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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Barmentlo NWG, Meirmans PG, Stiver WH, Yarkovich JG, McCann BE, Piaggio AJ, Wright D, Smyser TJ, Bosse M. Natural selection on feralization genes contributed to the invasive spread of wild pigs throughout the United States. Mol Ecol 2024; 33:e17383. [PMID: 38747342 DOI: 10.1111/mec.17383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 06/07/2024]
Abstract
Despite a long presence in the contiguous United States (US), the distribution of invasive wild pigs (Sus scrofa × domesticus) has expanded rapidly since the 1980s, suggesting a more recent evolutionary shift towards greater invasiveness. Contemporary populations of wild pigs represent exoferal hybrid descendants of domestic pigs and European wild boar, with such hybridization expected to enrich genetic diversity and increase the adaptive potential of populations. Our objective was to characterize how genetic enrichment through hybridization increases the invasiveness of populations by identifying signals of selection and the ancestral origins of selected loci. Our study focused on invasive wild pigs within Great Smoky Mountains National Park, which represents a hybrid population descendent from the admixture of established populations of feral pigs and an introduction of European wild boar to North America. Accordingly, we genotyped 881 wild pigs with multiple high-density single-nucleotide polymorphism (SNP) arrays. We found 233 markers under putative selection spread over 79 regions across 16 out of 18 autosomes, which contained genes involved in traits affecting feralization. Among these, genes were found to be related to skull formation and neurogenesis, with two genes, TYRP1 and TYR, also encoding for crucial melanogenesis enzymes. The most common haplotypes associated with regions under selection for the Great Smoky Mountains population were also common among other populations throughout the region, indicating a key role of putatively selective variants in the fitness of invasive populations. Interestingly, many of these haplotypes were absent among European wild boar reference genotypes, indicating feralization through genetic adaptation.
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Affiliation(s)
- Niek W G Barmentlo
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Blake E McCann
- Theodore Roosevelt National Park, Medora, North Dakota, USA
| | | | - Dominic Wright
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Timothy J Smyser
- USDA APHIS WS National Wildlife Research Center, Fort Collins, Colorado, USA
| | - Mirte Bosse
- Section Ecology & Evolution, Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wageningen University & Research - Animal Breeding and Genomics, Wageningen, The Netherlands
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3
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Guo P, Chen J, Luo L, Zhang X, Li X, Huang Y, Wu Z, Tian Y. Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese. Animals (Basel) 2024; 14:1508. [PMID: 38791725 PMCID: PMC11117251 DOI: 10.3390/ani14101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.
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Affiliation(s)
- Pengyun Guo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Junpeng Chen
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou 515800, China;
| | - Lei Luo
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xumeng Zhang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Xiujin Li
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunmao Huang
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Zhongping Wu
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
| | - Yunbo Tian
- College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (P.G.); (L.L.); (X.Z.); (X.L.); (Y.H.); (Y.T.)
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4
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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5
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Arenas-Báez P, Torres-Hernández G, Castillo-Hernández G, Hernández-Rodríguez M, Sánchez-Gutiérrez RA, Vargas-López S, González-Maldonado J, Domínguez-Martínez PA, Granados-Rivera LD, Maldonado-Jáquez JA. Coat Color in Local Goats: Influence on Environmental Adaptation and Productivity, and Use as a Selection Criterion. BIOLOGY 2023; 12:929. [PMID: 37508360 PMCID: PMC10376610 DOI: 10.3390/biology12070929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
This paper aims to review, systematically synthesize, and analyze fragmented information about the importance of coat color in local goats and its relationship with productivity and other important traits. Topics on current research on color expression are addressed, the relationship that has as a mechanism of environmental adaptation, its relationship with the production of meat, milk, and derivates, and the economic value of this characteristic. The use of this attribute as a tool to establish selection criteria in breeding programs based on results reported in the scientific literature is significant, particularly for low-income production systems, where the implementation of classic genetic improvement schemes is limited due to the lack of productive information, which is distinctive of extensive marginal or low scaled production systems around the world.
