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Maciel SVSA, Oliveira IPP, Senes BB, Silva JAIDV, Feitosa FLB, Alves JS, Costa RB, de Camargo GMF. Genomic regions associated with coat color in Gir cattle. Genome 2024. [PMID: 38579337 DOI: 10.1139/gen-2023-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.
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Rios ACH, Nasner SLC, Londoño-Gil M, Gonzalez-Herrera LG, Lopez-Herrera A, Flórez JCR. Genome-wide association study for reproduction traits in Colombian Creole Blanco Orejinegro cattle. Trop Anim Health Prod 2023; 55:429. [PMID: 38044379 DOI: 10.1007/s11250-023-03847-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
The profitability of the beef cattle production system relies heavily on reproductive traits. Unfortunately, certain traits, such as age at first calving (AFC), calving interval (CI), and gestation length (GL), can pose challenges in traditional breeding programs because of their low heritability (0.01-0.12) and sex-limited characteristics. Another important aspect is the conservation of the genetic resources of animals adapted to the Colombian regions, which implies the preservation and rational use of the creole breeds in the country market. Therefore, this study aimed to identify genomic regions in the creole cattle breed Blanco Orejinegro (BON) that influence the reproductive traits in females. The dataset comprised 439 animals and 118,116 single-nucleotide polymorphisms' (SNPs) markers. The GS3 program was used to identify the SNP effects employing the BAYES Cπ methodology. The number of SNPs with effect for AFC was 25, 1527 for CI, and 23 for GL. Some of the genes found associated with reproductive and growth traits as well as immune response and environmental adaptation ECE1, EPH, EPHB2, SMARCAL1, IGFBP5, IGFBP2, FCGRT, EGFR, MUL1, PINK1, STPG1, CNGB1, TGFB1, OXTR, IL22RA1, MYOM3, OXTR, CNR2, HIVEP3, CTPS1, CXCL8, FCGRT, MREG, TMEM169, PECR, and MC1R. Our results evidenced a high contribution of the genetic architecture of the Colombian creole cattle breed Blanco Orejinegro that may impact should be included in implementing genetic improvement and conservation programs.
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Affiliation(s)
- Ana Cristina Herrera Rios
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Carrera 65 N 59A-110, 050034, Medellín, Colombia.
- Grupo de Investigación Nutri-Solla, SOLLA S.A., Cra 42 #33-80, Itagüí, Antioquia, Colombia.
| | - Sindy Liliana Caivio Nasner
- Grupo de Investigación Biomolecular y Pecuaria BIOPEC, Universidad Tecnológica de Pereira, Cra. 27 N10-02, 660003, Pereira, Risaralda, Colombia
| | - Marisol Londoño-Gil
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Carrera 65 N 59A-110, 050034, Medellín, Colombia
| | - Luis Gabriel Gonzalez-Herrera
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Carrera 65 N 59A-110, 050034, Medellín, Colombia
| | - Albeiro Lopez-Herrera
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Carrera 65 N 59A-110, 050034, Medellín, Colombia
| | - Juan Carlos Rincón Flórez
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Carrera 65 N 59A-110, 050034, Medellín, Colombia
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Palmira, Carrera 32 N 12 - 00, PC 763352, Palmira, Colombia
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Kunene LM, Muchadeyi FC, Hadebe K, Mészáros G, Sölkner J, Dugmore T, Dzomba EF. Genetics of Base Coat Colour Variations and Coat Colour-Patterns of the South African Nguni Cattle Investigated Using High-Density SNP Genotypes. Front Genet 2022; 13:832702. [PMID: 35747604 PMCID: PMC9209731 DOI: 10.3389/fgene.2022.832702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
Nguni cattle are a Sanga type breed with mixed B. taurus and B. indicus ancestry and proven resistance to ticks, diseases and other harsh conditions of the African geographical landscape. The multi-coloured Nguni coats have found a niche market in the leather industry leading to breeding objectives towards the promotion of such diversity. However, there is limited studies on the genomic architecture underlying the coat colour and patterns hampering any potential breeding and improvement of such trait. This study investigated the genetics of base coat colour, colour-sidedness and the white forehead stripe in Nguni cattle using coat colour phenotyped Nguni