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniela C Kalthoff
- Swedish Museum of Natural History, Department of Zoology, Box 50007, 10405 Stockholm, Sweden
| | | | - Ben Lamm
- Colossal Biosciences, Dallas, TX 75247, USA
| | - Love Dalén
- Swedish Museum of Natural History, Department of Bioinformatics and Genetics, Box 50007, 10405 Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20c, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, 10691 Stockholm, Sweden.
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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3
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Honkanen L, Loechel R, Davison S, Donner J, Anderson H. Canine coat color E locus updates: Identification of a new MC1R variant causing 'sable' coat color in English Cocker Spaniels and a proposed update to the E locus dominance hierarchy. Anim Genet 2024; 55:291-295. [PMID: 38282569 DOI: 10.1111/age.13398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
The coat color phenotype 'sable' occurs in the English Cocker Spaniel dog breed. It closely resembles other canine color patterns known as domino/grizzle/pied (eA allele) and grizzle/domino (eG allele) determined by variants in the melanocortin 1 receptor gene (MC1R; 'extension' or E locus), a key multi-allele regulator of coat color. We examined genetic variation in MC1R, and found one new non-synonymous variant, c.250G>A (p.(Asp84Asn)), consistently associated with the English Cocker Spaniel 'sable' phenotype. We propose calling this newly identified allele eH and further show that the eA , eH and eG (previously known as EG ) alleles associate with similar phenotypes in dogs impacting genotypes regulated by beta-defensin 103 gene (CBD103; K locus) and agouti signaling protein gene (ASIP; A locus) in the absence of the EM and E alleles. This suggests that all three alleles are putative reduced-function variants of the MC1R gene. We propose the revised and updated E locus dominance hierarchy to be EM > E > eA /eH /eG > e1-3 .
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Affiliation(s)
- Leena Honkanen
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | | | - Stephen Davison
- Wisdom Panel, Mars Petcare Science & Diagnostics, Leicestershire, UK
| | - Jonas Donner
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
| | - Heidi Anderson
- Wisdom Panel, Mars Petcare Science & Diagnostics, Helsinki, Finland
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Hu Z, Su Y, Zong W, Niu N, Zhao R, Liang R, Wang L, Zhang Y, Zhang L. Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color. Animals (Basel) 2024; 14:699. [PMID: 38473084 DOI: 10.3390/ani14050699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 03/14/2024] Open
Abstract
The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.
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Affiliation(s)
- Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Ruiping Liang
- Beijing Changping District Center for Animal Disease Prevention and Control, Beijing 102200, China
| | - Lixian Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
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5
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Hong R, Yan Y, Zhu C, Zuo F, Zhang GW. Rapid genotyping of bovine MC1R gene c.296T>C and c.310delG haplotypes using high-resolution melting analysis. Anim Genet 2024; 55:173-174. [PMID: 37873887 DOI: 10.1111/age.13373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Affiliation(s)
- Rui Hong
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yi Yan
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Changhong Zhu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Chongqing, China
| | - Gong-Wei Zhang
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Chongqing, China
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6
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Liu S, Su J, Yang Q, Sun M, Wang Z, Yu J, Jafari H, Lei C, Sun Y, Dang R. Genome-wide analyses based on a novel donkey 40K liquid chip reveal the gene responsible for coat color diversity in Chinese Dezhou donkey. Anim Genet 2024; 55:140-146. [PMID: 37994172 DOI: 10.1111/age.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/28/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023]
Abstract
Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome-wide association analysis was performed for the differences in coat color traits between the Sanfen (n = 97) and Wutou (n = 108) strains using a novel donkey 40K liquid chip developed based on GenoBaits technology, to identify genomic regions and causal genes that could explain this variation. We also used FST and The cross-population composite likelihood ratio test (XPCLR) analyses to explore selected regions related to coat color differences. We identified one significant region on chromosome 15, with the most significant SNP located within the agouti signaling protein (ASIP) gene. At the same time, both FST and XPCLR methods detected the same selected region on chromosome 15, and ASIP was the gene with the strongest signal. ASIP and melanocortin 1 receptor (MC1R) control the ratio of eumelanin to pheomelanin through their protein activity. They are deeply involved in the process of melanosome organation and melanogenesis, thus affecting mammals' coat color variation. We used a range of genome-wide approach to identify the genetic basis of coat color variation in Dezhou donkeys. The results provide a supplement to the color variation study in Chinese donkeys at the genome-wide level, and preliminarily verified the reliability of the Molbreeding Donkey No. 1 40K liquid chip.
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Affiliation(s)
- Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jiangtian Su
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Qiwen Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Minhao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zhaofei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Halima Jafari
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
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7
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McFadden A, Vierra M, Martin K, Brooks SA, Everts RE, Lafayette C. Spotting the Pattern: A Review on White Coat Color in the Domestic Horse. Animals (Basel) 2024; 14:451. [PMID: 38338094 PMCID: PMC10854722 DOI: 10.3390/ani14030451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Traits such as shape, size, and color often influence the economic and sentimental value of a horse. Around the world, horses are bred and prized for the colors and markings that make their unique coat patterns stand out from the crowd. The underlying genetic mechanisms determining the color of a horse's coat can vary greatly in their complexity. For example, only two genetic markers are used to determine a horse's base coat color, whereas over 50 genetic variations have been discovered to cause white patterning in horses. Some of these white-causing mutations are benign and beautiful, while others have a notable impact on horse health. Negative effects range from slightly more innocuous defects, like deafness, to more pernicious defects, such as the lethal developmental defect incurred when a horse inherits two copies of the Lethal White Overo allele. In this review, we explore, in detail, the etiology of white spotting and its overall effect on the domestic horse to Spot the Pattern of these beautiful (and sometimes dangerous) white mutations.
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Affiliation(s)
- Aiden McFadden
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Micaela Vierra
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Katie Martin
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Samantha A. Brooks
- Department of Animal Sciences, UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA;
| | - Robin E. Everts
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
| | - Christa Lafayette
- Etalon Inc., Menlo Park, CA 94025, USA; (M.V.); (K.M.); (R.E.E.); (C.L.)
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8
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Wang J, Fan T, Du Z, Xu L, Chen Y, Zhang L, Gao H, Li J, Ma Y, Gao X. Genome-Wide Association Analysis Identifies the PMEL Gene Affecting Coat Color and Birth Weight in Simmental × Holstein. Animals (Basel) 2023; 13:3821. [PMID: 38136858 PMCID: PMC10740715 DOI: 10.3390/ani13243821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, PMEL_1, rs134930689, rs383170073, rs109924971, and rs109146332), and these were in RNF41, ZC3H10, ERBB3, PMEL, and OR10A7 on BTA5. Interestingly, rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, and PMEL_1 showed strong linkage disequilibrium (r2 > 0.8) and were significantly associated with coat color. Notably, Hypotrichosis_PMel17 and PMEL_1 were located in the gene PMEL (p = 2.22 × 10-18). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with Hypotrichosis_PMel17 and PMEL_1 genotypes was significantly greater than that of homozygous individuals (0.01 < p < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (p < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, PMEL appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight.
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Affiliation(s)
- Jing Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Tingting Fan
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Zhenwei Du
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
| | - Yi Ma
- Animal Husbandry Institute, Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (T.F.); (Z.D.); (L.X.); (Y.C.); (L.Z.); (H.G.); (J.L.)
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9
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Bellone RR, Tanaka J, Esdaile E, Sutton RB, Payette F, Leduc L, Till BJ, Abdel-Ghaffar AK, Hammond M, Magdesian KG. A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family. Anim Genet 2023; 54:752-762. [PMID: 37697831 DOI: 10.1111/age.13352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/12/2023] [Accepted: 08/19/2023] [Indexed: 09/13/2023]
Abstract
Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a de novo variant leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two single nucleotide variants (SNVs) in SOX10, four SNVs in MITF and a 2.3 kb deletion in MITF with the alternative allele present in this stallion but absent in the other 18 horses analyzed. All six SNVs were annotated as modifiers and were not further considered. The deletion in MITF (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses exon 9 encoding a part of the helix-loop-helix domain required for DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a de novo mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8. Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by brainstem auditory evoked response testing. This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants alone have not been connected to deafness. SW8 marks the fourth de novo MITF variant in horses reported to cause white patterning. The link between deafness and all MITF variants with and without other variants impacting melanocyte development and function needs to be further explored.