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Affiliation(s)
- Pablo Arenas-Báez
- Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, Bermejillo, Durango 35230, Mexico
| | | | - Gabriela Castillo-Hernández
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Cuautitlán Izcalli 54714, Mexico
| | | | - Ricardo Alonso Sánchez-Gutiérrez
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Zacatecas, Calera, Zacatecas 98500, Mexico
| | | | - Juan González-Maldonado
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali 21750, Mexico
| | - Pablo Alfredo Domínguez-Martínez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Valle del Guadiana, Durango 34170, Mexico
| | - Lorenzo Danilo Granados-Rivera
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Genera Terán, General Terán 67400, Mexico
| | - Jorge Alonso Maldonado-Jáquez
- Colegio de Postgraduados, Campus Montecillo, Montecillo, Texcoco 56264, Mexico
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental La Laguna, Matamoros 27440, Mexico
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6
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Guan S, Li W, Jin H, Zhang L, Liu G. Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat. Genes (Basel) 2023; 14:genes14051122. [PMID: 37239482 DOI: 10.3390/genes14051122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The source of SNPs in the panel were from the whole-genome resequencing of 110 dairy goats from three European and two Chinese indigenous dairy goat breeds. The performance of this liquid SNP chip panel was evaluated by genotyping 200 additional goats. Fifteen of them were randomly selected for whole-genome resequencing. The average capture ratio of the panel design loci was 98.41%, and the genotype concordance with resequencing reached 98.02%. We further used this chip panel to conduct genome-wide association studies (GWAS) to detect genetic loci that affect coat color in dairy goats. A single significant association signal for hair color was found on chromosome 8 at 31.52-35.02 Mb. The TYRP1 gene, which is associated with coat color in goats, was identified to be located at this genomic region (chromosome 8: 31,500,048-31,519,064). The emergence of high-precision and low-cost liquid microarrays will improve the analysis of genomics and breeding efficiency of dairy goats.
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Affiliation(s)
- Shengyu Guan
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Weining Li
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hai Jin
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China
| | - Lu Zhang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guoshi Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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7
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Voß K, Blaj I, Tetens JL, Thaller G, Becker D. Roan coat color in livestock. Anim Genet 2022; 53:549-556. [PMID: 35811453 DOI: 10.1111/age.13240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Since domestication, a wide variety of phenotypes including coat color variation has developed in livestock. This variation is mostly based on selective breeding. During the beginning of selective breeding, potential negative consequences did not become immediately evident due to low frequencies of homozygous animals and have been occasionally neglected. However, numerous studies of coat color genetics have been carried out over more than a century and, meanwhile, pleiotropic effects for several coat color genes, including disorders of even lethal impact, were described. Similar coat color phenotypes can often be found across species, caused either by conserved genes or by different genes. Even in the same species, more than one gene could cause the same or similar coat color phenotype. The roan coat color in livestock species is characterized by a mixture of white and colored hair in cattle, pig, sheep, goat, alpaca, and horse. So far, the genetic background of this phenotype is not fully understood, but KIT and its ligand KITLG (MGF) are major candidate genes in livestock species. For some of these species, pleiotropic effects such as subfertility in homozygous roan cattle or homozygous embryonic lethality in certain horse breeds have been described. This review aims to point out the similarities and differences of the roan phenotype across the following livestock species: cattle, pig, sheep, goat, alpaca, and horse; and provides the current state of knowledge on genetic background and pleiotropic effects.
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Affiliation(s)
- Katharina Voß
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Iulia Blaj
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Julia L Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel, Germany
| | - Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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8
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Pakpahan S, Widayanti R, Artama WT. Selection signatures and formation of the Samosir goat breed through the cultures of the Batak Toba Tribe in Samosir Island, Indonesia. Vet World 2022; 15:1044-1050. [PMID: 35698517 PMCID: PMC9178575 DOI: 10.14202/vetworld.2022.1044-1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: The Samosir goat has a high cultural value and is a source of germplasm in Indonesia. This study aimed to reveal the history and selection signatures of the Samosir goat. Materials and Methods: A total of 25 goats were divided into seven subpopulations of Indonesian goat breeds. Deoxyribonucleic acid (DNA) from blood samples was isolated with the use of the gSYNC™ DNA Mini Kit (Geneaid, Taipei, Taiwan). Cytb gene amplification was performed by the polymerase chain reaction (PCR) method, and the PCR products were sequenced. A phylogenetic tree was constructed by the neighbor-joining method using MEGA 11 software. A questionnaire was used to collect information related to the history and breeding practices of the Samosir goat on Samosir Island. Results: Samosir goats are divided into four groups based on their coat color: Completely white, white with brown spots, white with black spots, and white with brown and black spots. The body form of the Samosir goat is similar to that of the Kacang goat. The space below a traditional Toba Batak house is used as a goat pen. The genetic difference between the Samosir goat and the Kacang goat based on the Cytb gene was approximately 0.1%. Conclusion: Phylogenetic analysis between Samosir goats and other indigenous Indonesian goats revealed that Samosir goats form a single clade, with a very close genetic distance from other local goats, such as the Kacang goat. The Toba Batak culture on Samosir Island has significantly influenced the selection and formation of the Samosir goat breed.