cattle and Illumina Bovine HD (770K) genotypes. Base coat colour phenotypes were categorised into eumelanin (n = 45) and pheomelanin (n = 19). Animals were categorised into either colour-sided (n = 46) or non-colour-sided (n = 94) and similarly into presence (n = 15) or absence (n = 67) of white forehead stripe. Genome-wide association tests were conducted using 622,103 quality controlled SNPs and the Efficient Mixed Model Association eXpedited method (EMMAX) implemented in Golden Helix SNP Variation Suite. The genome-wide association studies for base coat colour (eumelanin vs. pheomelanin) resulted into four indicative SNPs on BTA18 and a well-known gene, MC1R, was observed within 1 MB from the indicative SNPs (p < 0.00001) and found to play a role in the melanogenesis (core pathway for melanin production) and the MAPK signalling pathway. GWAS for colour-sidedness resulted in four indicative SNPs, none of which were in close proximity to the KIT candidate gene known for colour-sidedness. GWAS for the white forehead stripe resulted in 17 indicative SNPs on BTA6. Four genes MAPK10, EFNA5, PPP2R3C and PAK1 were found to be associated with the white forehead stripe and were part of the MAPK, adrenergic and Wnt signalling pathways that are synergistically associated with the synthesis of melanin. Overall, our results prove prior knowledge of the role of MC1R in base coat colours in cattle and suggested a different genetic mechanism for forehead stripe phenotypes in Nguni cattle.
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Affiliation(s)
- Langelihle Mbali Kunene
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | | | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Onderstepoort, South Africa
| | - Gábor Mészáros
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Trevor Dugmore
- KZN Department of Agriculture and Rural Development, Pietermaritzburg, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Scottsville, South Africa
- *Correspondence: Edgar Farai Dzomba,
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Jiang L, Kon T, Chen C, Ichikawa R, Zheng Q, Pei L, Takemura I, Nsobi LH, Tabata H, Pan H, Omori Y, Ogura A. Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour. Sci Rep 2021; 11:17359. [PMID: 34462508 PMCID: PMC8405626 DOI: 10.1038/s41598-021-96896-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/05/2021] [Indexed: 12/04/2022] Open
Abstract
Zhoushan cattle are an endangered cattle breed in the Zhoushan islands in China. Since Zhoushan cattle have been bred in isolation, they show unique characteristics, such as dark black coat colour. However, no studies have been conducted on the genome of Zhoushan cattle. Here, we performed whole-genome sequencing of seven individuals of Zhoushan cattle and nine cattle in Wenling, geographically close to the Zhoushan islands. By integrating our data and publicly-available data, we found that Zhoushan cattle are genetically highly similar to Bos indicus cattle in south-eastern China. Furthermore, by identifying the genomic regions shared between Zhoushan cattle and Angus cattle, a Bos taurus breed, we found that the p.F195L mutation in melanocyte-stimulating hormone receptor (MC1R) could be associated with their dark black coat colour. Taken together, our results provide a valuable resource for characterising the uniqueness of Zhoushan cattle.
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Affiliation(s)
- Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China. .,Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
| | - Tetsuo Kon
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Chunyan Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ryota Ichikawa
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Qiyuan Zheng
- Zhoushan Sanxing Zhoushan Cattle Protection Institute, Zhoushan City, 316000, China
| | - Liyi Pei
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ikuyo Takemura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Lauden Hagai Nsobi
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Hiromasa Tabata
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Hao Pan
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Yoshihiro Omori
- Laboratory of Functional Genomics, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Atsushi Ogura
- Genomic Diversity Laboratory, Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan.
