犬基因组结构和多态性研究进展
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摘要
家犬是最早被驯化的家养动物,通过选择进化和培育,世界上注册的已有超过400多个犬品种,每个品种都具有独特的生理、行为和形态特征。利用高密度芯片技术进行犬全基因组多态性分析,并通过基因组多态信息扫描定位功能基因成为热点,总结和综述了犬基因组结构变异和多态信息的研究进展,为开展家犬基因组学研究提供新的方法和思路。
Domestic dog is the earliest domesticated animal.Through selection and evolution as well as breeding,400 dog breeds have been registered,and each of which has its unique physiological,behavioral,and morphological characteristics.With the publication of dog genome sequence,it has become a hot spot to use high-density chip technology for whole genome polymorphism analysis,and to locate functional genes through scanning genome polymorphism information.Based on a lot of literature,this paper summarizes and reviews the canine genome structure,the research progress of mutation and polymorphism information for domestic dogs genomics studies,providing a new method and thought on the scientific study on this aspect.
Domestic dog is the earliest domesticated animal.Through selection and evolution as well as breeding,400 dog breeds have been registered,and each of which has its unique physiological,behavioral,and morphological characteristics.With the publication of dog genome sequence,it has become a hot spot to use high-density chip technology for whole genome polymorphism analysis,and to locate functional genes through scanning genome polymorphism information.Based on a lot of literature,this paper summarizes and reviews the canine genome structure,the research progress of mutation and polymorphism information for domestic dogs genomics studies,providing a new method and thought on the scientific study on this aspect.
引文
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[35] WOHLKE A,PHILIPP U,BOCK P,et al.A one base pair deletion in the canine ATP13A2gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier[J].PLoS Genet,2011,7(10):e1002304.
[36] OLSSON M,MEADOWS J R,TRUVE K,et al.A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs[J].PLoS Genet,2011,7(3):e1001332.
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[38] MEURS K M,LAHMERS S,KEENE B W,et al.A splice site mutation in a gene encoding for PDK4,a mitochondrial protein,is associated with the development of dilated cardiomyopathy in the Doberman pinscher[J].Hum Genet,2012,131(8):1 319-1 325.
[39] BARTHELEMY I,PINTO-MARIZ F,YADA E,et al.Predictive markers of clinical outcome in the GRMD dog model of Duchenne muscular dystrophy[J].Dis Model Mech,2014,7(11):1 253-1 261.
[40] RICKETTS S L,PETTITT L,MCLAUGHLIN B,et al.A novel locus on canine chromosome 13is associated with cataract in the Australian Shepherd breed of domestic dog[J].Mamm Genome,2015,26(5-6):257-263.
[41] SWITONSKI M.Dog as a model in studies on human hereditary diseases and their gene therapy[J].Reprod Biol,2014,14(1):44-50.
[42] HAYWARD J J,CASTELHANO M G,OLIVEIRA K C,et al.Complex disease and phenotype mapping in the domestic dog[J].Nat Commun,2016,7:10 460-10 471.
[43] ROGERS N.Canine clues:Dog genomes explored in effort to bring human cancer to heel[J].Nat Med,2015,21(12):1374-1375.
[2] MELLERSH C S,LANGSTON A A,ACLAND G M,et al.A linkage map of the canine genome[J].Genomics,1997,46(3):326-336.
[3] NEFF M W,BROMAN K W,MELLERSH C S,et al.A second-generation genetic linkage map of the domestic dog,Canis familiaris[J].Genetics,1999,151(2):803-820.
[4] BREEN M,JOUQUAND S,RENIER C,et al.Chromosomespecific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes[J].Genome Res,2001,11(10):1 784-1 795.
[5] MELLERSH C S,HITTE C,RICHMAN M,et al.An integrated linkage-radiation hybrid map of the canine genome[J].Mamm Genome,2000,11(2):120-130.
[6] RICHMAN M,MELLERSH C S,ANDRE C,et al.Characterization of a minimal screening set of 172microsatellite markers for genome-wide screens of the canine genome[J].J Biochem Biophys Methods,2001,47(1-2):137-149.
[7] GUYON R,LORENTZEN T D,HITTE C,et al.A 1-Mb resolution radiation hybrid map of the canine genome[J].Proc Natl Acad Sci U S A,2003,100(9):5 296-5 301.
[8] BREEN M,HITTE C,LORENTZEN T D,et al.An integrated 4249marker FISH/RH map of the canine genome[J].BMC Genomics,2004,5(1):65-75.
[9] KIRKNESS E F,BAFNA V,HALPERN A L,et al.The dog genome:survey sequencing and comparative analysis[J].Science,2003,301(5641):1 898-1 903.
[10] LINDBLAD-TOH K,WADE C M,MIKKELSEN T S,et al.Genome sequence,comparative analysis and haplotype structure of the domestic dog[J].Nature,2005,438(7069):803-819.
[11] CHASE K,CARRIER D R,ADLER F R,et al.Genetic basis for systems of skeletal quantitative traits:principal component analysis of the canid skeleton[J].Proc Natl Acad Sci U S A,2002,99(15):9 930-9 935.
[12] AKEY J M,RUHE A L,AKEY D T,et al.Tracking footprints of artificial selection in the dog genome[J].Proc Natl Acad Sci U S A,2010,107(3):1 160-1 165.
[13] VAYSSE A,RATNAKUMAR A,DERRIEN T,et al.Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping[J].PLoS Genet,2011,7(10):e1002316.
[14] AXELSSON E,RATNAKUMAR A,ARENDT M L,et al.The genomic signature of dog domestication reveals adaptation to a starch-rich diet[J].Nature,2013,495(7441):360-364.