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Affiliation(s)
- Suhendra Pakpahan
- Museum Zoologicum Bogoriense, Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Rini Widayanti
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Wayan T. Artama
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Henkel J, Dubacher A, Bangerter E, Herren U, Ammann P, Drögemüller C, Flury C, Leeb T. Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats. J Hered 2021; 112:452-457. [PMID: 34050662 DOI: 10.1093/jhered/esab024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
The Valais Blackneck goat is a Swiss goat breed with a characteristic coat color phenotype. Before the revision of the breed standard in 1938, 4 different color varieties of Valais goats were known. Besides Blackneck animals resembling the modern breed standard, the brown and white Copperneck goat, the white Capra Sempione, and the greyish Grüenochte comprised the historic Valais goats. The brown pigmentation of Copperneck goats had previously been traced back to an introgression of a mutant TYRP1 allele from Toggenburg goats. In the present study, we identified additional introgression events of distinct ASIP alleles causing the remaining 2 rare coat color patterns within the Valais Blackneck goat breed. We identified the introgression of the AWt allele from Appenzell or Saanen goats in white Capra Sempione goats. Similarly, introgression of the Apc allele from Peacock goats resulted in the greyish Grüenochte phenotype. These results demonstrate past hybridization events between breeds that are separated today. A perfect genotype-phenotype association in 393 Valais goats supported the causality of the genotyped variants for the different coat color phenotypes. Our study gives insights into the introgression of functionally relevant copy number variant (CNV) alleles controlling pigmentation between goat breeds with strikingly different coat color patterns.
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Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Alexandra Dubacher
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Erika Bangerter
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | - Ursula Herren
- Swiss Goat Breeding Association, 3052 Zollikofen, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, 3052 Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,DermFocus, University of Bern, 3001 Bern, Switzerland
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10
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Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors. Animals (Basel) 2021; 11:ani11010081. [PMID: 33466315 PMCID: PMC7824738 DOI: 10.3390/ani11010081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [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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11
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Kiener S, Kehl A, Loechel R, Langbein-Detsch I, Müller E, Bannasch D, Jagannathan V, Leeb T. Novel Brown Coat Color (Cocoa) in French Bulldogs Results from a Nonsense Variant in HPS3. Genes (Basel) 2020; 11:genes11060636. [PMID: 32526956 PMCID: PMC7349258 DOI: 10.3390/genes11060636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Brown or chocolate coat color in many mammalian species is frequently due to variants at the B locus or TYRP1 gene. In dogs, five different TYRP1 loss-of-function alleles have been described, which explain the vast majority of dogs with brown coat color. Recently, breeders and genetic testing laboratories identified brown French Bulldogs that did not carry any of the known mutant TYRP1 alleles. We sequenced the genome of a TYRP1+/+ brown French Bulldog and compared the data to 655 other canine genomes. A search for private variants revealed a nonsense variant in HPS3, c.2420G>A or p.(Trp807*). The brown dog was homozygous for the mutant allele at this variant. The HPS3 gene encodes a protein required for the correct biogenesis of lysosome-related organelles, including melanosomes. Variants in the human HPS3 gene cause Hermansky–Pudlak syndrome 3, which involves a mild form of oculocutaneous albinism and prolonged bleeding time. A variant in the murine Hps3 gene causes brown coat color in the cocoa mouse mutant. We genotyped a cohort of 373 French Bulldogs and found a strong association of the homozygous mutant HPS3 genotype with the brown coat color. The genotype–phenotype association and the comprehensive knowledge on HPS3 function from other species strongly suggests that HPS3:c.2420G>A is the causative variant for the observed brown coat color in French Bulldogs. In order to clearly distinguish HPS3-related from the TYRP1-related brown coat color, and in line with the murine nomenclature, we propose to designate this dog phenotype as “cocoa”, and the mutant allele as HPS3co.
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Affiliation(s)
- Sarah Kiener
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.K.); (D.B.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Alexandra Kehl
- Laboklin, 97688 Bad Kissingen, Germany; (A.K.); (I.L.-D.); (E.M.)
| | | | | | - Elisabeth Müller
- Laboklin, 97688 Bad Kissingen, Germany; (A.K.); (I.L.-D.); (E.M.)
| | - Danika Bannasch
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.K.); (D.B.); (V.J.)