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Affiliation(s)
- R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - J Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - E Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - R B Sutton
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - F Payette
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - L Leduc
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania School of Veterinary Medicine, University School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - B J Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - A K Abdel-Ghaffar
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - M Hammond
- Veterinary Genetics Laboratory, School of Veterinary Medicine, UC Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, Davis, California, USA
| | - K G Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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10
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Awazu A, Takemoto D, Watanabe K, Sakamoto N. Possibilities of skin coat color-dependent risks and risk factors of squamous cell carcinoma and deafness of domestic cats inferred via RNA-seq data. Genes Cells 2023; 28:893-905. [PMID: 37864512 DOI: 10.1111/gtc.13076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/23/2023]
Abstract
The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color-related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white-spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the first intron of KIT by its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism.
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Affiliation(s)
- Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
| | - Daigo Takemoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kaichi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Naoaki Sakamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics, Hiroshima University, Hiroshima, Japan
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11
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Rajawat D, Panigrahi M, Nayak SS, Ghildiyal K, Sharma A, Kumar H, Parida S, Bhushan B, Gaur GK, Mishra BP, Dutt T. Uncovering genes underlying coat color variation in indigenous cattle breeds through genome-wide positive selection. Anim Biotechnol 2023; 34:3920-3933. [PMID: 37493405 DOI: 10.1080/10495398.2023.2240387] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Subhashree Parida
- Pharmacology and Toxicology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - B P Mishra
- Animal Biotechnology Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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12
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Chen J, Zhang S, Liu S, Dong J, Cao Y, Sun Y. Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds. Anim Biotechnol 2023; 34:1828-1839. [PMID: 35382683 DOI: 10.1080/10495398.2022.2053145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Yanhang Cao
- Modern Animal Husbandry Development Service Center of Dongying, Dongying, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
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13
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Gossett CL, Guyer D, Hein J, Brooks SA. Digital Phenotyping Reveals Phenotype Diversity and Epistasis among White Spotting Alleles in the American Paint Horse. Genes (Basel) 2023; 14:2011. [PMID: 38002953 PMCID: PMC10671537 DOI: 10.3390/genes14112011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/26/2023] Open
Abstract
White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat (% white coat) was measured using digital photograph analysis of 1195 registered American Paint Horses. Genotypes for nine white-spotting polymorphisms commonly found in Paint Horses, and two pigment-producing loci MCIR and ASIP genes, were also provided by the APHA. White-coat percent significantly increased in horses with more white-spotting alleles present, regardless of the number of loci bearing those alleles, likely due to a strong additive genetic effect at each white-spotting locus, as well as an additive epistatic effect among white spotting loci. Paint Horses with a chestnut base coat color (genotype e/e at MC1R) possessed a significantly higher white coat percentage, suggesting confirming an epistatic interaction between pigmentation signaling genes and loci for white spotting. The APHA registry categories of Regular versus Solid Paint-Bred also differed in their median white coat percentage (p < 0.0001), but not in the overall ranges of this phenotype, reenforcing the importance of the regional patterns of the depigmentation in the definition of the desired APHA phenotype. Multi-locus phenotype prediction models for white-coat percentage performed only moderately well, and improvements in the sample size and the number of loci genotyped will likely be needed before such an approach could be used practically by APHA breeders. In the future, models that enable phenotype prediction based on genotypes, and automated phenotype assessment could increase the production of valuable visual traits in the American Paint Horse population and improve the APHA member experience during the registration process.
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Affiliation(s)
- Chelby Lynn Gossett
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
| | - Danielle Guyer
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
| | - Jessica Hein
- American Paint Horse Association, Fort Worth, TX 76161-0023, USA
| | - Samantha A. Brooks
- UF Genetics Institute, University of Florida Department of Animal Sciences, Gainesville, FL 32611-0910, USA
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14
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Encina A, Ligero M, Sánchez-Guerrero MJ, Rodríguez-Sainz de los Terreros A, Bartolomé E, Valera M. Phenotypic and Genetic Study of the Presence of Hair Whorls in Pura Raza Español Horses. Animals (Basel) 2023; 13:2943. [PMID: 37760344 PMCID: PMC10525084 DOI: 10.3390/ani13182943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses with circular hair whorls than with linear whorls. The heritability ranges obtained were, in general, medium-high for both circular whorls (0.20 to 0.90) and linear whorls (0.44 to 0.84). High positive correlations were found on the between left and right positions, indicating a tendency to symmetry in certain locations. The laterality of hair whorls was also evidenced, with the biggest concentration on the left-hand side, particularly in gray horses, showing circular whorls below the central line of eyes, which has been associated in a previous paper with a calmer and more docile temperament.
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Affiliation(s)
- Ana Encina
- Real Asociación Nacional de Criadores de Caballos de Pura Raza Española (ANCCE), 41014 Sevilla, Spain;
| | - Manuel Ligero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - María José Sánchez-Guerrero
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | | | - Ester Bartolomé
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
| | - Mercedes Valera
- Departamento de Agronomía, Escuela Técnica Superior de Ingeniaría Agronómica, Universidad de Sevilla, Carretera de Utrera Km 1, 41013 Sevilla, Spain; (M.L.); (M.J.S.-G.); (E.B.); (M.V.)
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15
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Zhang K, Wang G, Wang L, Wen B, Fu X, Liu N, Yu Z, Jian W, Guo X, Liu H, Chen SY. A genome-wide association study of coat color in Chinese Rex rabbits. Front Vet Sci 2023; 10:1184764. [PMID: 37655262 PMCID: PMC10467280 DOI: 10.3389/fvets.2023.1184764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Coat color is an important phenotypic characteristic of the domestic rabbit (Oryctolagus cuniculus) and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, p = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, p = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein (ASIP) gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that ASIP is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
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Affiliation(s)
- Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Bin Wen
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Ning Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Zhiju Yu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Wensu Jian
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiaolin Guo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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Trigo BB, Alves NF, Milanesi M, Garcia JF, Terefe E, Hanotte O, Tijjani A, Utsunomiya YT. A structural variant at ASIP associated with the darkness of hair coat is found in multiple zebu cattle populations. Anim Genet 2023. [PMID: 37313778 DOI: 10.1111/age.13333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/29/2023] [Accepted: 05/27/2023] [Indexed: 06/15/2023]
Abstract
A structural variant (SV) in the agouti signaling protein gene (ASIP), namely ASIP-SV1, has been found to strongly correlate with the darkness of hair coat in specific regions of the body of bulls from the zebu (Bos indicus) Nellore breed. Here we visually analyzed the whole-genome sequence of zebu and taurine (Bos taurus) cattle to elucidate the extent of spread of ASIP-SV1 in different cattle populations. Of 216 sequences analyzed, 63 zebu (45.9%) and five taurine (6.3%) animals had at least one copy of ASIP-SV1. Four of the taurine animals presenting the SV were Romagnola cattle, a breed with history of zebu introgression. The remaining taurine animal was a Simmental, a breed frequently used in crossbreeding. These data provide evidence that ASIP-SV1 is commonly found in zebu populations, in addition to taurine animals with zebu admixture.