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Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-Wide Scanning for Signatures of Selection Revealed the Putative Genomic Regions and Candidate Genes Controlling Milk Composition and Coat Color Traits in Sahiwal Cattle. Front Genet 2021; 12:699422. [PMID: 34306039 PMCID: PMC8299338 DOI: 10.3389/fgene.2021.699422] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
Background In the evolutionary time scale, selection shapes the genetic variation and alters the architecture of genome in the organisms. Selection leaves detectable signatures at the genomic coordinates that provide clues about the protein-coding regions. Sahiwal is a valuable indicine cattle adapted to tropical environments with desirable milk attributes. Insights into the genomic regions under putative selection may reveal the molecular mechanisms affecting the quantitative and other important traits. To understand this, the present investigation was undertaken to explore signatures of selection in the genome of Sahiwal cattle using a medium-density genotyping INDUS chip. Result De-correlated composite of multiple selection signals (DCMS), which combines five different univariate statistics, was computed in the dataset to detect the signatures of selection in the Sahiwal genome. Gene annotations, Quantitative Trait Loci (QTL) enrichment, and functional analyses were carried out for the identification of significant genomic regions. A total of 117 genes were identified, which affect a number of important economic traits. The QTL enrichment analysis highlighted 14 significant [False Discovery Rate (FDR)-corrected p-value ≤ 0.05] regions on chromosomes BTA 1, 3, 6, 11, 20, and 21. The top three enriched QTLs were found on BTA 6, 20, and 23, which are associated with exterior, health, milk production, and reproduction traits. The present study on selection signatures revealed some key genes related with coat color (PDGFRA, KIT, and KDR), facial pigmentation (LEF), milk fat percent (MAP3K1, HADH, CYP2U1, and SGMS2), sperm membrane integrity (OSTC), lactation persistency (MRPS30, NNT, CCL28, HMGCS1, NIM1K, ZNF131, and CCDC152), milk yield (GHR and ZNF469), reproduction (NKX2-1 and DENND1A), and bovine tuberculosis susceptibility (RNF144B and PAPSS1). Further analysis of candidate gene prioritization identified four hub genes, viz., KIT, KDR, MAP3K1, and LEF, which play a role in coat color, facial pigmentation, and milk fat percentage in cattle. Gene enrichment analysis revealed significant Gene ontology (GO) terms related to breed-specific coat color and milk fat percent. Conclusion The key candidate genes and putative genomic regions associated with economic traits were identified in Sahiwal using single nucleotide polymorphism data and the DCMS method. It revealed selection for milk production, coat color, and adaptability to tropical climate. The knowledge about signatures of selection and candidate genes affecting phenotypes have provided a background information that can be further utilized to understand the underlying mechanism involved in these traits in Sahiwal cattle.
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Affiliation(s)
- Satish Kumar Illa
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sabyasachi Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Sapna Nath
- Artificial Breeding Research Center, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
| | - Anupama Mukherjee
- Division of Animal Genetics and Breeding, Indian Council of Agricultural Research-National Dairy Research Institute, Karnal, India
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Reverter A, Hudson NJ, McWilliam S, Alexandre PA, Li Y, Barlow R, Welti N, Daetwyler H, Porto-Neto LR, Dominik S. A low-density SNP genotyping panel for the accurate prediction of cattle breeds. J Anim Sci 2021; 98:5924388. [PMID: 33057688 DOI: 10.1093/jas/skaa337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Genomic tools to better define breed composition in agriculturally important species have sparked scientific and commercial industry interest. Knowledge of breed composition can inform multiple scientifically important decisions of industry application including DNA marker-assisted selection, identification of signatures of selection, and inference of product provenance to improve supply chain integrity. Genomic tools are expensive but can be economized by deploying a relatively small number of highly informative single-nucleotide polymorphisms (SNP) scattered evenly across the genome. Using resources from the 1000 Bull Genomes Project we established calibration (more stringent quality criteria; N = 1,243 cattle) and validation (less stringent; N = 864) data sets representing 17 breeds derived from both taurine and indicine bovine subspecies. Fifteen successively smaller panels (from 500,000 to 50 SNP) were built from those SNP in the calibration data that increasingly satisfied 2 criteria, high differential allele frequencies across the breeds as measured by average Euclidean distance (AED) and high uniformity (even spacing) across the physical genome. Those SNP awarded the highest AED were in or near genes previously identified as important signatures of selection in cattle such as LCORL, NCAPG, KITLG, and PLAG1. For each panel, the genomic breed composition (GBC) of each animal in the validation dataset was estimated using a linear regression model. A systematic exploration of the predictive accuracy of the various sized panels was then undertaken on the validation population using 3 benchmarking approaches: (1) % error (expressed relative to the estimated GBC made from over 1 million SNP), (2) % breed misassignment (expressed relative to each individual's breed recorded), and (3) Shannon's entropy of estimated GBC across the 17 target breeds. Our analyses suggest that a panel of just 250 SNP represents an adequate balance between accuracy and cost-only modest gains in accuracy are made as one increases panel density beyond this point.