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.K.); (D.B.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (S.K.); (D.B.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
- Correspondence: ; Tel.: +41-3163-123-26
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12
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Scholtens M, Jiang A, Smith A, Littlejohn M, Lehnert K, Snell R, Lopez-Villalobos N, Garrick D, Blair H. Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats. J Anim Sci Biotechnol 2020; 11:55. [PMID: 32489662 PMCID: PMC7247195 DOI: 10.1186/s40104-020-00453-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background Identifying associations between genetic markers and traits of economic importance will provide practical benefits for the dairy goat industry, enabling genomic prediction of the breeding value of individuals, and facilitating discovery of the underlying genes and mutations. Genome-wide association studies were implemented to detect genetic regions that are significantly associated with effects on lactation yields of milk (MY), fat (FY), protein (PY) and somatic cell score (SCS) in New Zealand dairy goats. Methods A total of 4,840 goats were genotyped with the Caprine 50 K SNP chip (Illumina Inc., San Diego, CA). After quality filtering, 3,732 animals and 41,989 SNPs were analysed assuming an additive linear model. Four GWAS models were performed, a single-SNP additive linear model and three multi-SNP BayesC models. For the single-SNP GWAS, SNPs were fitted individually as fixed covariates, while the BayesC models fit all SNPs simultaneously as random effects. A cluster of significant SNPs were used to define a haplotype block whose alleles were fitted as covariates in a Bayesian model. The corresponding diplotypes of the haplotype block were then fit as class variables in another Bayesian model. Results Across all four traits, a total of 43 genome-wide significant SNPs were detected from the SNP GWAS. At a genome-wide significance level, the single-SNP analysis identified a cluster of variants on chromosome 19 associated with MY, FY, PY, and another cluster on chromosome 29 associated with SCS. Significant SNPs mapped in introns of candidate genes (45%), in intergenic regions (36%), were 0-5 kb upstream or downstream of the closest gene (14%) or were synonymous substitutions (5%). The most significant genomic window was located on chromosome 19 explaining up to 9.6% of the phenotypic variation for MY, 8.1% for FY, 9.1% for PY and 1% for SCS. Conclusions The quantitative trait loci for yield traits on chromosome 19 confirms reported findings in other dairy goat populations. There is benefit to be gained from using these results for genomic selection to improve milk production in New Zealand dairy goats.
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Affiliation(s)
- Megan Scholtens
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ashley Smith
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Mathew Littlejohn
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Russell Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Lopez-Villalobos
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Hugh Blair
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
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13
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Simon R, Lischer HEL, Pieńkowska-Schelling A, Keller I, Häfliger IM, Letko A, Schelling C, Lühken G, Drögemüller C. New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Anim Genet 2020; 51:439-448. [PMID: 32060960 DOI: 10.1111/age.12918] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023]
Abstract
In domestic goats, the polled intersex syndrome (PIS) refers to XX female-to-male sex reversal associated with the absence of horn growth (polled). The causal variant was previously reported as a 11.7 kb deletion at approximately 129 Mb on chromosome 1 that affects the transcription of both FOXL2 and several long non-coding RNAs. In the meantime the presence of different versions of the PIS deletion was postulated and trials to establish genetic testing with the existing molecular genetic information failed. Therefore, we revisited this variant by long-read whole-genome sequencing of two genetically female (XX) goats, a PIS-affected and a horned control. This revealed the presence of a more complex structural variant consisting of a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG. Publicly available short-read whole-genome sequencing data, Sanger sequencing of the breakpoints and FISH using BAC clones corresponding to both involved genome regions confirmed this structural variant. A diagnostic PCR was developed for simultaneous genotyping of carriers for this variant and determination of their genetic sex. We showed that the variant allele was present in all 334 genotyped polled goats of diverse breeds and that all analyzed 15 PIS-affected XX goats were homozygous. Our findings enable for the first time a precise genetic diagnosis for polledness and PIS in goats and add a further genomic feature to the complexity of the PIS phenomenon.
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Affiliation(s)
- R Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - H E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, 3001, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - A Pieńkowska-Schelling
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.,Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - I Keller
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.,Department for BioMedical Research, University of Bern, Bern, 3001, Switzerland
| | - I M Häfliger
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
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14
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Henkel J, Saif R, Jagannathan V, Schmocker C, Zeindler F, Bangerter E, Herren U, Posantzis D, Bulut Z, Ammann P, Drögemüller C, Flury C, Leeb T. Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes. PLoS Genet 2019; 15:e1008536. [PMID: 31841508 PMCID: PMC6936872 DOI: 10.1371/journal.pgen.1008536] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/30/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (AWt), Swiss markings (Asm), badgerface (Ab), and the newly proposed peacock (Apc) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats. Domestic animals have been selected for hundreds or sometimes even thousands of years for traits that were appreciated by their human owners. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. We conducted a comprehensive screen for selection signatures in 20 phenotypically and genetically diverse modern goat breeds and identified a total of 2,239 putative selection signatures in our dataset. Follow-up experiments on selection signatures harboring known candidate genes for coat color revealed six different copy number variants (CNVs). Two of these CNVs were located in the 3’-flanking region of KIT and associated with a completely white coat color phenotype in Pak Angora goats and a white-spotted coat color phenotype in Barbari goats, respectively. The other four CNVs were located at the ASIP locus. They were associated with four different types of coat color patterning in seven Swiss goat breeds. Their functional effect is mediated by region-specific quantitative changes in ASIP mRNA expression. Our study illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.
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Affiliation(s)
- Jan Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Rashid Saif
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Biotechnology, Gulab Devi Educational Complex, Lahore, Pakistan
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Corinne Schmocker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Flurina Zeindler
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | | | - Ursula Herren
- Swiss Goat Breeding Association, Zollikofen, Switzerland
| | | | - Zafer Bulut
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Konya, Turkey
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
| | - Christine Flury
- School of Agricultural, Forest and Food Sciences, Bern University of Applied Sciences, Zollikofen, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- DermFocus, University of Bern, Bern, Switzerland
- * E-mail:
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15
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Peng Y, Wang Y, Wang R, Geng L, Ma R, Zhang C, Liu Z, Gong Y, Li J, Li X. Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.
