全基因组选择信号检测方法在家畜研究中的应用进展
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摘要
长期的自然和人为选择使家畜品种经济性状得到了显著改善,其相关的基因组区域也发生了特定遗传变异。随着时间的推移部分基因多态性已经下降或消失,而在群体中保留包含单一单倍型的多个基因。这种基因组上特定区域基因多态性频率的变异被称为选择信号。识别选择信号可以提供家畜驯化机制并进一步揭示表型相关的基因变异。目前,高密度SNP芯片及大规模重测序技术已成功应用于家畜选择信号鉴定研究。全基因组选择信号检测方法有等位基因频率检测法、连锁不平衡检测法和群体分化分析法。作者综述了全基因组范围内选择信号检测方法及其在家畜研究中的应用进展,为从事家畜育种及生物进化研究人员提供参考。
The economic traits of livestock has been significantly improved due to long-term under natural and artificial selection,and the specific variation characterizations emerged from the selected genome regions.As time goes on,the some polymorphism frequency of gene has dropped or disappeared,and keep in a group contains a single haploid type of multiple genes.This frequency variation of gene in specific region on the genomes is called the signatures of selection.Identifying signatures of selection can provide a straightforward insight into the mechaism of domestication and further uncover the casual genes related to the phenotypic variation.The high density SNP chips and large scale resequencing technology have been successfully applied to genomic selection signature in livestock breeds.The methods to detect selection signatures can be classed into three categories:Site frequency spectrum based methods,haplotyped based methods and population differentiation based methods.In the present article,we summarized the methods of selection signature detection and development and application of genomic selection signature methods in livestock.It will provide useful information for researchers working with breeding and evolutionary biology.
The economic traits of livestock has been significantly improved due to long-term under natural and artificial selection,and the specific variation characterizations emerged from the selected genome regions.As time goes on,the some polymorphism frequency of gene has dropped or disappeared,and keep in a group contains a single haploid type of multiple genes.This frequency variation of gene in specific region on the genomes is called the signatures of selection.Identifying signatures of selection can provide a straightforward insight into the mechaism of domestication and further uncover the casual genes related to the phenotypic variation.The high density SNP chips and large scale resequencing technology have been successfully applied to genomic selection signature in livestock breeds.The methods to detect selection signatures can be classed into three categories:Site frequency spectrum based methods,haplotyped based methods and population differentiation based methods.In the present article,we summarized the methods of selection signature detection and development and application of genomic selection signature methods in livestock.It will provide useful information for researchers working with breeding and evolutionary biology.
引文
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[33]Clop A,Marcq F,Takeda H,et al.A mutation creating apotential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep[J].Nature Genetics,2006,38(7):813-818.
[34]Moradi M H,Nejati-Javaremi A,Moradi-Shahrbabak M,et al.Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition[J].Bmc Genet,2012,13:10.
[35]Gu J J,Orr N,Park S D,et al.A genome scan for positive selection in Thoroughbred horses[J].PLoS One,2009,4(6):e5767.
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[37]Kader A,Li Y,Dong K,et al.Population variation reveals independent selection towards small body size in Chinese Debao pony[J].Genome Biology and Evolution,2015,8(1):42-50.
[38]Andersson L S,Larhammar M,Memic F,et al.Mutations in DMRT3affect locomotion in horses and spinal circuit function in mice[J].Nature,2012,488(7413):642-646.
[2]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):1613-1616.
[3]Diamond J.Evolution,consequences and future of plant and animal domestication[J].Nature,2002,418(6898):700-707.
[4]Flori L,Fritz S,Jaffrezic F,et al.The genome response to artificial selection:A case study in dairy cattle[J].PLoS One,2009,4(8):e6595.
[5]Nielsen R,Hellmann I,Hubisz M,et al.Recent and ongoing selection in the human genome[J].Nat Rev Genet,2007,8(11):857-868.
[6]López M E,Neira R,Yáez J M.Applications in the search for genomic selection signatures in fish[J].Frontiers in Genetics,2015,5:458.
[7]Biswas S,Akey J M.Genomic insights into positive selection[J].Trends Genet,2006,22(8):437-446.
[8]Elsik C G,Tellam R L,Worley K C,et al.The genome sequence of taurine cattle:A window to ruminant biology and evolution[J].Science,2009,324(5926):522-528.
[9]Archibald A L,Cockett N E,Dalrymple B P,et al.The sheep genome reference sequence:A work in progress[J].Anim Genet,2010,41(5):449-453.