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Affiliation(s)
- Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Road, St. Lucia, Brisbane, QLD, Australia
| | - Nicholas J Hudson
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
| | - Sean McWilliam
- CSIRO Agriculture & Food, 306 Carmody Road, St. Lucia, Brisbane, QLD, Australia
| | - Pamela A Alexandre
- CSIRO Agriculture & Food, 306 Carmody Road, St. Lucia, Brisbane, QLD, Australia
| | - Yutao Li
- CSIRO Agriculture & Food, 306 Carmody Road, St. Lucia, Brisbane, QLD, Australia
| | | | - Nina Welti
- CSIRO Agriculture & Food, Waite Road, Urrbrae, SA, Australia
| | - Hans Daetwyler
- Agriculture Victoria Research, AgriBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Sonja Dominik
- CSIRO Agriculture & Food, Chiswick, New England Highway, Armidale, NSW, Australia
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Goud TS, Upadhyay RC, Pichili VBR, Onteru SK, Chadipiralla K. Molecular characterization of coat color gene in Sahiwal versus Karan Fries bovine. J Genet Eng Biotechnol 2021; 19:22. [PMID: 33512595 DOI: 10.1186/s43141-021-00117-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/06/2021] [Indexed: 01/12/2023]
Abstract
Background Melanocortin-1-receptor gene (MC1R) plays a significant role in signaling cascade of melanin production. In cattle, the coat colors, such as red and black, are an outcome of eumelanin and pheomelanin pigments, respectively. The coat colors have become critical factors in the animal selection process. This study is therefore aimed at the molecular characterization of reddish-brown coat-colored Sahiwal cattle in comparison to the black and white-colored Karan Fries. Results The Sequence length of the MC1R gene was 954 base pairs in Sahiwal cattle. The sequences were examined and submitted to GenBank Acc.No. MG373575 to MG373605. Alignment of both (Sahiwal and Karan Fries) protein sequences by applying ClustalO multiple sequence alignment programs revealed 99.8–96.8% sequence similarity within the bovine. MC1R gene phylogenetic studies were analyzed by MEGA X. The gene MC1R tree, protein confines, and hereditary difference of cattle were derived from Ensemble Asia Cow Genome Browser 97. One unique single-nucleotide polymorphism (c.844C>A) (SNP) was distinguished. Single amino acid changes were detected in the seventh transmembrane structural helix region, with SNP at p.281 T>N of MC1R gene in Karan Fries cattle. Conclusions In this current research, we first distinguished the genomic sequence of the MC1R gene regions that showed evidence of coat variation between Indian indigenous Sahiwal cattle breed correlated with crossbreed Karan Fries. These variations were found in the Melanocortin 1 receptor coding regions of the diverse SNPs. The conclusions of this research provide new insights into understanding the coat color variation in crossbreed compared to the Indian Sahiwal cattle. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00117-2.
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Xu J, Fu Y, Hu Y, Yin L, Tang Z, Yin D, Zhu M, Yu M, Li X, Zhou Y, Zhao S, Liu X. Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features. J Anim Sci Biotechnol 2020; 11:115. [PMID: 33292532 PMCID: PMC7713148 DOI: 10.1186/s40104-020-00520-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/15/2023] Open
Abstract
Background A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds. Results In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color). Conclusion Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits. Supplementary Information Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.