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Affiliation(s)
- Yongdong Peng
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Yaqi Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Ruining Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Liying Geng
- College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, Hebei 071001, People’s Republic of China
| | - Ruxue Ma
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Chuansheng Zhang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Zhengzhu Liu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Yuanfang Gong
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
| | - Jingshi Li
- College of Animal Science and Technology, Agricultural University of Hebei Province, Baoding, Hebei 071001, People’s Republic of China
| | - Xianglong Li
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei 066004, People’s Republic of China
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16
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Guan D, Mármol-Sánchez E, Cardoso TF, Such X, Landi V, Tawari NR, Amills M. Genomic analysis of the origins of extant casein variation in goats. J Dairy Sci 2019; 102:5230-5241. [PMID: 30928270 DOI: 10.3168/jds.2018-15281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 02/05/2019] [Indexed: 12/29/2022]
Abstract
The variation in the casein genes has a major impact on the milk composition of goats. Even though many casein polymorphisms have been identified so far, we do not know yet whether they are evolutionarily ancient (i.e., they existed before domestication) or young (i.e., they emerged after domestication). Herewith, we identified casein polymorphisms in a data set of 106 caprine whole-genome sequences corresponding to bezoars (Capra aegagrus, the ancestor of domestic goats) and 4 domestic goat (Capra hircus) populations from Europe, Africa, the Far East, and the Near East. Domestic and wild goat populations shared a substantial number of casein SNP, from 36.1% (CSN2) to 55.1% (CSN1S2). The comparison of casein variation among bezoars and the 4 domestic goat populations demonstrated that more than 50% of the casein SNP are shared by 2 or more populations, and 18 to 44% are shared by all populations. Moreover, the majority of casein alleles reported in domestic goats also segregate in the bezoar, including several alleles displaying significant associations with milk composition (e.g., the A/B alleles of the CSN1S1 and CSN3 genes, the A allele of the CSN2 gene). We conclude that much of the current diversity of the caprine casein genes comes from ancient standing variation segregating in the ancestor of modern domestic goats.
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Affiliation(s)
- D Guan
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - E Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - T F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F., 70.040-020 Brazil
| | - X Such
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - V Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - N R Tawari
- Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona (CSIC-IRTA-UAB-UB), Campus 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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17
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Yang W, Han J, Ma J, Feng Y, Hou Q, Wang Z, Yu T. Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontology. Exp Ther Med 2019; 17:2561-2566. [PMID: 30906446 PMCID: PMC6425128 DOI: 10.3892/etm.2019.7216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/23/2019] [Indexed: 12/21/2022] Open
Abstract
Guilt by association (GBA) algorithm has been widely used to predict gene functions statistically, and a network-based approach may increase the confidence and veracity of identifying molecular signatures for diseases. The aim of the present study was to suggest a gene ontology (GO)-based method by integrating the GBA algorithm and network, to identify key gene functions for spinal muscular atrophy (SMA). The inference of predicting key gene functions was comprised of four steps, preparing gene lists and sets; extracting differentially expressed genes (DEGs) using microarray data [linear models for microarray data (limma)] package; constructing a co-expression matrix on gene lists using the Spearman correlation coefficient method; and predicting gene functions by GBA algorithm. Ultimately, key gene functions were predicted according to the area under the curve (AUC) index for GO terms and the GO terms with AUC >0.7 were determined as the optimal gene functions for SMA. A total of 484 DEGs and 466 background GO terms were regarded as gene lists and sets for the subsequent analyses, respectively. The predicted results obtained from the network-based GBA approach showed 141 gene sets had a good classified performance with AUC >0.5. Most significantly, 3 gene sets with AUC >0.7 were denoted as seed gene functions for SMA, including cell morphogenesis, which is involved in differentiation and ossification. In conclusion, we have predicted 3 key gene functions for SMA compared with control utilizing network-based GBA algorithm. The findings may provide great insights to reveal pathological and molecular mechanism underlying SMA.