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Affiliation(s)
- Beatriz Batista Trigo
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
- International Atomic Energy Agency (IAEA), Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Natália Fonseca Alves
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
- International Atomic Energy Agency (IAEA), Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Marco Milanesi
- AgroPartners Consulting, Araçatuba, Brazil
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - José Fernando Garcia
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
- International Atomic Energy Agency (IAEA), Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
- AgroPartners Consulting, Araçatuba, Brazil
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Endashaw Terefe
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Habor, Maine, USA
| | - Yuri Tani Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, Brazil
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Jakaria J, Kholijah K, Darwati S, Rahman Q, Daulay WL, Suhendro I, Londra IM, Ulum MF, Noor RR. Open AccessLack of association between coat color abnormalities in Bali cattle ( Bos javanicus) and the coding regions of the MC1R and KIT genes. Vet World 2023; 16:1312-1318. [PMID: 37577199 PMCID: PMC10421557 DOI: 10.14202/vetworld.2023.1312-1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/18/2023] [Indexed: 08/15/2023] Open
Abstract
Background and Aim Coat color variations in cattle are known to be influenced by the melanocortin 1 receptor (MC1R) and receptor tyrosine kinase (KIT) genes. The presence of coat color abnormalities, such as white spots and albinism, in Bali cattle was the focus of this study. This study aimed to identify single nucleotide polymorphisms (SNPs) in the coding region of MC1R and exons 2 and 3 of KIT associated with coat color abnormalities in Bali cattle. Materials and Methods The study included the analysis of 48 Bali cattle, including 20 individuals with standard coat color, 15 with white spots, and 13 with albinism. Total DNA was extracted using a DNA Extraction Kit, and MC1R (coding region) and KIT (exons 2 and 3) gene amplifications were analyzed using forward and reverse primers with polymerase chain reaction product lengths of 1071, 234, and 448 bp, respectively. The determination of MC1R and KIT gene diversity was analyzed through direct sequencing. Melanocortin 1 receptor and KIT gene sequence data were analyzed using BioEdit and MEGA6 to identify SNPs associated with standard and abnormal coat color phenotypes (white-spotted and albino) in Bali cattle. Results No SNPs associated with coat color abnormalities were found in the coding region of MC1R and exons 2 and 3 of KIT genes in Bali cattle. However, the intron two regions of KIT contained the SNP g.70208534A>G, which showed a high degree of diversity. The AA genotype frequency was highest in albino Bali cattle, whereas the G allele frequency was highest and the A allele frequency was lowest in white-spotted Bali cattle. Conclusion The results indicated that standard, white-spotted, and albino coat colors in Bali cattle could not be distinguished by analyzing the MC1R and KIT genes.
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Affiliation(s)
- Jakaria Jakaria
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Kholijah Kholijah
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Sri Darwati
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Qonita Rahman
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Winni Liani Daulay
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Ikhsan Suhendro
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - I. Made Londra
- Agricultural Technology Study Center (BPTP), JL. By Pass Ngurah Rai, Pesanggaran, Denpasar Selatan 80222, Bali, Indonesia
| | - Mokhamad Fakhrul Ulum
- Division of Reproduction and Obstetrics, School of Veterinary Medicine and Biomedical Sciences, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
| | - Ronny Rachman Noor
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University (Bogor Agricultural University), Bogor 16680, Indonesia
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18
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Zhou Q, Cao C, Zhang H, Liang Y, Zhang X, Kang Y, Wenwen F, Lan X, Pan C, Li R. Convergent changes in MC1R gene are associated with black-headed coat color in sheep. J Anim Sci 2023; 101:7080500. [PMID: 36933185 PMCID: PMC10100648 DOI: 10.1093/jas/skad084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
As one of the most obvious phenotypic traits, the coat color of sheep is an ideal model to study the genetic mechanisms underlying coat color varieties of mammals. One distinguishable coat color is the black-headed type, such as the famous black-headed Dorper sheep from Africa and Bayinbuluke sheep from Asia. In this study, we compared the genome sequences of black-headed and all-white sheep to identify causative genes for the black-headed sheep, including black-headed Dorper versus white-headed Dorper, as well as Bayinbuluke (black-headed) versus Small-tailed Han (all-white). The most differentiating region between black-headed sheep and all-white sheep was found to harbor a haplotype covering melanocortin receptor 1 (MC1R) gene. The share of this haplotype by the black-headed sheep from Africa and Asia suggested that the convergent change in the MC1R region is likely to determine this unique coat color. Two missense mutations (g. 14251947T>A and g. 14252090G>A) within this haplotype of MC1R gene were found. We further analyzed whole genome sequence data of 460 world-wide sheep with diverse coat colors and confirmed the association between the MC1R haplotype with pigmentation variations. Our study provides novel insights into coat color genetics in sheep and expands our knowledge of the link between MC1R gene and varying pigmentation patterns in sheep.
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Affiliation(s)
- Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunna Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huanhuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yilin Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyue Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang Wenwen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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19
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Kennah JL, Peers MJL, Vander Wal E, Majchrzak YN, Menzies AK, Studd EK, Boonstra R, Humphries MM, Jung TS, Kenney AJ, Krebs CJ, Boutin S. Coat color mismatch improves survival of a keystone boreal herbivore: Energetic advantages exceed lost camouflage. Ecology 2023; 104:e3882. [PMID: 36208219 DOI: 10.1002/ecy.3882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 02/03/2023]
Abstract
Climate warming is causing asynchronies between animal phenology and environments. Mismatched traits, such as coat color change mismatched with snow, can decrease survival. However, coat change does not serve a singular adaptive benefit of camouflage, and alternate coat change functions may confer advantages that supersede mismatch costs. We found that mismatch reduced, rather than increased, autumn mortality risk of snowshoe hares in Yukon by 86.5% when mismatch occurred. We suggest that the increased coat insulation and lower metabolic rates of winter-acclimatized hares confer energetic advantages to white mismatched hares that reduce their mortality risk. We found that white mismatched hares forage 17-77 min less per day than matched brown hares between 0°C and -10°C, thus lowering their predation risk and increasing survival. We found no effect of mismatch on spring mortality risk, during which mismatch occurred at warmer temperatures, suggesting a potential temperature limit at which the costs of conspicuousness outweigh energetic benefits.
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Affiliation(s)
- Joanie L Kennah
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Michael J L Peers
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Eric Vander Wal
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Yasmine N Majchrzak
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Allyson K Menzies
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Emily K Studd
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Rudy Boonstra
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Murray M Humphries
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
| | - Thomas S Jung
- Department of Environment, Government of Yukon, Whitehorse, Yukon, Canada.,Department of Renewable Resources, University of Alberta, Edmonton, Alberta, Canada
| | - Alice J Kenney
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charles J Krebs
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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20
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Wang L, Zhou S, Liu G, Lyu T, Shi L, Dong Y, He S, Zhang H. The Mechanisms of Fur Development and Color Formation in American Mink Revealed Using Comparative Transcriptomics. Animals (Basel) 2022; 12:ani12223088. [PMID: 36428316 PMCID: PMC9686883 DOI: 10.3390/ani12223088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
American mink fur is an important economic product, but the molecular mechanisms underlying its color formation and fur development remain unclear. We used RNA-seq to analyze the skin transcriptomes of young and adult mink with two different hair colors. The mink comprised black adults (AB), white adults (AW), black juveniles (TB), and white juveniles (TW) (three each). Through pair comparison and cross-screening among different subgroups, we found that 13 KRTAP genes and five signaling pathways (the JAK-STAT signaling pathway (cfa04630), signaling pathways regulating pluripotency of stem cells (cfa04550), ECM-receptor interaction (cfa04512), focal adhesion (cfa04510), and the Ras signaling pathway (cfa04014)) were related to mink fur development. We also found that members of a tyrosinase family (TYR, TYRP1, and TYRP2) are involved in mink hair color formation. The expression levels of TYR were higher in young black mink than in young white mink, but this phenomenon was not observed in adult mink. Our study found significant differences in adult and juvenile mink skin transcriptomes, which may shed light on the mechanisms of mink fur development. At the same time, the skin transcriptomes of black and white mink also showed differences, with the results varying by age, suggesting that the genes regulating hair color are active in early development rather than in adulthood. The results of this study provide molecular support in breeding for mink coat color and improving fur quality.
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Affiliation(s)
- Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Guangshuai Liu
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Tianshu Lyu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Shangbin He
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu 273165, China
- Correspondence:
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21
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Cosso G, Carcangiu V, Luridiana S, Fiori S, Columbano N, Masala G, Careddu GM, Sanna Passino E, Mura MC. Characterization of the Sarcidano Horse Coat Color Genes. Animals (Basel) 2022; 12:2677. [PMID: 36230420 DOI: 10.3390/ani12192677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/24/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
The goal of this study was to contribute to the general knowledge of the Sarcidano Horse, both by the identification of the genetic basis of the coat color and by updating the exact locations of the genotyping sites, based on the current EquCab3.0 genome assembly version. One-hundred Sarcidano Horses, living in semi-feral condition, have been captured to perform health and biometric checks. From that total number, 70 individual samples of whole blood were used for DNA extraction, aimed to characterize the genetic basis of the coat color. By genotyping and sequencing analyses of the MC1R Exon 1 and ASIP Exon 3, a real image of the coat color distribution in the studied population has been obtained. Chestnut and Black resulted in the most representative coat colors both from a phenotypic and genotypic point of view, that is suggestive of no human domestication or crossbreeding with domestic breed. Due to its ancient origin and genetic isolation, an active regional plan for the conservation of this breed would be desirable, focused on maintenance of resident genotypes and genetic resources. Collection and management of DNA, sperm, embryos, with the involvement of research centers and Universities, could be a valid enhancing strategy.