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Affiliation(s)
- Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
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Reiner G, Weber T, Nietfeld F, Fischer D, Wurmser C, Fries R, Willems H. A genome-wide scan study identifies a single nucleotide substitution in MC1R gene associated with white coat colour in fallow deer (Dama dama). BMC Genet 2020; 21:126. [PMID: 33213385 PMCID: PMC7678172 DOI: 10.1186/s12863-020-00950-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background The coat colour of fallow deer is highly variable and even white animals can regularly be observed in game farming and in the wild. Affected animals do not show complete albinism but rather some residual pigmentation resembling a very pale beige dilution of coat colour. The eyes and claws of the animals are pigmented. To facilitate the conservation and management of such animals, it would be helpful to know the responsible gene and causative variant. We collected 102 samples from 22 white animals and from 80 animals with wildtype coat colour. The samples came from 12 different wild flocks or game conservations located in different regions of Germany, at the border to Luxembourg and in Poland. The genomes of one white hind and her brown calf were sequenced. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies (http://www.ifpcs.org/albinism/), a variant in the MC1R gene (NM_174108.2:c.143 T > C) resulting in an amino acid exchange from leucine to proline at position 48 of the MC1R receptor protein (NP_776533.1:p.L48P) was identified as a likely cause of coat colour dilution. A gene test revealed that all animals of the white phenotype were of genotype CC whereas all pigmented animals were of genotype TT or TC. The study showed that 14% of the pigmented (brown or dark pigmented) animals carried the white allele. Conclusions A genome-wide scan study led to a molecular test to determine the coat colour of fallow deer. Identification of the MC1R gene provides a deeper insight into the mechanism of dilution. The gene marker is now available for the conservation of white fallow deer in wild and farmed animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00950-3.
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Affiliation(s)
- Gerald Reiner
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany. .,Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany.
| | - Tim Weber
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Florian Nietfeld
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
| | - Dominik Fischer
- Arbeitskreis Wildbiologie e.V., Justus-Liebig-University, Giessen, Germany
| | - Christine Wurmser
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Ruedi Fries
- Department of Animal Breeding, Technical University of Munich, Liesel-Beckmann-Strasse 1, D-85354, Freising-Weihenstephan, Germany
| | - Hermann Willems
- Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany
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Marín-Garzón NA, Magalhães AFB, Mota LFM, Fonseca LFS, Chardulo LAL, Albuquerque LG. Genome-wide association study identified genomic regions and putative candidate genes affecting meat color traits in Nellore cattle. Meat Sci 2020; 171:108288. [PMID: 32949820 DOI: 10.1016/j.meatsci.2020.108288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 01/08/2023]
Abstract
Single and multiple-trait GWAS were conducted to detect genomic regions and candidate genes associated with meat color traits (L*, lightness; a*, redness; b*, yellowness) in Nellore cattle. Phenotypic records of 5000 animals, and 3794 genotypes for 614,274 SNPs were used. The BLUPF90 family programs were used through single step GWAS approach. The top 10 genomic regions from single-trait GWAS explained 13.64%, 15.12% and 13% of genetic variance of L*, a* and b*, which harbored 129, 70, and 84 candidate genes, respectively. Regarding multiple-trait GWAS, the top 10 SNP windows explained 17.46%, 18.98% and 13.74% of genetic variance of L*, a* and b*, and harbored 124, 86, and 82 candidate genes, respectively. Pleiotropic effects were evidenced by the overlapping regions detected on BTA 15 and 26 associated with L* and a* (genetic correlation of -0.53), and on BTA 18 associated with a* and b* (genetic correlation of 0.60). Similar genomic regions located on BTA 2, 5, 6, and 18 were detected through single and multi-trait GWAS. Overlapped regions harbored a total of 30 functional candidate genes involved in mitochondrial activity, structural integrity of muscles, lipid oxidation, anaerobic metabolism, and muscular pH.
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Affiliation(s)
- N A Marín-Garzón
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil.