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Affiliation(s)
- Wenjiu Yang
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Jing Han
- Department of Ophthalmology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Jinfeng Ma
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Yujie Feng
- Hepatobiliary Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Qingxian Hou
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Zhijie Wang
- Department of Spine Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Tengbo Yu
- Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266071, P.R. China
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18
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Li J, Bed’hom B, Marthey S, Valade M, Dureux A, Moroldo M, Péchoux C, Coville J, Gourichon D, Vieaud A, Dorshorst B, Andersson L, Tixier‐Boichard M. A missense mutation in
TYRP1
causes the chocolate plumage color in chicken and alters melanosome structure. Pigment Cell Melanoma Res 2018; 32:381-390. [DOI: 10.1111/pcmr.12753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 09/19/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Jingyi Li
- Department of Animal and Poultry Sciences Virginia Tech Blacksburg Virginia
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas
| | - Bertrand Bed’hom
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Sylvain Marthey
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Mathieu Valade
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Audrey Dureux
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Marco Moroldo
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Christine Péchoux
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Jean‐Luc Coville
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | | | - Agathe Vieaud
- GABI, AgroParisTech, INRA Université Paris‐Saclay Jouy‐en‐Josas France
| | - Ben Dorshorst
- Department of Animal and Poultry Sciences Virginia Tech Blacksburg Virginia
| | - Leif Andersson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station Texas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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19
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Kumar C, Song S, Dewani P, Kumar M, Parkash O, Ma Y, Malhi KK, Yang N, Mwacharo JM, He X, Jiang L. Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations. Anim Genet 2018; 49:592-604. [PMID: 30229969 DOI: 10.1111/age.12722] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).
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Affiliation(s)
- C Kumar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan.,Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - S Song
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - P Dewani
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - M Kumar
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - O Parkash
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - Y Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - K K Malhi
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - N Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - J M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - X He
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - L Jiang
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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20
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Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 2018; 361:85-88. [PMID: 29976826 DOI: 10.1126/science.aas9411] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, Israel
| | - François Pompanon
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Tristan Cumer
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Groningen University, Groningen, Netherlands
| | - Azadeh Fatemeh Mohaseb
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Delphine Decruyenaere
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Hossein Davoudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Özlem Çevik
- Trakya Universitesi, Edebiyat Fakültesi, Arkeoloi Bölümü, Edirne, Turkey
| | - Gary Rollefson
- Department of Anthropology, Whitman College, Walla Walla, WA 99362, USA
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Roya Khazaeli
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Sanaz Beizaee Doost
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord, Iran
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Edinburgh EH8 9AG, UK
| | | | - Sepideh Maziar
- Institut für Archäologische Wissenschaften, Goethe Universität, Frankfurt am Main, Germany
| | - Boris Gasparian
- Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Louise Martin
- Institute of Archeology, University College London, London, UK
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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21
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Nazari-Ghadikolaei A, Mehrabani-Yeganeh H, Miarei-Aashtiani SR, Staiger EA, Rashidi A, Huson HJ. Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat. Front Genet 2018; 9:105. [PMID: 29670642 PMCID: PMC5893768 DOI: 10.3389/fgene.2018.00105] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/16/2018] [Indexed: 12/31/2022] Open
Abstract
The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.
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Affiliation(s)
- Anahit Nazari-Ghadikolaei
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hassan Mehrabani-Yeganeh
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Seyed R. Miarei-Aashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Amir Rashidi
- Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan, Sanandaj, Iran
| | - Heather J. Huson
- Department of Animal Science, Cornell University, Ithaca, NY, United States
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22
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Li G, Xiong H, Xi D, Memon S, Wang L, Liu X, Deng W. An examination of melanogenic traits and <i>TYRP1</i> polymorphism in Nanping and Romney Marsh sheep breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-131-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The effects of mutations of the gene for tyrosinase-related
protein 1 (TYRP1) on the black muscles and coat color in Nanping
black-boned sheep were investigated. Tyrosinase activity and melanin content
in plasma were measured and compared in three random groups of sheep: Nanping
black-boned (101 heads), Nanping normal (106 heads) and Romney Marsh sheep
(82 heads, Ovis aries). Eight exons and their partial flanking
regions of the TYRP1 gene were amplified. Six intronic mutations and
six exonic polymorphisms including two non-synonymous mutations [c.203C > T
(p.A68V) and c.1202T > C (p.V401A)] were identified. Using a
bi-directional polymerase chain reaction allele-specific amplification
(bi-PASA) of the mutation c.203C > T it was shown that the frequencies of
allele C in the Nanping black-boned, Nanping normal and Romney Marsh sheep
were respectively 0.955, 0.967 and 0.744. For the mutation c.1202T > C,
the frequencies of allele T in the three populations of sheep were
respectively 0.777, 0.745 and 0.793 as measured using the single-strand
conformation polymorphism. When the data from sheep of all three populations
with the CC genotype of SNP c.203C > T were pooled, it was found that there
was significantly higher (P < 0.05) tyrosinase activity, content of
alkali-soluble melanin and ratio of eumelanin : total melanin than
in the plasma of sheep with the CT and TT genotypes. This was not so within each
of the three groups of sheep. No significant effect of the TRYP1
genotype on coat color was found. Further studies will be necessary to
determine the cause of the black traits in Nanping black-boned sheep.