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22
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Esdaile E, Till B, Kallenberg A, Fremeux M, Bickel L, Bellone RR. A de novo missense mutation in KIT is responsible for dominant white spotting phenotype in a Standardbred horse. Anim Genet 2022; 53:534-537. [PMID: 35641888 DOI: 10.1111/age.13222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Brad Till
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Angelica Kallenberg
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Michelle Fremeux
- InfogeneNZ, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Leslie Bickel
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, California, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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23
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Du Z, D’Alessandro E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes. Animals (Basel) 2022; 12:ani12080969. [PMID: 35454216 PMCID: PMC9031378 DOI: 10.3390/ani12080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 12/17/2022] Open
Abstract
The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, Italy;
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
- Correspondence:
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24
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Lan J, Wang M, Qin K, Liu X, Shi X, Sun G, Liu X, Chen Y, He Z. Functional characterization of cAMP signaling of variant porcine MC1R alleles in PK15 cells. Anim Genet 2022; 53:317-326. [PMID: 35292981 DOI: 10.1111/age.13189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/21/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
The melanocortin 1 receptor (MC1R), encoded by the classical extension (E) coat color locus, is expressed on the surface of melanocytes and plays a critical role in switching melanin synthesis from pheomelanin (red/yellow) to eumelanin (black/brown). Different MC1R alleles associated with various coat color patterns in pigs have been identified over the past decades. However, functional analysis of variant porcine MC1R alleles has not yet been performed. Therefore, in this study, we examined the subcellular localization and cyclic adenosine monophosphate (cAMP) signaling capability of MC1R variants in porcine kidney epithelial cells (PK15) overexpressing different MC1R alleles. Transcriptional slippage may partially restore the reading frame of the EP allele, possibly accounting for the observed spot phenotype. The A243T substitution in the e allele severely disrupted the membrane localization of the MC1R receptor, resulting in a severely impaired cAMP signaling capability. Both the V95M and L102P substitutions in the ED1 allele may contribute to the constitutively active function of MC1R, thus accounting for the dominant black phenotype. The D124N substitution in the ED2 allele severely attenuated the cAMP signaling capability of MC1R; however, whether this mutation contributes to the distinct phenotype of Hampshire pigs requires further investigation. Thus, our results provide new insights into the functional characteristics of MC1R variants and their roles in porcine coat color formation.
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Affiliation(s)
- Jin Lan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ke Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaofeng Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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25
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Esdaile E, Kallenberg A, Avila F, Bellone RR. Identification of W13 in the American Miniature Horse and Shetland Pony Populations. Genes (Basel) 2021; 12:1985. [PMID: 34946933 DOI: 10.3390/genes12121985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 11/16/2022] Open
Abstract
Coat color is a trait of economic significance in horses. Variants in seven genes have been documented to cause white patterning in horses. Of the 34 variants that have been identified in KIT proto-oncogene, receptor tyrosine kinase (KIT), 27 have only been reported in a single individual or family and thus not all are routinely offered for genetic testing. Therefore, to enable proper use of marker-assisted selection, determining breed specificity for these alleles is warranted. Screening 19 unregistered all-white Shetland ponies for 16 white patterning markers identified 14 individuals whose phenotype could not be explained by testing results. In evaluating other known dominant white variants, 14 horses were heterozygous for W13. W13 was previously only reported in two quarter horses and a family of Australian miniature horses. Genotyping known white spotting variants in 30 owner-reported white animals (25 Miniature Horses and five Shetland ponies) identified two additional W13/N American Miniature Horses. The estimated allele frequency of W13 in the American Miniature Horse was 0.0063 (79 N/N, 1 W13/N) and the allele was not detected in a random sample (n = 59) of Shetland ponies. No homozygous W13 individuals were identified and W13/N ponies had a similar all-white coat with pink skin phenotype, regardless of the other white spotting variants present, demonstrating that W13 results in a Mendelian inherited dominant white phenotype and homozygosity is likely lethal. These findings document the presence of W13 in the American Miniature Horse and Shetland pony populations at a low frequency and illustrate the importance of testing for this variant in additional breeds.
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26
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Abstract
MiRNAs as a series of small noncoding RNAs that play a crucial part in regulating coat color and hair follicle development. In the previous Solexa sequencing experiments, there were many miRNAs expressed differentially in alpacas with different coat color, including miR-193b.But the mechanism of miR-193b in mammalian pigmentation is still unknown. In this study, bioinformatics analysis showed that WNT10A and GNAI2 might be the target genes of miR-193b. qRT-PCR showed the expression of miR-193b in white Cashmere goats' skins was obviously lower than that in browns, and the expression of WNT10A and GNAI2 were similar with miR-193b. The protein levels of WNT10A and GNAI2 indicated the same findings. Furthermore, the expression of WNT10A and GNAI2 in keratinocytes were analyzed from mRNA and protein levels, the results manifested that the group of overexpression of miR-193b in HaCaT cells increased the expressions of target genes, and miR-193b inhibition group reduced expressions. Luciferase report assays confirmed that the targeting relationship between miR-193b and target genes (WNT10A and GNAI2), the results showed that miR-193b was positively correlated with target genes. These experimental data showed that miR-193b might participate in adjustment of coat color in skin tissue of Cashmere goat by targeting WNT10A and GNAI2.
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Affiliation(s)
- Ba Xiang
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yumei Li
- College of Animal Science, Jilin University, Changchun, China
| | - Jianping Li
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Jianyu Li
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - HuaiZhi Jiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - QiaoLing Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China
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27
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Guan D, Martínez A, Luigi-Sierra MG, Delgado JV, Landi V, Castelló A, Fernández Álvarez J, Such X, Jordana J, Amills M. Detecting the footprint of selection on the genomes of Murciano-Granadina goats. Anim Genet 2021; 52:683-693. [PMID: 34196982 DOI: 10.1111/age.13113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2021] [Indexed: 01/14/2023]
Abstract
Artificial selection is one of the major forces modifying the genetic composition of livestock populations. Identifying genes under selection could be useful to elucidate their impact on phenotypic variation. We aimed to identify genomic regions targeted by selection for dairy and pigmentation traits in Murciano-Granadina goats. Performance of a selection scan based on the integrated haplotype score test in a population of 1183 Murciano-Granadina goats resulted in the identification of 77 candidate genomic regions/SNPs. The most significant selective sweeps mapped to chromosomes 1 (69.86 Mb), 4 (41.80-49.95 Mb), 11 (65.74 Mb), 12 (31.24 and 52.51 Mb), 17 (34.76-37.67 Mb), 22 (31.75 Mb), and 26 (26.69-31.05 Mb). By using previously generated RNA-Seq data, we built a catalogue of 6414 genes that are differentially expressed across goat lactation (i.e. 78 days post-partum, early lactation; 216 days post-partum, late lactation; 285 days post-partum, dry period). Interestingly, 183 of these genes mapped to selective sweeps and several of them display functions related with lipid, protein, and carbohydrate metabolism, insulin signaling, cell proliferation, as well as mammary development and involution. Of particular interest are the CSN3 and CSN1S2 genes, which encode two major milk proteins. Additionally, we found three pigmentation genes (GLI3, MC1R, and MITF) co-localizing with selective sweeps. Performance of a genome-wide association study and Sanger sequencing and TaqMan genotyping experiments revealed that the c.801C>G (p.Cys267Trp) polymorphism in the melanocortin 1 receptor (MC1R) gene is the main determinant of the black (GG or GC genotypes) and brown (CC genotypes) colorations of Murciano-Granadina goats.