[10]Nielsen R.Statistical tests of selective neutrality in the age of genomics[J].Heredity,2001,86:641-647.
[11]Schlotterer C.Hitchhiking mapping-functional genomics from the population genetics perspective[J].Trends Genet,2003,19(1):32-38.
[12]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[13]Charlesworth D.Balancing selection and its effects on sequences in nearby genome regions[J].PLoS Genetics,2006,2(4):e64.
[14]Navarro A,Barton N H.The effects of multilocus balancing selection on neutral variability[J].Genetics,2002,161(2):849-863.
[15]Fay J C,Wu C I.Hitchhiking under positive Darwinian selection[J].Genetics,2000,155(3):1405-1413.
[16]Sabeti P C,Reich D E,Higgins J M,,et al.Detecting recent positive selection in the human genome from haplotype structure[J].Nature,2002,419(6909):832-837.
[17]Hanchard N A,Rockett K A,Spencer C,et al.Screening for recently selected alleles by analysis of human haplotype similarity[J].Am J Hum Genet,2006,78(1):153-159.
[18]Lewontin R C,Krakauer J.Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms[J].Genetics,1973,74(1):175-195.
[19]Andersson L,Georges M.Domestic-animal genomics:Deciphering the genetics of complex traits[J].Nat Rev Genet,2004,5(3):202-212.
[20]Gibbs R A,Taylor J F,Van Tassell C P,et al.Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds[J].Science,2009,324(5926):528-532.
[21]Barendse W,Reverter A,Bunch R J,et al.A validated whole-genome association study of efficient food conversion in cattle[J].Genetics,2007,176(3):1893-1905.
[22]Prasad A,Schnabel R D,Mckay S D,et al.Linkage disequilibrium and signatures of selection on chromosomes 19and 29in beef and dairy cattle[J].Anim Genet,2008,39(6):597-605.
[23]Gautier M,Flori L,Riebler A,et al.A whole genome Bayesian scan for adaptive genetic divergence in West African cattle[J].Bmc Genomics,2009,10:550.
[24]Hosokawa D,Ishii A,Yamaji K,et al.Identification of divergently selected regions between Japanese Black and Holstein cattle using bovine 50kSNP array[J].Anim Sci J,2012,83(1):7-13.
[25]Hayes B J,Lien S,Nilsen H,et al.The origin of selection signatures on bovine chromosome 6[J].Animal Genetics,2008,39(2):105-111.
[26]Cole J B,Van Raden P M,O’Connell J R,et al.Distribution and location of genetic effects for dairy traits[J].J Dairy Sci,2009,92(7):3542-3542.
[27]Kefei C,Tara B,Muir W M,et al.Genetic resources,genome mapping and evolutionary genomics of the pig(Sus scrofa)[J].International Journal of Biological Sciences,2007,3(3):153-165.
[28]Van Laere A S,Nguyen M,Braunschweig M,et al.A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig[J].Nature,2003,425(6960):832-836.
[29]Rubin C J,Megens H J,Barrio A M,et al.Strong signatures of selection in the domestic pig genome[J].P Natl Acad Sci USA,2012,109(48):19529-19536.
[30]Amaral A J,Ferretti L,Megens H J,et al.Genomewide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA[J].PLoS One,2011,6(4):e14782.
[31]Esteve-Codina A,Paudel Y,Ferretti L,et al.Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs[J].Bmc Genomics,2013,14:148.
[32]Kijas J W,Lenstra J A,Hayes B,et al.Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection[J].PLoS Biology,2012,10(2):e1001258.
[33]Clop A,Marcq F,Takeda H,et al.A mutation creating apotential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep[J].Nature Genetics,2006,38(7):813-818.
[34]Moradi M H,Nejati-Javaremi A,Moradi-Shahrbabak M,et al.Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition[J].Bmc Genet,2012,13:10.
[35]Gu J J,Orr N,Park S D,et al.A genome scan for positive selection in Thoroughbred horses[J].PLoS One,2009,4(6):e5767.
[36]Hill E W,Gu J,McGivney B A,et al.Targets of selection in the Thoroughbred genome contain exerciserelevant gene SNPs associated with elite racecourse performance[J].Animal Genetics,2010,41(2):56-63.
[37]Kader A,Li Y,Dong K,et al.Population variation reveals independent selection towards small body size in Chinese Debao pony[J].Genome Biology and Evolution,2015,8(1):42-50.
[38]Andersson L S,Larhammar M,Memic F,et al.Mutations in DMRT3affect locomotion in horses and spinal circuit function in mice[J].Nature,2012,488(7413):642-646.