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23
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Mucha S, Mrode R, Coffey M, Kizilaslan M, Desire S, Conington J. Genome-wide association study of conformation and milk yield in mixed-breed dairy goats. J Dairy Sci 2017; 101:2213-2225. [PMID: 29290434 DOI: 10.3168/jds.2017-12919] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/08/2017] [Indexed: 11/19/2022]
Abstract
Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log10(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log10(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.
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Affiliation(s)
- Sebastian Mucha
- Poznan University of Life Sciences, 33 Wolynska, 60-637 Poznan, Poland; Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Raphael Mrode
- Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Mike Coffey
- Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - Mehmet Kizilaslan
- Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom; International Center for Livestock Research and Training, Breeding and Genetics Department, 06852, Ankara, Turkey
| | - Suzanne Desire
- Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom.
| | - Joanne Conington
- Animal and Veterinary Sciences, Scotland's Rural College, Easter Bush, Midlothian EH25 9RG, United Kingdom
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24
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Song X, Xu C, Liu Z, Yue Z, Liu L, Yang T, Cong B, Yang F. Comparative Transcriptome Analysis of Mink (Neovison vison) Skin Reveals the Key Genes Involved in the Melanogenesis of Black and White Coat Colour. Sci Rep 2017; 7:12461. [PMID: 28963476 PMCID: PMC5622100 DOI: 10.1038/s41598-017-12754-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022] Open
Abstract
Farmed mink (Neovison vison) is one of the most important fur-bearing species worldwide, and coat colour is a crucial qualitative characteristic that contributes to the economic value of the fur. To identify additional genes that may play important roles in coat colour regulation, Illumina/Solexa high-throughput sequencing technology was used to catalogue the global gene expression profiles in mink skin with two different coat colours (black and white). RNA-seq analysis indicated that a total of 12,557 genes were differentially expressed in black versus white minks, with 3,530 genes up-regulated and 9,027 genes down-regulated in black minks. Significant differences were not observed in the expression of MC1R and TYR between the two different coat colours, and the expression of ASIP was not detected in the mink skin of either coat colour. The expression levels of KITLG, LEF1, DCT, TYRP1, PMEL, Myo5a, Rab27a and SLC7A11 were validated by qRT-PCR, and the results were consistent with RNA-seq analysis. This study provides several candidate genes that may be associated with the development of two coat colours in mink skin. These results will expand our understanding of the complex molecular mechanisms underlying skin physiology and melanogenesis in mink and will provide a foundation for future studies.
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Affiliation(s)
- Xingchao Song
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Chao Xu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zongyue Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Zhigang Yue
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Linling Liu
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Tongao Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Bo Cong
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Fuhe Yang
- Key Laboratory of Special Economic Animal Genetic Breeding and Reproduction, Ministry of Agriculture, State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China.
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25
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Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat. Sci Rep 2017; 7:8621. [PMID: 28819310 PMCID: PMC5561203 DOI: 10.1038/s41598-017-09285-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/14/2017] [Indexed: 01/24/2023] Open
Abstract
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals. Verification of this 66 K SNP chip with the whole-genome sequencing data of 436 cashmere goats showed that the SNP call rates was between 95.3% and 99.8%. The average sequencing depth for target SNPs were 40X. The capture regions were shown to be 200 bp that flank target SNPs. This chip was further tested in a genome-wide association analysis of cashmere fineness (fiber diameter). Several top hit loci were found marginally associated with signaling pathways involved in hair growth. These results demonstrate that the 66 K SNP chip is a useful tool in the genomic analyses of cashmere goats. The successful chip design shows that the SHS-based target enrichment strategy could be applied to SNP chip design in other species.
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26
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Peng Y, Liu X, Geng L, Ma R, Li L, Li J, Zhang C, Liu Z, Gong Y, Li X. Illumina-sequencing based transcriptome study of coat color phenotypes in domestic goats. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0543-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Talenti A, Bertolini F, Pagnacco G, Pilla F, Ajmone-Marsan P, Rothschild MF, Crepaldi P. The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions. Mamm Genome 2017; 28:114-128. [PMID: 28255622 DOI: 10.1007/s00335-017-9678-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/26/2017] [Indexed: 01/10/2023]
Abstract
The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed's main purpose is to produce milk and meat, but is peculiar for its involvement in the "Batailles de Chèvres," a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed.
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Affiliation(s)
- Andrea Talenti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | | | - Giulio Pagnacco
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via Francesco De Sanctis s.n.c., 86100, Campobasso, Italy
| | - Paolo Ajmone-Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Paola Crepaldi
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
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28
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Burren A, Neuditschko M, Signer-Hasler H, Frischknecht M, Reber I, Menzi F, Drögemüller C, Flury C. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds. Anim Genet 2016; 47:727-739. [PMID: 27436146 DOI: 10.1111/age.12476] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2016] [Indexed: 01/03/2023]
Abstract
We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.