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Affiliation(s)
- D Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - M G Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain.,Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, Valenzano, 70010, Italy
| | - A Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Fernández Álvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), Fuente Vaqueros, Granada, 18340, Spain
| | - X Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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28
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Magdesian KG, Tanaka J, Bellone RR. A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse. J Hered 2021; 111:287-293. [PMID: 32242630 PMCID: PMC7238438 DOI: 10.1093/jhered/esaa009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/01/2020] [Indexed: 11/14/2022] Open
Abstract
Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.
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Affiliation(s)
- K Gary Magdesian
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA
| | - Rebecca R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA
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29
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Yuxing Z, Hong W, Li Y. Progress on coat color regulation mechanism and its association with the adaptive evolution in mammals. Yi Chuan 2021; 43:118-133. [PMID: 33724215 DOI: 10.16288/j.yczz.20-390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The various coat colorations exhibited in different mammalian groups is an attractive biological phenomenon, and is also one of the excellent models for studying and understanding mammalian adaptive evolution. Coat color polymorphism in mammals plays an important role in avoiding predator, predation, courtship, and protection against UV radiation. The coloration of hair or coat in mammal is determined by the quantity, quality and distribution of melanin in the body. Pigmentation in cells is a complicated cell process, including the differentiation and maturation of melanocytes, the morphogenesis of melanosome, the anabolism of melanin and the transportation of melanin in melanocytes. Every stage or phase of pigmentation in cells can always proceed with the participation of some important functional genes. The complex regulatory network formed through interactions between these genes has greatly led to different coat colors. With the coat color polymorphisms, mammals can adapt to various environments. Revealing the genetic basis of different coat colors in mammals has been an important research focus in genetics and evolutionary biology. In this review, we summarize the main advance in molecular mechanisms of pigmentation in cells and the genetic basis of coloration-related adaptations in mammals. Our review is expected to provide new clues for molecular mechanism studies on coat color polymorphism and adaptive evolutions in mammals.
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Affiliation(s)
- Zhang Yuxing
- School of Life Sciences of Yunnan University, State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, China
| | - Wu Hong
- School of Life Sciences of Yunnan University, State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, China
| | - Yu Li
- School of Life Sciences of Yunnan University, State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming 650091, China
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30
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Floriot S, Duchesne A, Grohs C, Hozé C, Deloche MC, Fayolle G, Vilotte JL, Boichard D, Fritz S, Boussaha M. A missense mutation in the FZD7 gene is associated with dilution of the red areas of the coat in Montbéliarde cattle. Anim Genet 2021; 52:351-355. [PMID: 33686687 DOI: 10.1111/age.13055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 10/22/2022]
Abstract
Recently, a new genetically autosomal recessive color phenotype emerged in the red pied bovine Montbéliarde breed. It is characterized by a dilution of the red areas of the coat and was denominated 'milca'. A genome-wide homozygosity scan of 106 cases followed by haplotype analysis revealed a candidate region within BTA2 between positions 89.95 and 91.63 Mb. Analysis of whole-genome sequence data generated from milca animals identified a strong candidate variant within the coding region of the Frizzled-7 gene (FZD7). This gene encodes for a G-protein coupled receptor for Wnt signaling proteins. The variant induces a glycine to alanine substitution in the second extracellular loop, p.(Gly414Ala). Cross-species amino acid alignments revealed that this glycine is conserved among orthologs and most paralogs, suggesting that it plays an important role in FZD function. In addition, genotyping data revealed that the mutant allele is restricted to the Montbéliarde breed, at a 3.7% frequency. All homozygous cows for the mutant allele exhibited the milca phenotype whereas all heterozygotes had no coat color defects. In conclusion, this study strongly suggests that, in cattle, a mutation of FZD7 alone is sufficient to cause a coat color phenotype without any strong other adverse effect.
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Affiliation(s)
- S Floriot
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
| | - A Duchesne
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
| | - C Grohs
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
| | - C Hozé
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France.,Allice, Paris, 75595, France
| | | | | | - J L Vilotte
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
| | - D Boichard
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
| | - S Fritz
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France.,Allice, Paris, 75595, France
| | - M Boussaha
- INRAE, AgroParisTech, Université Paris-Saclay, GABI, Jouy-en-Josas, 78350, France
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Manakhov AD, Mintseva MY, Andreeva TV, Filimonov PA, Onokhov AA, Chernova IЕ, Kashtanov SN, Rogaev EI. Genome Analysis of Sable Fur Color Links a Lightened Pigmentation Phenotype to a Frameshift Variant in the Tyrosinase-Related Protein 1 Gene. Genes (Basel) 2021; 12:157. [PMID: 33503951 DOI: 10.3390/genes12020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022] Open
Abstract
Sable (Martes zibellina) is one of the most valuable species of fur animals. Wild-type sable fur color varies from sandy-yellow to black. Farm breeding and 90 years of directional selection have resulted in a generation of several sable breeds with a completely black coat color. In 2005, an unusually chocolate (pastel) puppy was born in the Puschkinsky State Fur Farm (Russia). We established that the pastel phenotype was inherited as a Mendelian autosomal recessive trait. We performed whole-genome sequencing of the sables with pastel fur color and identified a frameshift variant in the gene encoding membrane-bound tyrosinase-like enzyme (TYRP1). TYRP1 is involved in the stability of the tyrosinase enzyme and participates in the synthesis of eumelanin. These data represent the first reported variant linked to fur color in sables and reveal the molecular genetic basis for pastel color pigmentation. These data are also useful for tracking economically valuable fur traits in sable breeding programs.
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Jia X, Ding P, Chen S, Zhao S, Wang J, Lai S. Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors. Animals (Basel) 2021; 11:E81. [PMID: 33466315 DOI: 10.3390/ani11010081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Coat color is an important breed characteristic and economic trait for rabbits, and it is regulated by a few genes. In this study, the gene frequencies of some pigmentation genes were investigated in four Chinese native rabbit breeds with different coat colors. A total of 14 genetic variants were detected in the gene fragments of MC1R, MITF, TYR, TYRP1, and MLPH genes, and there was low-to-moderate polymorphism in the populations. The gene frequency showed significant differences among the four rabbit populations. The above results suggest that these genetic variations play an important role in regulating the coat color of rabbits. This study will provide potential molecular markers for the breeding of coat color traits in rabbits. Abstract Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources.
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Abstract
The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.
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Affiliation(s)
- Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul 90619-900, Brazil;
| | - Fernanda J Trindade
- Laboratory of Genomics and Molecular Biology, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Rio Grande do Sul 90619-900, Brazil;
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Nguyen TB, Paul RC, Okuda Y, LE TNA, Pham PTK, Kaissar KJ, Kazhmurat A, Bibigul S, Bakhtin M, Kazymbet P, Maratbek SZ, Meldebekov A, Nishibori M, Ibi T, Tsuji T, Kunieda T. Genetic characterization of Kushum horses in Kazakhstan based on haplotypes of mtDNA and Y chromosome, and genes associated with important traits of the horses. J Equine Sci 2020; 31:35-43. [PMID: 33061782 PMCID: PMC7538259 DOI: 10.1294/jes.31.35] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
The Kushum is a relatively new breed of horses in Kazakhstan that was established in the
middle of the 20th century through a cross between mares of Kazakhstan local horses and
stallions of Thoroughbred, Trotter, and Russian Don breeds to supply military horses. To
reveal the genetic characteristics of this breed, we investigated haplotypes of
mitochondrial DNA (mtDNA) and single-nucleotide polymorphisms of the Y chromosome, as well
as genotypes of five functional genes associated with coat color, body composition, and
locomotion traits. We detected 10 mtDNA haplotypes that fell into 8 of the 17 major
haplogroups of horse mtDNA, indicating a unique haplotype composition with high genetic
diversity. We also found two Y-chromosomal haplotypes in Kushum horses, which likely
originated from Trotter and/or Don breeds. The findings regarding the mtDNA and
Y-chromosomal haplotypes are concordant with the documented maternal and paternal origins
of the Kushum horses. The allele frequencies of ASIP, MC1R, and MATP associated with coat
color were consistent with the coat color variations of Kushum horses. The allele
frequencies of MSTN associated with endurance performance and those of DMRT3 associated
with gait suggested that the observed allele frequencies of these genes were the result of
selective breeding for these traits. As a result of this study, we were able to obtain
useful information for a better understanding of the origin and breeding history of the
Kushum horse breed using molecular markers.
