1
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Zheng X, Chen J, Nie R, Miao H, Chen Z, He J, Xie Y, Zhang H. Differential expression of ASIP transcripts reveals genetic mechanism underpinning black-tail independence from body plumage in yellow-bodied chickens. Anim Genet 2024; 55:249-256. [PMID: 38194424 DOI: 10.1111/age.13395] [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: 11/30/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
The genetic foundation of chicken body plumage color has been extensively studied. However, little attention has been paid to the inheritance patterns and molecular mechanisms underlying the formation of distal feather colors (tail and wingtip). Differences in these colors are common; for example, the Chinese Huiyang Beard chicken has black tail feathers, but yellow body plumage. Here, the hybrid offspring of Huiyang Beard and White Leghorn chickens were used to study the inheritance patterns of tail-feather color. The expression levels of pigment genes in differently colored feather follicles were analyzed using quantitative real-time PCR. The results showed that genetic regulation of tail-feather color was independent of body-plumage color. The Dominant White locus inhibited eumelanin synthesis in tail feathers without affecting the formation of yellow body plumage, whereas the Silver locus had the opposite effect. The expression of agouti signaling protein (ASIP) gene class 1 transcripts was significantly lower in black tail-feather follicles than in yellow body follicles, whereas tyrosinase-related protein 1 (TYRP1) gene expression was significantly higher in black tail feathers. These differentially expressed genes were confirmed to exert an effect on eumelanin and pheomelanin formation in feathers, thus influencing the regulation of chicken tail-feather color. In conclusion, this study lays the foundation for further research on the genetic mechanisms of regional differences in feather color, contributing to a better understanding of plumage pigmentation in chickens.
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Affiliation(s)
- Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ruixue Nie
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huanhuan Miao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ziwei Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jiaheng He
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yinku Xie
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Hao Zhang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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2
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Ballan M, Bovo S, Bertolini F, Schiavo G, Schiavitto M, Negrini R, Fontanesi L. Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds. J Anim Breed Genet 2023; 140:663-678. [PMID: 37435689 DOI: 10.1111/jbg.12818] [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: 03/18/2023] [Revised: 06/25/2023] [Accepted: 07/02/2023] [Indexed: 07/13/2023]
Abstract
Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources.
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Affiliation(s)
- Mohamad Ballan
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Samuele Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Giuseppina Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Michele Schiavitto
- Associazione Nazionale Coniglicoltori Italiani (ANCI), Volturara Appula, Italy
| | | | - Luca Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
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3
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Zhang K, Wang G, Wang L, Wen B, Fu X, Liu N, Yu Z, Jian W, Guo X, Liu H, Chen SY. A genome-wide association study of coat color in Chinese Rex rabbits. Front Vet Sci 2023; 10:1184764. [PMID: 37655262 PMCID: PMC10467280 DOI: 10.3389/fvets.2023.1184764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Coat color is an important phenotypic characteristic of the domestic rabbit (Oryctolagus cuniculus) and has specific economic importance in the Rex rabbit industry. Coat color varies considerably among different populations of rabbits, and several causal genes for this variation have been thoroughly studied. Nevertheless, the candidate genes affecting coat color variation in Chinese Rex rabbits remained to be investigated. In this study, we collected blood samples from 250 Chinese Rex rabbits with six different coat colors. We performed genome sequencing using a restriction site-associated DNA sequencing approach. A total of 91,546 single nucleotide polymorphisms (SNPs), evenly distributed among 21 autosomes, were identified. Genome-wide association studies (GWAS) were performed using a mixed linear model, in which the individual polygenic effect was fitted as a random effect. We detected a total of 24 significant SNPs that were located within a genomic region on chromosome 4 (OCU4). After re-fitting the most significant SNP (OCU4:13,434,448, p = 1.31e-12) as a covariate, another near-significant SNP (OCU4:11,344,946, p = 7.03e-07) was still present. Hence, we conclude that the 2.1-Mb genomic region located between these two significant SNPs is significantly associated with coat color in Chinese Rex rabbits. The well-studied coat-color-associated agouti signaling protein (ASIP) gene is located within this region. Furthermore, low genetic differentiation was also observed among the six coat color varieties. In conclusion, our results confirmed that ASIP is a putative causal gene affecting coat color variation in Chinese Rex rabbits.
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Affiliation(s)
- Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Bin Wen
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Ning Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Zhiju Yu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Wensu Jian
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Xiaolin Guo
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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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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Belyakin SN, Maksimov DA, Pobedintseva MA, Laktionov PP, Voronova D. ASIP Promoter Variants Predict the Sesame Coat Color in Shiba Inu Dogs. Vet Sci 2022; 9:vetsci9050222. [PMID: 35622750 PMCID: PMC9146165 DOI: 10.3390/vetsci9050222] [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: 02/23/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Animals exhibit a wide variety of genetically determined coat colors and pigmentation patterns that serve important roles in adaptation and communication. Although the genetics of the main coat colors in dogs have been studied extensively, there are types of coat pigmentation that have not been explained yet. Recently, an association between the variants in the ASIP gene Ventral (VP) and Hair Cycle (HCP) promoters with different coat colors in dogs has been established. Here, we used the new findings as a basis to investigate the genetics of the red sesame coat color in Shiba Inu dogs. Our study revealed that red sesame dogs carry a specific heterozygous ASIP promoter diplotype, VP2-HCP1/VP2-HCP3, where VP2-HCP1 is responsible for the red coat with a dark overlay, and VP2-HCP3 for a tan point-like pattern. This finding explains the inheritance of this coat color pattern and can be used by breeders to produce dogs with this rare phenotype. A comparison of sesame dogs (VP2-HCP1/VP2-HCP3) to a dog homozygous for the VP2-HCP1 promoter haplotype suggests that the incomplete dominance between the ASIP alleles may be involved in the sesame coat formation. These results are in good agreement with the new model explaining how different levels of ASIP gene expression affect the regulation of pigment synthesis in melanocytes.
