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Zhou H, Ma R, Gao L, Zhang J, Zhang A, Zhang X, Ren F, Zhang W, Liao L, Yang Q, Xu S, Otieno Ogutu C, Zhao J, Yu M, Jiang Q, Korban SS, Han Y. A 1.7-Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:192-205. [PMID: 32722872 PMCID: PMC7769229 DOI: 10.1111/pbi.13455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/16/2020] [Indexed: 05/06/2023]
Abstract
Flat peaches have become popular worldwide due to their novelty and convenience. The peach flat fruit trait is genetically controlled by a single gene at the S locus, but its genetic basis remains unclear. Here, we report a 1.7-Mb chromosomal inversion downstream of a candidate gene encoding OVATE Family Protein, designated PpOFP1, as the causal mutation for the peach flat fruit trait. Genotyping of 727 peach cultivars revealed an occurrence of this large inversion in flat peaches, but absent in round peaches. Ectopic overexpression of PpOFP1 resulted in oval-shaped leaves and shortened siliques in Arabidopsis, suggesting its role in repressing cell elongation. Transcriptional activation of PpOFP1 by the chromosomal inversion may repress vertical elongation in flat-shaped fruits at early stages of development, resulting in the flat fruit shape. Moreover, PpOFP1 can interact with fruit elongation activator PpTRM17, suggesting a regulatory network controlling fruit shape in peach. Additionally, screening of peach wild relatives revealed an exclusive presence of the chromosomal inversion in P. ferganensis, supporting that this species is the ancestor of the domesticated peach. This study provides new insights into mechanisms underlying fruit shape evolution and molecular tools for genetic improvement of fruit shape trait in peach breeding programmes.
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Affiliation(s)
- Hui Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural CropsInstitute of HorticultureAnhui Academy of Agricultural SciencesHefeiChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Ruijuan Ma
- Institute of HorticultureJiangsu Academy of Agricultural SciencesNanjingChina
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNYUSA
| | - Jinyun Zhang
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural CropsInstitute of HorticultureAnhui Academy of Agricultural SciencesHefeiChina
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Fei Ren
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Weihan Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Liao Liao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
| | - Qiurui Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
| | - Shengli Xu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
| | - Collins Otieno Ogutu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Jianbo Zhao
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Mingliang Yu
- Institute of HorticultureJiangsu Academy of Agricultural SciencesNanjingChina
| | - Quan Jiang
- Institute of Forestry and PomologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Schuyler S. Korban
- Department of Natural Resources and Environmental SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenThe Innovative Academy of Seed DesignChinese Academy of SciencesWuhanChina
- Center of Economic BotanyCore Botanical GardensChinese Academy of SciencesWuhanChina
- Sino‐African Joint Research CenterChinese Academy of SciencesWuhanChina
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Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses. Genes (Basel) 2020; 11:genes11060680. [PMID: 32580410 PMCID: PMC7348759 DOI: 10.3390/genes11060680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 11/26/2022] Open
Abstract
Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed.
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The Genetic Basis of Piebald Coat Colour in Hucul Horses in the Context of White Markings and Crypto-Tobiano as a Breeding Problem in Poland. ANNALS OF ANIMAL SCIENCE 2019. [DOI: 10.2478/aoas-2019-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The aim of the study was to analyse the genetic basis of piebald coat colour in Hucul horses and to verify their coat colour in breeding records. Tests were performed with DNA purified from the whole blood samples of 242 Hucul horses with different coat colour patterns. DNA was analysed to identify an inversion in ECA3 (PCR). The results confirmed that the inversion on ECA3 is a direct factor determining piebald (tobiano) colour in the analysed Hucul horses. No inversion was observed in any of the solid coloured horses, but it was present in all the piebald ones. It was also identified in 18% (11 of 61) of the horses from the group of horses qualified in the passport as solid coloured with white markings. In fact, these horses had the tobiano gene that is phenotypically identifiable as crypto-tobiano, which may give the false impression of having white markings and lead to error when describing a horse. This is an important issue, in particular with regard to the breed standard, which eliminates Hucul horses with white markings from breeding.