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Affiliation(s)
- Trung B Nguyen
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,An Giang University, Vietnam National University, An Giang, Vietnam
| | - Ripon C Paul
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Yu Okuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Okayama University of Science, Okayama 700-0005, Japan
| | - Thu N A LE
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,University of Agriculture & Forestry, Hue University, Hue, Vietnam
| | - Phuong T K Pham
- An Giang University, Vietnam National University, An Giang, Vietnam
| | - Kushaliye J Kaissar
- Zhangir Khan West Kazakhstan Agrarian-Technical University, Uralsk, Kazakhstan
| | | | | | - Meirat Bakhtin
- Radiobiological Research Institute, JSC Astana Medical University, Astana, Kazakhstan
| | - Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University, Astana, Kazakhstan
| | | | | | - Masahide Nishibori
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takayuki Ibi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takehito Tsuji
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
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Carini RM, Sinski J, Weber JD. Coat Color and Cat Outcomes in an Urban U.S. Shelter. Animals (Basel) 2020; 10:ani10101720. [PMID: 32977402 PMCID: PMC7597961 DOI: 10.3390/ani10101720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/02/2022] Open
Abstract
Simple Summary There is continuing debate as to whether individuals prefer companion cats of varying coat colors, and if so, how color preferences may affect whether cats in shelters are euthanized, adopted, or transferred to another organization. This study analyzed outcomes for nearly 8000 cats admitted to an urban public shelter in Kentucky, USA from 2010 through 2011. While coat color overall was not an important predictor of cat outcomes, a tiered pattern among particular colors was detected. Specifically, black and white cats experienced the highest and lowest chances of euthanasia, respectively, while brown and gray cats experienced more middling chances. Orange cats’ relative chances of euthanasia were more difficult to gauge, but orange and white cats had similar euthanasia and adoption outcomes in the most nuanced model. In addition, there has been persistent speculation that the public’s interest in—and preference for—black cats might spike before Halloween due to cats’ associations with the holiday. However, the present study found that a subsample of more than 1200 entirely black cats did not experience improved chances of adoption or transfer to a rescue organization in October compared to other months. Overall, this study provides weak evidence for what has been termed “Black Cat Bias” by others, and hints that black cats in public shelters should receive extra consideration for rehoming. Abstract Some nonhuman animal shelters have developed rehoming programs for black cats to remedy what they believe are their higher rates of euthanasia and lower rates of adoption. This study reviews humans’ preferences/aversions to cats of various coat colors and uses contingency tables and multinomial logistic regression to test possible differences in outcomes (euthanasia, adoption, or transfer) for 7983 cats that entered an urban public shelter in Kentucky, USA from 2010 through 2011. While coat color overall was negligibly associated with cat outcomes in a contingency table, the pairwise difference between black and white cats was significant (p < 0.05) and nontrivial in strength. Specifically, black cats experienced the highest euthanasia and lowest adoption rates, while white cats had the lowest euthanasia and highest adoption rates. Brown, gray, and orange cats experienced similar outcomes, but middling between those of black and white cats. These patterns by color remained weak but significant after controlling for breed and stray status in regression analysis, with the exception of orange and white, which did not differ significantly. A subsample of 1219 entirely black cats was analyzed to assess whether they had different outcomes during the run-up to Halloween; their October percentages of adoption and transfer were comparable to or lower than all other months of the calendar year. Thus, this study did not find that outcomes improved for black cats during October. Overall, this study provides weak support for what has been termed “Black Cat Bias” by others, and hints that black cats in public shelters should receive extra consideration for rehoming, particularly if such efforts do not substantially redirect resources from other initiatives.
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Affiliation(s)
- Robert M. Carini
- Department of Sociology, University of Louisville, Louisville, KY 40292, USA;
- Correspondence:
| | - Jennifer Sinski
- Department of Sociology, Bellarmine University, Louisville, KY 40205, USA;
| | - Jonetta D. Weber
- Department of Sociology, University of Louisville, Louisville, KY 40292, USA;
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36
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Senczuk G, Guerra L, Mastrangelo S, Campobasso C, Zoubeyda K, Imane M, Marletta D, Kusza S, Karsli T, Gaouar SBS, Pilla F, Ciani E. Fifteen Shades of Grey: Combined Analysis of Genome-Wide SNP Data in Steppe and Mediterranean Grey Cattle Sheds New Light on the Molecular Basis of Coat Color. Genes (Basel) 2020; 11:genes11080932. [PMID: 32823527 PMCID: PMC7464420 DOI: 10.3390/genes11080932] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Coat color is among the most distinctive phenotypes in cattle. Worldwide, several breeds share peculiar coat color features such as the presence of a fawn pigmentation of the calf at birth, turning over time to grey, and sexual dichromatism. The aim of this study was to search for polymorphisms under differential selection by contrasting grey cattle breeds displaying the above phenotype with non-grey cattle breeds, and to identify the underlying genes. Using medium-density SNP array genotype data, a multi-cohort FST-outlier approach was adopted for a total of 60 pair-wise comparisons of the 15 grey with 4 non-grey cattle breeds (Angus, Limousin, Charolais, and Holstein), with the latter selected as representative of solid and piebald phenotypes, respectively. Overall, more than 50 candidate genes were detected; almost all were either directly or indirectly involved in pigmentation, and some of them were already known for their role in phenotypes related with hair graying in mammals. Notably, 17 relevant genes, including SDR16C5, MOS, SDCBP, and NSMAF, were located in a signal on BTA14 convergently observed in all the four considered scenarios. Overall, the key stages of pigmentation (melanocyte development, melanogenesis, and pigment trafficking/transfer) were all represented among the pleiotropic functions of the candidate genes, suggesting the complex nature of the grey phenotype in cattle.
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Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Lorenzo Guerra
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128 Palermo, Italy;
| | - Claudia Campobasso
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
| | - Kaouadji Zoubeyda
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Meghelli Imane
- Department of Biology, University Abou Bekr Bélkaid, Tlemcen 13000, Algeria; (K.Z.); (M.I.); (S.B.S.G.)
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, 95123 Catania, Italy;
| | - Szilvia Kusza
- Animal Genetics Laboratory, University of Debrecen, 4032 Debrecen, Hungary;
| | - Taki Karsli
- Department of Animal Science, Akdeniz University, 07070 Antalya, Turkey;
| | | | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, 86100 Campobasso, Italy; (G.S.); (F.P.)
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari, 70125 Bari, Italy; (L.G.); (C.C.)
- Correspondence:
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Friedrich J, Talenti A, Arvelius P, Strandberg E, Haskell MJ, Wiener P. Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits. Adv Genet (Hoboken) 2020; 1:e10024. [PMID: 36619250 PMCID: PMC9744541 DOI: 10.1002/ggn2.10024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 01/11/2023]
Abstract
Strong selection has resulted in substantial morphological and behavioral diversity across modern dog breeds, which makes dogs interesting model animals to study the underlying genetic architecture of these traits. However, results from between-breed analyses may confound selection signatures for behavior and morphological features that were coselected during breed development. In this study, we assess population genetic differences in a unique resource of dogs of the same breed but with systematic behavioral selection in only one population. We exploit these different breeding backgrounds to identify signatures of recent selection. Selection signatures within populations were found on chromosomes 4 and 19, with the strongest signals in behavior-related genes. Regions showing strong signals of divergent selection were located on chromosomes 1, 24, and 32, and include candidate genes for both physical features and behavior. Some of the selection signatures appear to be driven by loci associated with coat color (Chr 24; ASIP) and length (Chr 32; FGF5), while others showed evidence of association with behavior. Our findings suggest that signatures of selection within dog breeds have been driven by selection for morphology and behavior. Furthermore, we demonstrate that combining selection scans with association analyses is effective for dissecting the traits under selection.