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Affiliation(s)
- Stepan N. Belyakin
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
- VetGenomics Laboratory, 630090 Novosibirsk, Russia
- Correspondence:
| | - Daniil A. Maksimov
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
| | - Maria A. Pobedintseva
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
| | - Petr P. Laktionov
- Genomics Laboratory, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; (D.A.M.); (M.A.P.); (P.P.L.)
- Laboratory of Epigenetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Dinara Voronova
- Russian Nihonken Hozonkai (NIPPO) Club, 129626 Moscow, Russia;
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6
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Demars J, Labrune Y, Iannuccelli N, Deshayes A, Leroux S, Gilbert H, Aymard P, Benitez F, Riquet J. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities. Genomics 2022; 114:110361. [PMID: 35378242 DOI: 10.1016/j.ygeno.2022.110361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023]
Abstract
Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.
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Affiliation(s)
- Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Yann Labrune
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Nathalie Iannuccelli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Alice Deshayes
- UMR967, CEA, INSERM, Institut de Radiobiologie Cellulaire et Moléculaire, Télomères et réparation du chromosome, F- 92265 Fontenay-aux-Roses, France.
| | - Sophie Leroux
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Patrick Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Florence Benitez
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
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7
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Ballan M, Bovo S, Schiavo G, Schiavitto M, Negrini R, Fontanesi L. Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data. Genet Sel Evol 2022; 54:3. [PMID: 35062866 PMCID: PMC8780294 DOI: 10.1186/s12711-022-00696-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/07/2022] [Indexed: 11/23/2022] Open
Abstract
Background Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00696-9.
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8
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Trigo BB, Utsunomiya ATH, Fortunato AAAD, Milanesi M, Torrecilha RBP, Lamb H, Nguyen L, Ross EM, Hayes B, Padula RCM, Sussai TS, Zavarez LB, Cipriano RS, Caminhas MMT, Lopes FL, Pelle C, Leeb T, Bannasch D, Bickhart D, Smith TPL, Sonstegard TS, Garcia JF, Utsunomiya YT. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol 2021; 53:40. [PMID: 33910501 PMCID: PMC8082809 DOI: 10.1186/s12711-021-00633-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. RESULTS We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. CONCLUSIONS Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
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Affiliation(s)
- Beatriz B Trigo
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | - Adam T H Utsunomiya
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Alvaro A A D Fortunato
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,Personal-PEC, R. Sebastião Lima, 1336-Centro, Campo Grande, MS, 79004-600, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Rafaela B P Torrecilha
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Harrison Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Loan Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Ben Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | - Thayla S Sussai
- Centro Universitário Católico Salesiano, Araçatuba, SP, Brazil
| | - Ludmilla B Zavarez
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | | | - Maria M T Caminhas
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | - Flavia L Lopes
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland
| | - Danika Bannasch
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Derek Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Timothy P L Smith
- US. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | | | - José F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.,School of Agriculture and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Yuri T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil. .,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.
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9
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Dog colour patterns explained by modular promoters of ancient canid origin. Nat Ecol Evol 2021; 5:1415-1423. [PMID: 34385618 PMCID: PMC8484016 DOI: 10.1038/s41559-021-01524-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.
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10
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Pallotti S, Chandramohan B, Pediconi D, Nocelli C, La Terza A, Renieri C. Interaction between the melanocortin 1 receptor (MC1R) and agouti signalling protein genes (ASIP), and their association with black and brown coat colour phenotypes in peruvian alpaca. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1850216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Stefano Pallotti
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | | | - Dario Pediconi
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | - Cristina Nocelli
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
| | - Antonietta La Terza
- Scuola di Bioscienze e Medicina Veterinaria, University of Camerino, Camerino, Italy
| | - Carlo Renieri
- Scuola di Scienze del Farmaco e dei Prodotti della salute, University of Camerino, Camerino, Italy
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Dorożyńska K, Maj D. Rabbits - their domestication and molecular genetics of hair coat development and quality. Anim Genet 2020; 52:10-20. [PMID: 33216407 DOI: 10.1111/age.13024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
The European rabbit (Oryctolagus cuniculus) is the only representative of its genus living in present-day Europe and North Africa, and all domestic rabbits are descendants of this one species, which is native to the Iberian Peninsula. There are over 300 breeds of rabbits that differ in size, coat color, length of ears and type of fur. Rabbits are bred for various reasons, such as for laboratory animals and a source of meat, wool and fur, as well as for pets and exhibition animals. The hair coat is a important economic trait of rabbits. Its development and quality are influenced by various factors, both environmental and genetic. The genetic mechanisms underlying its development have not been thoroughly researched. The aim of this review is to discuss the domestication of rabbits and the different aspects of rabbit genetics. A brief review of the properties of rabbit hair coat, hair coat development and hair cycle will be provided, followed by discussion of the factors regulating hair coat development, molecular control of hair coat development and the role of non-coding RNAs in the regulation of gene expression in the hair follicles of rabbits. Information about genetic regulation of pathways could provide useful tools for improving hair coat quality and be of practical use in rabbit breeding.
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Affiliation(s)
- K Dorożyńska
- Department of Genetics, Animal Breeding and Ethology, University of Agriculture in Krakow, al. Mickiewicza 24/28, Krakow, 30-059, Poland
| | - D Maj
- Department of Genetics, Animal Breeding and Ethology, University of Agriculture in Krakow, al. Mickiewicza 24/28, Krakow, 30-059, Poland
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