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Henkel J, Lafayette C, Brooks SA, Martin K, Patterson-Rosa L, Cook D, Jagannathan V, Leeb T. Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness. Anim Genet 2019; 50:172-174. [PMID: 30644113 DOI: 10.1111/age.12762] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2018] [Indexed: 01/18/2023]
Abstract
White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white-spotting phenotype were deaf. We obtained whole-genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63-kb deletion spanning exons 6-9 of the MITF gene (chr16:21 503 211-21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR-based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.
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Affiliation(s)
- J Henkel
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | | | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - K Martin
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - L Patterson-Rosa
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611-0910, USA
| | - D Cook
- Etalon Inc., Menlo Park, CA, 94025, USA
| | - V Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.,DermFocus, University of Bern, 3001, Bern, Switzerland
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Kim NY, Bhuiyan MSA, Chae HS, Baek KS, Son JK, Shin SM, Woo JH, Park SH, Lee SH. Genome-wide association study for tobiano spotting coat color in Korean Jeju × Thoroughbred horse population. Anim Genet 2017; 48:728-729. [PMID: 28850680 DOI: 10.1111/age.12596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Nam Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | | | - Hyun Seok Chae
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Kwang Soo Baek
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Jun Kyu Son
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Sang Min Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Jae Hoon Woo
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Seol Hwa Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, 593-50, Sanrokbuk-ro, Jeju, 63242, Korea
| | - Seung Hwan Lee
- Division of Animal & Dairy Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 34134, Korea
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Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T. Whole genome sequencing reveals a novel deletion variant in the KIT
gene in horses with white spotted coat colour phenotypes. Anim Genet 2017; 48:483-485. [DOI: 10.1111/age.12556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 01/24/2023]
Affiliation(s)
- N. Dürig
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - R. Jude
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- RJC; 53919 Weilerswist Germany
| | - H. Holl
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
- Etalon Inc.; Menlo Park CA 94025 USA
| | - S. A. Brooks
- Department of Animal Sciences; University of Florida; Gainesville FL 32611-0910 USA
| | | | - V. Jagannathan
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - T. Leeb
- Vetsuisse Faculty; Institute of Genetics; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
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Dobigny G, Britton-Davidian J, Robinson TJ. Chromosomal polymorphism in mammals: an evolutionary perspective. Biol Rev Camb Philos Soc 2015; 92:1-21. [PMID: 26234165 DOI: 10.1111/brv.12213] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/23/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
Abstract
Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.
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Affiliation(s)
- Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Cc065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7062, South Africa
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Abstract
PRACTICAL RELEVANCE The health of the cat is a complex interaction between its environment (nurture) and its genetics (nature). Over 70 genetic mutations (variants) have been defined in the cat, many involving diseases, structural abnormalities and clinically relevant health concerns. As more of the cat's genome is deciphered, less commonly will the term 'idiopathic' be used regarding the diagnosis of diseases and unique health conditions. State-of-the-art health care will include DNA profiling of the individual cat, and perhaps its tumor, to establish the best treatment approaches. Genetic testing and eventually whole genome sequencing should become routine diagnostics for feline health care. GLOBAL IMPORTANCE Cat breeds have disseminated around the world. Thus, practitioners should be aware of the breeds common to their region and the mutations found in those regional populations. Specific random-bred populations can also have defined genetic characteristics and mutations. AUDIENCE This review of 'the good, the bad and the ugly' DNA variants provides the current state of knowledge for genetic testing and genetic health management for cats. It is aimed at feline and general practitioners wanting to update and review the basics of genetics, what tests are available for cats and sources for genetic testing. The tables are intended to be used as references in the clinic. Practitioners with a high proportion of cat breeder clientele will especially benefit from the review. EVIDENCE BASE The data presented is extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning the heritable trait and/or disease. The author also draws upon personal experience and expertise in feline genetics.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO 65201, USA