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Affiliation(s)
- Juliane Friedrich
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
| | - Andrea Talenti
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
| | - Per Arvelius
- Swedish Armed Forces Dog Training CenterMärstaSweden
| | - Erling Strandberg
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Marie J. Haskell
- Animal & Veterinary SciencesScotland's Rural College (SRUC)EdinburghUK
| | - Pamela Wiener
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothianUK
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38
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Dreger DL, Anderson H, Donner J, Clark JA, Dykstra A, Hughes AM, Ekenstedt KJ. Atypical Genotypes for Canine Agouti Signaling Protein Suggest Novel Chromosomal Rearrangement. Genes (Basel) 2020; 11:E739. [PMID: 32635139 DOI: 10.3390/genes11070739] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 02/05/2023] Open
Abstract
Canine coat color is a readily observed phenotype of great interest to dog enthusiasts; it is also an excellent avenue to explore the mechanisms of genetics and inheritance. As such, multiple commercial testing laboratories include basic color alleles in their popular screening panels, allowing for the creation of genotyped datasets at a scale not before appreciated in canine genetic research. These vast datasets have revealed rare genotype anomalies that encourage further exploration of color and pattern inheritance. We previously reported the simultaneous presence of greater than two allele variants at the Agouti Signaling Protein (ASIP) locus in a commercial genotype cohort of 11,790 canids. Here we present additional data to characterize the occurrence of anomalous ASIP genotypes. We document the detection of combinations of three or four ASIP allele variants in 17 dog breeds and Dingoes, at within-breed frequencies of 1.32–63.34%. We analyze the potential impact on phenotype that these allele combinations present, and propose mechanisms that could account for the findings, including: gene recombination, duplication, and incorrect causal variant identification. These findings speak to the accuracy of industry-wide protocols for commercial ASIP genotyping and imply that ASIP should be analyzed via haplotype, rather than using only the existing allele hierarchy, in the future.
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39
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Voß K, Tetens J, Thaller G, Becker D. Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses. Genes (Basel) 2020; 11:E680. [PMID: 32580410 DOI: 10.3390/genes11060680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed.
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40
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Varga L, Lénárt X, Zenke P, Orbán L, Hudák P, Ninausz N, Pelles Z, Szőke A. Being Merle: The Molecular Genetic Background of the Canine Merle Mutation. Genes (Basel) 2020; 11:E660. [PMID: 32560567 DOI: 10.3390/genes11060660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022] Open
Abstract
The intensity of the merle pattern is determined by the length of the poly(A) tail of a repeat element which has been inserted into the boundary of intron 10 and exon 11 of the PMEL17 locus in reverse orientation. This poly(A) tail behaves as a microsatellite, and due to replication slippage, longer and shorter alleles of it might be generated during cell divisions. The length of the poly(A) tail regulates the splicing mechanism. In the case of shorter tails, the removal of intron 10 takes place at the original splicing, resulting in a normal premelanosome protein (PMEL). Longer tails generate larger insertions, forcing splicing to a cryptic splice site, thereby coding for an abnormal PMEL protein, which is unable to form the normal fibrillar matrix of the eumelanosomes. Thus, eumelanin deposition ensuring the dark color formation is reduced. In summary, the longer the poly(A) tail, the lighter the coat color intensity of the melanocytes. These mutations can occur in the somatic cells and the resulting cell clones will shape the merle pattern of the coat. When they take place in the germ line, they occasionally produce offspring with unexpected color variations which are different from those of their parents.
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41
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Reissmann M, Lutz W, Lieckfeldt D, Sandoval-Castellanos E, Ludwig A. An Agouti-Signaling-Protein Mutation is Strongly Associated with Melanism in European Roe Deer ( Capreolus capreolus). Genes (Basel) 2020; 11:E647. [PMID: 32545389 DOI: 10.3390/genes11060647] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022] Open
Abstract
Although the European roe deer (Capreolus capreolus) population of North-West Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and 2039 bp of ASIP were sequenced in 24 specimens and several SNPs were detected. But only the ASIP-SNP c.33G>T completely segregated both phenotypes leading to the amino acid substitution p.Leu11Phe. The SNP was further evaluated in additional 471 samples. Generally, all black specimens (n = 33) were homozygous TT, whereas chestnut individuals were either homozygote GG (n = 436) or heterozygote GT (n = 26). Considering the fact that all melanistic animals shared two mutated alleles of the strongly associated SNP, we concluded that melanism is inherited in a recessive mode in European roe deer.
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Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020; 10:E1005. [PMID: 32521830 DOI: 10.3390/ani10061005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Abstract Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
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Posbergh CJ, Staiger EA, Huson HJ. A Stop-Gain Mutation within MLPH Is Responsible for the Lilac Dilution Observed in Jacob Sheep. Genes (Basel) 2020; 11:genes11060618. [PMID: 32512769 PMCID: PMC7349772 DOI: 10.3390/genes11060618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
A coat color dilution, called lilac, was observed within the Jacob sheep breed. This dilution results in sheep appearing gray, where black would normally occur. Pedigree analysis suggested an autosomal recessive inheritance. Whole-genome sequencing of a dilute case, a known carrier, and sixteen non-dilute sheep was used to identify the molecular variant responsible for the coat color change. Through investigation of the genes MLPH, MYO5A, and RAB27A, we discovered a nonsynonymous mutation within MLPH, which appeared to match the reported autosomal recessive nature of the lilac dilution. This mutation (NC_019458.2:g.3451931C>A) results in a premature stop codon being introduced early in the protein (NP_001139743.1:p.Glu14*), likely losing its function. Validation testing of additional lilac Jacob sheep and known carriers, unrelated to the original case, showed a complete concordance between the mutation and the dilution. This stop-gain mutation is likely the causative mutation for dilution within Jacob sheep.
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Affiliation(s)
- Christian J. Posbergh
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: (C.J.P.); (H.J.H.)
| | - Elizabeth A. Staiger
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Department of Animal Sciences, Auburn University, Auburn, AL 36849, USA
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY 14853, USA;
- Correspondence: (C.J.P.); (H.J.H.)
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Matsumoto H, Kojya M, Takamuku H, Kimura S, Kashimura A, Imai S, Yamauchi K, Ito S. MC1R c.310G>- and c.871G > A determine the coat color of Kumamoto sub-breed of Japanese Brown cattle. Anim Sci J 2020; 91:e13367. [PMID: 32285552 DOI: 10.1111/asj.13367] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 11/28/2022]
Abstract
Coat color is one of the important factors characterizing breeds for domestic animals. Melanocortin 1 receptor (MC1R) is a representative responsible gene for this phenotype. Two single-nucleotide polymorphisms (SNPs) in bovine MC1R gene, c.296T > C and c.310G>-, have been well characterized, but these SNPs are not enough to explain cattle coat color. As far as we know, MC1R genotypes of Kumamoto sub-breed of Japanese Brown cattle have not been analyzed. In the current study, genotyping for c.296T > C and c.310G>- was performed to elucidate the role of MC1R in determining the coat color of this sub-breed. As a result, most animals were e/e genotype, suggesting the coat color of this sub-breed is derived from the e allele of MC1R gene. However, we found six animals with E/e genotype, which coat color would be black theoretically. Subsequently, sequence comparison was performed with these animals to identify other polymorphisms affecting coat color, elucidating that these animals possessed the A allele of c.871G > A commonly. c.871G > A was a non-synonymous mutation in the seventh transmembrane domain, suggesting alteration of the function and/or the structure of MC1R protein. Our data indicated that the A allele of c.871G > A might be a loss-of-function mutation.
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Affiliation(s)
- Hirokazu Matsumoto
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Masatake Kojya
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Hiroko Takamuku
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Satoshi Kimura
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Atsushi Kashimura
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Saki Imai
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
| | - Kenji Yamauchi
- Kumamoto Station, National Livestock Breeding Center, Kumamoto, Japan
| | - Shuichi Ito
- Department of Animal Science, School of Agriculture, Tokai University, Kumamoto, Japan
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Abstract
Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.
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Affiliation(s)
- Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China;
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Abstract
Coat color is one of the major quality traits of animals, and miR-129-5p acts as an important regulator for melanin biosynthesis in mammals. In this study, real-time PCR and western blotting were used to examine the expression of miR-129-5p and its targets genes in the skin of different coat color goats. The results showed that the expression of miR-129-5p in the skin samples of Inner Mongolia cashmere goats (IMCG) was higher than that of Dazu black goat (DBG). Also, the target genes (tyrosinase (TYR), frizzled 6 (FZD6) and glycogen synthase kinase 3β (GSK3β)) of miR-129-5p was highly expressed in the skin samples of DBG. The expression of miR-129-5p firstly increased and then decreased with age in F1 hybrid generation of DBG and IMCG. In addition, the expression of TYR decreased with age, while the expression of MITF increased with age but then decreased. The expression of FZD6 and GSK3β in the skin samples of F1 of different ages were irregular. Our results indicated that miR-129-5p mainly affects the formation of coat color of goats by decreasing the expression of TYR. This study suggests that miR-129-5p can act as a suppressor in the formation of coat color to lay the foundation for studying the effect of miR-129-5p on melanin synthesis.