| | - A F B Magalhães
- APTA Beef Cattle Center, Animal Science Institute, Sertãozinho, São Paulo, Brazil
| | - L F M Mota
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L F S Fonseca
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil
| | - L A L Chardulo
- São Paulo State University (Unesp), College of Veterinary and Animal Science, Botucatu, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
| | - L G Albuquerque
- São Paulo State University (Unesp), College of Agricultural and Veterinarian Sciences, Via de Acesso Professor Paulo Donato Castelane Castellane S/N - Vila Industrial, 14884-900 Jaboticabal, SP, Brazil; National Council for Science and Technological Development (CNPq), Brasília, Brazil
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11
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Reiner G, Tramberend K, Nietfeld F, Volmer K, Wurmser C, Fries R, Willems H. A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population. BMC Genet 2020; 21:14. [PMID: 32041521 DOI: 10.1186/s12863-020-0814-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022] Open
Abstract
Background Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene. For this purpose, samples of one white hind and her brown calf were available for whole genome sequencing to identify the single nucleotide polymorphism(s) responsible for the white phenotype. Subsequently, samples from 194 brown and 11 white animals were genotyped. Results Based on a list of colour genes of the International Federation of Pigment Cell Societies, a non-synonymous mutation with exchange of a glycine residue at position 291 of the tyrosinase protein by arginine was identified as the cause of dilution of the coat colour. A gene test led to exactly matching genotypes in all examined animals. The study showed that 14% of the brown animals carry the white gene. This provides a simple and reliable way of conservation for the white animals. However, results could not be transferred to another, unrelated red deer population with white animals. Although no brown animals with a white tyrosinase genotype were detected, the cause for the white colouring in this population was different. Conclusions A gene test for the conservation of white red deer is available for the population of the Reinhardswald. While mutations in the tyrosinase are commonly associated with oculocutaneous albinism type 1, the amino acid exchange at position 291 was found to be associated with coat colour dilution in Cervus elaphus.
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Baazaoui I, McEwan J, Anderson R, Brauning R, McCulloch A, Van Stijn T, Bedhiaf-Romdhani S. GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds. Animals (Basel) 2019; 10:ani10010005. [PMID: 31861491 PMCID: PMC7022847 DOI: 10.3390/ani10010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker FST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.
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Affiliation(s)
- Imen Baazaoui
- Faculty of Science of Bizerte, University of Carthage, Carthage 1054, Tunisia
| | - John McEwan
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Rayna Anderson
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Alan McCulloch
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Tracey Van Stijn
- AgResearch Ltd., Invermay Agricultural Centre; Mosgiel 9092, New Zealand
| | - Sonia Bedhiaf-Romdhani
- National Agricultural Research Institute of Tunisia, Laboratory of Animal and forage Production, University of Carthage, Ariana 1004, Tunisia
- Correspondence: ; Tel.: +216-25-113-344
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Goud TS, Upadhyay RC, Onteru SK, Pichili VBR, Chadipiralla K. Identification and sequence characterization of melanocortin 1 receptor gene ( MC1R) in Bos indicus versus ( Bos taurus X Bos indicus). Anim Biotechnol 2019; 31:283-294. [PMID: 30890019 DOI: 10.1080/10495398.2019.1585866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Melanocortin 1 receptor (MC1R) plays a vital role in melanogenesis and determines coat color of mammals. Polymorphic variants in MC1R, causing coat color variation, were described in few mammals; however, such studies were not done in cattle. The objective of the study was to explore the association of MC1R gene polymorphism within Tharparkar (Bos indicus) and Karan Fries (B. indicus X Bos taurus) cattle. Genomic DNA isolated from blood samples of Tharparkar breed by modified Phenol: Chloroform; Isoamyl alcohol method. Using genomic DNA as template for PCR, MC1R gene was amplified and sequenced. The sequences were analyzed and submitted to Genbank with Acc.No MG373615-MG373644. Comparison of sequence alignment with other bovine species using ClustalW revealed 99-96% similarity. MC1R gene phylogenetic analyses were analyzed using MEGA X. The MC1R gene tree, protein domains and genetic variation of cattle were retrieved from Ensemble Asia Cattle Genome Browser. Eight single nucleotide polymorphisms (SNPs) (c.296T > C, c.583T > C, c.663C > T, c.830T > C, c.853G > A, c.880G > A, c.906C > G, c.927C > T) in CDS reveal high genetic variability. Subsequent to amino acid changes p.L99P, p.F195L, p.F277S, p.A285T and p.D293N, p.R302S, respectively found in seven-transmembrane. Mutations appeared in MC1R of B. taurus with white and black coat color as compared to B. indicus with white coat.