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Hauswirth R, Jude R, Haase B, Bellone RR, Archer S, Holl H, Brooks SA, Tozaki T, Penedo MCT, Rieder S, Leeb T. Novel variants in theKITandPAX3genes in horses with white-spotted coat colour phenotypes. Anim Genet 2013; 44:763-5. [DOI: 10.1111/age.12057] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Regula Hauswirth
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
| | - Rony Jude
- Certagen GmbH; Marie-Curie-Str. 1 53359 Rheinbach Germany
| | - Bianca Haase
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
- Faculty of Veterinary Science; University of Sydney; Sydney 2006 NSW Australia
| | | | | | - Heather Holl
- Department of Animal Science; Cornell University, Ithaca; NY 14853 USA
| | | | - Teruaki Tozaki
- Department of Molecular Genetics; Laboratory of Racing Chemistry; Utsunomiya Tochigi 320-0851 Japan
| | - Maria Cecilia T. Penedo
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - Stefan Rieder
- Agroscope ALP-Haras; Swiss National Stud Farm; 1580 Avenches Switzerland
| | - Tosso Leeb
- Institute of Genetics; Vetsuisse Faculty; University of Bern; 3001 Bern Switzerland
- DermFocus; University of Bern; 3001 Bern Switzerland
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Abstract
Color variation in companion animals has long been of interest to the breeding and scientific communities. Simple traits, like black versus brown or yellow versus black, have helped to explain principles of transmission genetics and continue to serve as models for studying gene action and interaction. We present a molecular genetic review of pigmentary variation in dogs and cats using a nomenclature and logical framework established by early leaders in the field. For most loci in which molecular variants have been identified (nine in dogs and seven in cats), homologous mutations exist in laboratory mice and/or humans. Exceptions include the K locus in dogs and the Tabby locus in cats, which give rise to alternating stripes or marks of different color, and which illustrate the continued potential of coat color genetics to provide insight into areas that transcend pigment cell biology.
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Affiliation(s)
- Christopher B. Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
| | - Gregory S. Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 and Department of Genetics, Stanford University, Stanford, California 94305;,
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Kim NY, Shin KY, Lee CE, Han SH, Lee SS, Park YS, Ko MS, Hong HJ, Yang JH, Jang DJ, Yang YH. Genetic Characterization of Wolla Coat Color in Jeju Horses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.5.375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kim NY, Han SH, Lee SS, Lee CE, Park NG, Ko MS, Yang YH. Relationship Between MC1R and ASIP Genotypes and Basic Coat Colors in Jeju Horses. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5187/jast.2011.53.2.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat-colour-associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat-colour variants. Recent studies demonstrate that this selection for coat-colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat-colour-associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat-colour-associated genes act.
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Affiliation(s)
- Michael Cieslak
- Leibniz Institute for Zoo and Wildlife Research, Research Group of Evolutionary Genetics, Berlin, Germany
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Haase B, Rieder S, Tozaki T, Hasegawa T, Penedo MCT, Jude R, Leeb T. Five novel KIT mutations in horses with white coat colour phenotypes. Anim Genet 2011; 42:337-9. [DOI: 10.1111/j.1365-2052.2011.02173.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yang H, Ma YH, Li B, Dugarjaviin M. [Progress on horse genome project]. YI CHUAN = HEREDITAS 2010; 32:211-8. [PMID: 20233697 DOI: 10.3724/sp.j.1005.2010.00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There is unique genetic information belonging to various kinds of living beings. Understanding of the formation process of organisms and a variety of vital movement is associated with the achievements of genome study. As horse has a notable health condition and great record of the genealogy in the world, thus it becomes a valuable model animal for studying life science. Despite of a late start, the map of the horse genome has undergone unprecedented expansion during the last few years. The current progresses of the horse genome, including genetic map, physical map, comparative genomic map, and functional genomics, were reviewed in this paper. The maps are currently used worldwide to discover genes associated with various traits of significance in horse including general health, disease resistance, reproduction, fertility, athletic performance, phenotypic characteristics like coat color, etc. The results are believed to provide new ideas and approaches for prevention, diagnostics, and therapeutic for horses, and also better foundation of breed selection and equine genetic breeding.
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Affiliation(s)
- Hong Yang
- College of Animal Science and Animal Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China.
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Kakoi H, Tozaki T, Nagata S, Gawahara H, Kijima-Suda I. Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan. J Anim Breed Genet 2010; 126:425-31. [PMID: 19912416 DOI: 10.1111/j.1439-0388.2009.00841.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot(TM) technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.