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Affiliation(s)
- Jialu Li
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
| | - Lei Cheng
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
| | - Lingtong Ren
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Beibei, Chongqing, P. R. China.,Chongqing Key Laboratory of Forage and Herbivore, Beibei, Chongqing, P. R. China.,Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Beibei, Chongqing, P. R. China
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Huang M, Yang B, Chen H, Zhang H, Wu Z, Ai H, Ren J, Huang L. The fine-scale genetic structure and selection signals of Chinese indigenous pigs. Evol Appl 2020; 13:458-475. [PMID: 31993089 PMCID: PMC6976964 DOI: 10.1111/eva.12887] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 01/24/2023] Open
Abstract
Genome-wide SNP profiling has yielded insights into the genetic structure of China indigenous pigs, but has focused on a limited number of populations. Here, we present an analysis of population structure and signals of positive selection in 42 Chinese pig populations that represent the most extensive pig phenotypic diversity in China, using genotype data of 1.1 million SNPs on customized Beadchips. This unravels the fine-scale genetic diversity, phylogenic relationships, and population structure of these populations, which shows remarkably concordance between genetic clusters and geography with few exceptions. We also reveal the genetic contribution to North Chinese pigs from European modern pigs. Furthermore, we identify possible targets of selection in the Tibetan pig, including the well-characterized hypoxia gene (EPAS1) and several previously unrecognized candidates. Intriguingly, the selected haplotype in the EPAS1 gene is associated with higher hemoglobin contents in Tibetan pigs, which is different from the protective role of EPAS1 in the high-altitude adaptation in Tibetan dogs and their owners. Additionally, we present evidence for the causality between EDNRB variants and the two-end-black (TEB) coat color phenotype in all Chinese pig populations except the Jinhua pig. We hypothesize that distinct targets have been independently selected for the formation of the TEB phenotype in Chinese pigs of different geographic origins. This highlights the importance of characterizing population-specific genetic determinants for heritable phenotype in diverse pig populations.
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Affiliation(s)
- Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
- Present address:
College of Animal ScienceSouth China Agricultural UniversityGuangzhouChina
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchangChina
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Weich K, Affolter V, York D, Rebhun R, Grahn R, Kallenberg A, Bannasch D. Pigment Intensity in Dogs is Associated with a Copy Number Variant Upstream of KITLG. Genes (Basel) 2020; 11:genes11010075. [PMID: 31936656 PMCID: PMC7017362 DOI: 10.3390/genes11010075] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 01/14/2023] Open
Abstract
Dogs exhibit a wide variety of coat color types, and many genes have been identified that control pigment production, appearance, and distribution. Some breeds, such as the Nova Scotia Duck Tolling Retriever (NSDTR), exhibit variation in pheomelanin pigment intensity that is not explained by known genetic variants. A genome-wide association study comparing light red to dark red in the NSDTR identified a significantly associated region on canine chromosome 15 (CFA 15:23 Mb–38 Mb). Coverage analysis of whole genome sequence data from eight dogs identified a 6 kb copy number variant (CNV) 152 kb upstream of KITLG. Genotyping with digital droplet PCR (ddPCR) confirmed a significant association between an increased copy number with the dark-red coat color in NSDTR (p = 6.1 × 10−7). The copy number of the CNV was also significantly associated with coat color variation in both eumelanin and pheomelanin-based Poodles (p = 1.5 × 10−8, 4.0 × 10−9) and across other breeds. Moreover, the copy number correlated with pigment intensity along the hair shaft in both pheomelanin and eumelanin coats. KITLG plays an important role in melanogenesis, and variants upstream of KITLG have been associated with coat color variation in mice as well as hair color in humans consistent with its role in the domestic dog.
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Affiliation(s)
- Kalie Weich
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA;
| | - Verena Affolter
- Department of Pathology, Microbiology, and Immunology, University of California-Davis, Davis, CA 95616, USA;
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California-Davis, Davis, CA 95616, USA; (D.Y.); (R.R.)
| | - Robert Rebhun
- Department of Surgical and Radiological Sciences, University of California-Davis, Davis, CA 95616, USA; (D.Y.); (R.R.)
| | - Robert Grahn
- Veterinary Genetics Laboratory, University of California-Davis, Davis, CA 95616, USA; (R.G.); (A.K.)
| | - Angelica Kallenberg
- Veterinary Genetics Laboratory, University of California-Davis, Davis, CA 95616, USA; (R.G.); (A.K.)
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California-Davis, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-754-8728
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Miller H, Ward M, Beatty JA. Population Characteristics of Cats Adopted from an Urban Cat Shelter and the Influence of Physical Traits and Reason for Surrender on Length of Stay. Animals (Basel) 2019; 9:ani9110940. [PMID: 31717438 PMCID: PMC6912321 DOI: 10.3390/ani9110940] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/06/2019] [Accepted: 11/06/2019] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Every year, millions of cats are admitted to shelters around the world. Reducing the amount of time that cats stay in a shelter environment (length of stay, LOS) promotes animal welfare by reducing illness and stress, as well as supporting more efficient use of shelter resources. Understanding the factors that might influence LOS supports evidence-based interventions aimed at improving the flow of animals through shelters. Whether the same factors affect LOS in shelters of different types and from different geographic regions is poorly understood. We studied cats adopted from an urban shelter in Sydney, Australia, and found that stray cats have a longer LOS than owner-relinquished cats, supporting the results of previous studies. Surprisingly, in contrast to the widely held view that black cats stay in shelters longer than white cats, the opposite was true here—overall, white cats stayed longer than black cats in the shelter, even when other factors such as age were taken into consideration. Shelters might consider analyzing their own data, where possible, to inform strategies to reduce LOS. Abstract Measures aimed at reducing the length of stay (LOS) of cats in shelters can promote animal welfare and more efficient use of resources. The extent to which variables shown to impact LOS are broadly applicable is unclear. The aim of this study was to describe a population of cats adopted from an urban shelter, and to analyze the association between potential predictor variables and LOS. A study cohort was identified retrospectively from shelter records (n = 2584), 48.8% of which were < 12 weeks old at admission, and 80.7% were stray. Among 445 cats relinquished by owners, reasons for surrender were primarily owner-related (87.2%). Overall, reason for surrender and coat color were significantly associated with LOS. Hazard ratios showed that all reasons for surrender for owner-relinquished cats were associated with a shorter LOS than stray cats and this association was significant (p < 0.05) for all except cat behavioral or medical reasons. In contrast to previous reports, white cats had a significantly (p < 0.05) longer LOS than black cats. This study highlights an important role for shelter-specific baseline data to inform and measure the effect of interventional studies aimed at improving animal welfare by reducing LOS in shelter-housed cats
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Tanaka J, Leeb T, Rushton J, Famula TR, Mack M, Jagannathan V, Flury C, Bachmann I, Eberth J, McDonnell SM, Penedo MCT, Bellone RR. Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies. Genes (Basel) 2019; 10:E826. [PMID: 31635058 DOI: 10.3390/genes10100826] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 01/09/2023] Open
Abstract
Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (Pcorrected = 2.08 × 10−10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of various breeds, uncovered a frameshift variant, p.Asp201fs, in the MFSD12 gene encoding the major facilitator superfamily domain containing 12 protein. This variant was perfectly concordant with phenotype in 96 Shetland Ponies (P = 1.15 × 10−22), was identified in the closely related Miniature Horse for which the mushroom phenotype is suspected to occur (fmu = 0.02), and was absent in 252 individuals from seven additional breeds not reported to have the mushroom phenotype. MFSD12 is highly expressed in melanocytes and variants in this gene in humans, mice, and dogs impact pigmentation. Given the role of MFSD12 in melanogenesis, we propose that p.Asp201fs is causal for the dilution observed in mushroom ponies.
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