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Affiliation(s)
- Talla Sridhar Goud
- Climate Resilient Live Stock Research Centre, ICAR-National Dairy Research Institute, Karnal, India.,Department of Biotechnology, Vikrama Simhapuri University, Nellore, India
| | - Ramesh Chandra Upadhyay
- Climate Resilient Live Stock Research Centre, ICAR-National Dairy Research Institute, Karnal, India
| | - Suneel Kumar Onteru
- Molecular Endocrinology and Structural Biology, Animal Biochemistry Division, ICAR-National Dairy Research Institute, Karnal, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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15
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Abstract
Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.
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Affiliation(s)
- Imtiaz A. S. Randhawa
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
- * E-mail:
| | - Mehar S. Khatkar
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Peter C. Thomson
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
| | - Herman W. Raadsma
- Reprogen - Animal Bioscience Group, Faculty of Veterinary Science, The University of Sydney, 425 Werombi Road, Camden, 2570, NSW, Australia
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Knaust J, Hadlich F, Weikard R, Kuehn C. Epistatic interactions between at least three loci determine the "rat-tail" phenotype in cattle. Genet Sel Evol 2016; 48:26. [PMID: 27037038 PMCID: PMC4818457 DOI: 10.1186/s12711-016-0199-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 03/03/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The "rat-tail" syndrome (RTS) is an inherited hypotrichosis in cattle, which is exclusively expressed in diluted coloured hair. The affected animals also suffer from disturbed thermoregulation, which impairs their health and growth performance. Phenotypic features that are similar to RTS are observed in dogs with black hair follicle dysplasia. RESULTS We used a resource cross population between German Holstein and Charolais cattle breeds to prove that epistatic interactions between at least three independent genetic loci are required for the expression of the RTS phenotype. In this population, the RTS is exclusively expressed in animals with a eumelanic background that is due to the dominant E (D) allele at the melanocortin 1 receptor gene located on Bos taurus autosome (BTA) 18. In addition, only the individuals that are heterozygous at the dilution locus on BTA5 that corresponds to the premelanosome protein or silver gene variant c.64G>A were classified as displaying a RTS phenotype. Linkage and whole-genome association analyses using different models and different pedigrees allowed us to map a third locus (hereafter referred to as the RTS locus) that is essential for the expression of the RTS phenotype to the chromosomal region between 14 and 22 Mb on BTA5. Our findings clearly demonstrate that the RTS and dilution loci are distinct loci on BTA5. CONCLUSIONS Our study provides evidence that the RTS locus has effects on hair conformation and coat colour dilution and that the effect on coat colour dilution is clearly independent from that of the dilution locus. Finally, our results excluded several other loci that were previously reported to be associated with or to underlie hair conformation or pigmentation traits as the causal mutations of RTS and also several major functional candidate genes that are associated with hypotrichosis in humans. Our finding on the identification of a three-locus interaction that underlies RTS provides a prime example of epistatic interaction between several independent loci that is required for the expression of a distinct phenotype.
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Affiliation(s)
- Jacqueline Knaust
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Frieder Hadlich
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Rosemarie Weikard
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany
| | - Christa Kuehn
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196, Dummerstorf, Mecklenburg-Vorpommern, Germany. .,Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059, Rostock, Germany.
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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] [What about the content of this article? (0)] [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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18
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Cardoso C, Peripolli V, Amador S, Brandão E, Esteves G, Sousa C, França M, Gonçalves F, Barbosa F, Montalvão T, Martins C, Neto AF, McManus C. Physiological and thermographic response to heat stress in zebu cattle. Livest Sci 2015. [DOI: 10.1016/j.livsci.2015.10.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds. Front Genet 2015; 6:167. [PMID: 26029239 PMCID: PMC4429627 DOI: 10.3389/fgene.2015.00167] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/13/2015] [Indexed: 12/11/2022] Open
Abstract
This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity.
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Affiliation(s)
| | - Juan J Arranz
- Departamento de Producción Animal, Universidad de León León, Spain
| | - Pamela Wiener
- Division of Genetics and Genomics, Roslin Institute and R(D)SVS, University of Edinburgh Midlothian, UK
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