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Affiliation(s)
- H Kakoi
- Laboratory of Racing Chemistry, Utsunomiya City, Tochigi, Japan.
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18
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Hollister JD, Ross-Ibarra J, Gaut BS. Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol 2009; 27:409-16. [PMID: 19825943 DOI: 10.1093/molbev/msp249] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A recently proposed mutational mechanism, indel-associated mutation (IDAM), posits that heterozygous insertions/deletions (indels) increase the point mutation rate at nearby nucleotides due to errors during meiosis. This mechanism could have especially dynamic consequences for the evolution of plant genomes, because the high degree of variation in the rate of self-fertilization among plant species causes differences in the heterozygosity of alleles, including indel alleles, segregating in plant species. In this study, we investigated the consequences of IDAM for species differing in mating system using both forward population genetic simulations and genomewide DNA resequencing data from Arabidopsis thaliana, Oryza sativa, and Oryza rufipogon. Simulations of different levels of selfing suggest that the effect of IDAM on surrounding nucleotide diversity should decrease with increasing selfing rate. Further simulations incorporating selfing rates and the time of onset of selfing suggest that the time since the switch to selfing also affects patterns of nucleotide diversity due to IDAM. Population genetic analyses of A. thaliana and Oryza DNA sequence data sets empirically confirmed our simulation results, revealing the strongest effect of IDAM in the outcrossing O. rufipogon, a weaker effect in the recently evolved selfer O. sativa, and the weakest effect in the relatively ancient selfer A. thaliana. These results support the novel idea that differences in life history, such as the level of selfing, can affect the per-individual mutation rate among species.
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Affiliation(s)
- Jesse D Hollister
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA.
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Haase B, Brooks SA, Tozaki T, Burger D, Poncet PA, Rieder S, Hasegawa T, Penedo C, Leeb T. Seven novel KIT mutations in horses with white coat colour phenotypes. Anim Genet 2009; 40:623-9. [PMID: 19456317 DOI: 10.1111/j.1365-2052.2009.01893.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
White coat colour in horses is inherited as a monogenic autosomal dominant trait showing a variable expression of coat depigmentation. Mutations in the KIT gene have previously been shown to cause white coat colour phenotypes in pigs, mice and humans. We recently also demonstrated that four independent mutations in the equine KIT gene are responsible for the dominant white coat colour phenotype in various horse breeds. We have now analysed additional horse families segregating for white coat colour phenotypes and report seven new KIT mutations in independent Thoroughbred, Icelandic Horse, German Holstein, Quarter Horse and South German Draft Horse families. In four of the seven families, only one single white horse, presumably representing the founder for each of the four respective mutations, was available for genotyping. The newly reported mutations comprise two frameshift mutations (c.1126_1129delGAAC; c.2193delG), two missense mutations (c.856G>A; c.1789G>A) and three splice site mutations (c.338-1G>C; c.2222-1G>A; c.2684+1G>A). White phenotypes in horses show a remarkable allelic heterogeneity. In fact, a higher number of alleles are molecularly characterized at the equine KIT gene than for any other known gene in livestock species.
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Affiliation(s)
- B Haase
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland
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Crews N, Wittwer CT, Montgomery J, Pryor R, Gale B. Spatial DNA Melting Analysis for Genotyping and Variant Scanning. Anal Chem 2009; 81:2053-8. [DOI: 10.1021/ac801495w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Niel Crews
- Departments of Mechanical Engineering and Pathology, University of Utah, Salt Lake City, Utah 84112
| | - Carl T. Wittwer
- Departments of Mechanical Engineering and Pathology, University of Utah, Salt Lake City, Utah 84112
| | - Jesse Montgomery
- Departments of Mechanical Engineering and Pathology, University of Utah, Salt Lake City, Utah 84112
| | - Rob Pryor
- Departments of Mechanical Engineering and Pathology, University of Utah, Salt Lake City, Utah 84112
| | - Bruce Gale
- Departments of Mechanical Engineering and Pathology, University of Utah, Salt Lake City, Utah 84112
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