[15] CLUTTON-BROCK J,The Domestic Dog:Its Evolution,Behavior and interactions with People[M].Cambridge University Press,1995.
[16] OVODOV N D,CROCKFORD S J,KUZMIN Y V,et al.A33,000-year-old incipient dog from the Altai Mountains of Siberia:evidence of the earliest domestication disrupted by the Last Glacial Maximum[J].PLoS One,2011,6(7):e22821.
[17] DAVIS S J M,VALLA F R.Evidence for domestication of the dog 12,000years ago in the Natufian of Israel[J].Nature,1978,276(5688):608-610.
[18]VILA C,SAVOLAINEN P,MALDONADO J E,et al.Multiple and ancient origins of the domestic dog[J].Science,1997,276(5319):1 687-1 689.
[19] SAVOLAINEN P,ZHANG Y P,LUO J,et al.Genetic evidence for an East Asian origin of domestic dogs[J].Science,2002,298(5598):1 610-1 613.
[20] LEONARD J A, WAYNE R K, WHEELER J,et al.Ancient DNA evidence for Old World origin of New World dogs[J].Science,2002,298(5598):1 613-1 616.
[21] KOSKINEN M T.Individual assignment using microsatellite DNA reveals unambiguous breed identification in the domestic dog[J].Anim Genet,2003,34(4):297-301.
[22] NEFF M W,ROBERTSON K R,WONG A K,et al.Breed distribution and history of canine mdr1-1Delta,apharmacogenetic mutation that marks the emergence of breeds from the collie lineage[J].Proc Natl Acad Sci U S A,2004,101(32):11 725-11 730.
[23] PARKER H G,KIM L V,SUTTER N B,et al.Genetic structure of the purebred domestic dog[J].Science,2004,304(5674):1 160-1 164.
[24] VONHOLDT B M,POLLINGER J P,LOHMUELLER K E,et al.Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication[J].Nature,2010,464(7290):898-902.
[25] WANG G D,ZHAI W,YANG H C,et al.Out of southern East Asia:the natural history of domestic dogs across the world[J].Cell Res,2016,26(1):21-33.
[26] SHANNON L M,BOYKO R H,CASTELHANO M,et al.Genetic structure in village dogs reveals a Central Asian domestication origin[J].Proc Natl Acad Sci U S A,2015,112(44):13 639-13 644.
[27] BARSH G S.How the dog got its spots[J].Nat Genet,2007,39(11):1 304-1 306.
[28] DROGEMULLER C,KARLSSON E K,HYTONEN M K,et al.A mutation in hairless dogs implicates FOXI3in ectodermal development[J].Science,2008,321(5895):1 462.
[29] WIIK A C,WADE C,BIAGI T,et al.A deletion in nephronophthisis 4(NPHP4)is associated with recessive cone-rod dystrophy in standard wire-haired dachshund[J].Genome Res,2008,18(9):1 415-1 421.
[30] DROGEMULLER C,BECKER D,BRUNNER A,et al.A missense mutation in the SERPINH1 gene in Dachshunds with osteogenesis imperfecta[J].PLoS Genet,2009,5(7):e1000579.
[31] AWANO T,JOHNSON G S,WADE C M,et al.,Genomewide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis[J].Proc Natl Acad Sci U S A,2009,106(8):2 794-2 799.
[32] WILBE M,ZIENER M L,ARONSSON A,et al.DLA class II alleles are associated with risk for canine symmetrical lupoid onychodystrophy(SLO)[J].PLoS One,2010,5(8):e12332.
[33] DROGEMULLER C,BECKER D,KESSLER B,et al.A deletion in the N-myc downstream regulated gene 1(NDRG1)gene in Greyhounds with polyneuropathy[J].PLoS One,2010,5(6):e11258.
[34] MEURS K,M MAUCELI E,LAHMERS S,et al.Genomewide association identifies a deletion in the 3'untranslated region of striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy[J].Hum Genet,2010,128(3):315-324.
[35] WOHLKE A,PHILIPP U,BOCK P,et al.A one base pair deletion in the canine ATP13A2gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier[J].PLoS Genet,2011,7(10):e1002304.
[36] OLSSON M,MEADOWS J R,TRUVE K,et al.A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs[J].PLoS Genet,2011,7(3):e1001332.
[37] DOWNS L M,WALLIN-HAKANSSON B,BOURSNELL M,et al.A frameshift mutation in golden retriever dogs with progressive retinal atrophy endorses SLC4A3as a candidate gene for human retinal degenerations[J].PLoS One,2011,6(6):e21452.
[38] MEURS K M,LAHMERS S,KEENE B W,et al.A splice site mutation in a gene encoding for PDK4,a mitochondrial protein,is associated with the development of dilated cardiomyopathy in the Doberman pinscher[J].Hum Genet,2012,131(8):1 319-1 325.
[39] BARTHELEMY I,PINTO-MARIZ F,YADA E,et al.Predictive markers of clinical outcome in the GRMD dog model of Duchenne muscular dystrophy[J].Dis Model Mech,2014,7(11):1 253-1 261.
[40] RICKETTS S L,PETTITT L,MCLAUGHLIN B,et al.A novel locus on canine chromosome 13is associated with cataract in the Australian Shepherd breed of domestic dog[J].Mamm Genome,2015,26(5-6):257-263.
[41] SWITONSKI M.Dog as a model in studies on human hereditary diseases and their gene therapy[J].Reprod Biol,2014,14(1):44-50.
[42] HAYWARD J J,CASTELHANO M G,OLIVEIRA K C,et al.Complex disease and phenotype mapping in the domestic dog[J].Nat Commun,2016,7:10 460-10 471.
[43] ROGERS N.Canine clues:Dog genomes explored in effort to bring human cancer to heel[J].Nat Med,2015,21(12):1374-1375.