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Affiliation(s)
- A Burren
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
| | - M Neuditschko
- Swiss National Stud Farm, Agroscope Research Station, Les Longs-Prés, 1580, Avenches, Switzerland
| | - H Signer-Hasler
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
| | - M Frischknecht
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
| | - I Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - F Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - C Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland
| | - C Flury
- School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland
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Menzi F, Keller I, Reber I, Beck J, Brenig B, Schütz E, Leeb T, Drögemüller C. Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation. Sci Rep 2016; 6:28438. [PMID: 27329507 PMCID: PMC4916431 DOI: 10.1038/srep28438] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023] Open
Abstract
The South African Boer goat displays a characteristic white spotting phenotype, in which the pigment is limited to the head. Exploiting the existing phenotype variation within the breed, we mapped the locus causing this white spotting phenotype to chromosome 17 by genome wide association. Subsequent whole genome sequencing identified a 1 Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats. We propose a hypothesis that ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely lead to an absence of melanocytes in the non-pigmented body areas of Boer goats. Our findings demonstrate the value of domestic animals as reservoir of unique mutants and for identifying a precisely defined functional CNV.
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Affiliation(s)
- Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Irene Keller
- Department of Clinical Research and Swiss Institute of Bioinformatics, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Irene Reber
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
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Hepp D, Gonçalves GL, Moreira GRP, de Freitas TRO. Epistatic Interaction of the Melanocortin 1 Receptor and Agouti Signaling Protein Genes Modulates Wool Color in the Brazilian Creole Sheep. J Hered 2016; 107:544-52. [PMID: 27288530 DOI: 10.1093/jhered/esw037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/29/2016] [Indexed: 02/01/2023] Open
Abstract
Different pigmentation genes have been associated with color diversity in domestic animal species. The melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are candidate genes responsible for variation in wool color among breeds of sheep. Although the influence of these genes has been described in some breeds, in many others the effect of interactions among genes underlying wool color has not been investigated. The Brazilian Creole sheep is a local breed with a wide variety of wool color, ranging from black to white with several intermediate hues. We analyzed in this study the influence of the genes MC1R, ASIP, TYRP1, and KIT on the control of wool color in this breed. A total of 410 samples were analyzed, including 148 white and 262 colored individuals. The MC1R and ASIP polymorphisms were significantly associated with the segregation of either white or colored wool. The dominant MC1R allele (E(D) p.M73K and p.D121N) was present only in colored animals. All white individuals were homozygous for the MC1R recessive allele (E(+)) and carriers of the duplicated copy of ASIP A gene expression assay showed that only the carrier of the duplicated copy of ASIP produces increased levels in skin, not detectable in the single homozygous copy. These results demonstrate that the epistatic interaction of the genotypes in the MC1R and ASIP gene is responsible for the striking color variation in the Creole breed.
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Affiliation(s)
- Diego Hepp
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp).
| | - Gislene Lopes Gonçalves
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Gilson Rudinei Pires Moreira
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
| | - Thales Renato Ochotorena de Freitas
- From the Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp, Gonçalves, and de Freitas); Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile (Gonçalves); Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Moreira); and Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil (Hepp)
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31
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Wu X, Zhang Y, Shen L, Du J, Luo J, Liu C, Pu Q, Yang R, Li X, Bai L, Tang G, Zhang S, Zhu L. A 6-bp deletion in exon 8 and two mutations in introns of TYRP1 are associated with blond coat color in Liangshan pigs. Gene 2016; 578:132-6. [DOI: 10.1016/j.gene.2015.12.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/26/2015] [Accepted: 12/07/2015] [Indexed: 01/02/2023]
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32
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Corrigendum. Anim Genet 2015; 46:470. [PMID: 26207940 DOI: 10.1111/age.12308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dietrich J, Menzi F, Ammann P, Drögemüller C, Leeb T. A breeding experiment confirms the dominant mode of inheritance of the brown coat colour associated with the (496) Asp TYRP1 allele in goats. Anim Genet 2015; 46:587-8. [PMID: 26153465 DOI: 10.1111/age.12320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Joëlle Dietrich
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bern, 3001, Switzerland.,Swiss Competence Center of Animal Breeding and Genetics, Bern University of Applied Sciences HAFL & Agroscope, University of Bern, Bern, 3001, Switzerland
| | - Fiona Menzi
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bern, 3001, Switzerland.,Swiss Competence Center of Animal Breeding and Genetics, Bern University of Applied Sciences HAFL & Agroscope, University of Bern, Bern, 3001, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bern, 3001, Switzerland.,Swiss Competence Center of Animal Breeding and Genetics, Bern University of Applied Sciences HAFL & Agroscope, University of Bern, Bern, 3001, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,DermFocus, University of Bern, Bern, 3001, Switzerland.,Swiss Competence Center of Animal Breeding and Genetics, Bern University of Applied Sciences HAFL & Agroscope, University of Bern, Bern, 3001, Switzerland
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