麦洼牦牛基因组三碱基重复微卫星的挖掘及其遗传多态性分析
|
摘要
为了解麦洼牦牛现有群体的遗传多样性及种群遗传分化特征,试验通过生物信息学方法从已公布的牦牛基因组中筛选到9 466个三碱基重复微卫星位点,以191个麦洼牦牛基因组DNA样品为模板对各个位点进行PCR扩增和聚丙烯酰胺凝胶电泳基因分型。经过哈迪-温伯格平衡检验,在15个三碱基微卫星位点中,有5个位点偏离哈迪-温伯格平衡(P<0.05)。15个微卫星位点均为高度多态性(PIC>0.5),群体平均观测杂合度(Ho)、平均期望杂合度(He)和平均多态信息含量(PIC)分别达到0.5041、0.8152和0.7831。进一步通过Structure 3.0软件分析发现,麦洼牦牛群体结构单一,无分化特征,表明麦洼牦牛品种虽然具有较高的遗传多态性但是无分化迹象。
In order to study the genetic diversity and differentiation characteristics of the existing population of Maiwa yak and provide a theoretical basis for utilization in the future,a total of9 466tri-nucleotide repeats microsatellites loci were screened based on the release of genome of yaks by bioinformatics method.The tri-nucleotide repeats microsatellites were amplified by PCR using the genomic DNA of 191 Maiwa yaks as templates,and the polymorphic microsatellite loci were genotyped through polyacrylamide electrophoresis experiment.After the Hardy-Weinberg equilibrium test,5tri-nucleotide microsatellite loci were deviated from the Hardy-Weinberg equilibrium(P<0.05).15 microsatellite loci were highly polymorphic(PIC>0.5),the mean observed heterozygosity(Ho),mean expected heterozygosity(He)and mean polymorphic information content(PIC)were 0.5041,0.8152and0.7831,respectively.Maiwa yak population exhibited no characteristics of differentiation by Structure3.0software analysis.Therefore,Maiwa yak had plentiful genetic polymorphism while no signs of genetic differentiation were observed within the population.
In order to study the genetic diversity and differentiation characteristics of the existing population of Maiwa yak and provide a theoretical basis for utilization in the future,a total of9 466tri-nucleotide repeats microsatellites loci were screened based on the release of genome of yaks by bioinformatics method.The tri-nucleotide repeats microsatellites were amplified by PCR using the genomic DNA of 191 Maiwa yaks as templates,and the polymorphic microsatellite loci were genotyped through polyacrylamide electrophoresis experiment.After the Hardy-Weinberg equilibrium test,5tri-nucleotide microsatellite loci were deviated from the Hardy-Weinberg equilibrium(P<0.05).15 microsatellite loci were highly polymorphic(PIC>0.5),the mean observed heterozygosity(Ho),mean expected heterozygosity(He)and mean polymorphic information content(PIC)were 0.5041,0.8152and0.7831,respectively.Maiwa yak population exhibited no characteristics of differentiation by Structure3.0software analysis.Therefore,Maiwa yak had plentiful genetic polymorphism while no signs of genetic differentiation were observed within the population.
引文
[1]钟金城,陈志华,马志杰,等.牦牛分子育种的理论与实践[J].西南民族大学学报(自然科学版),2006,32(1):114-119.
[2]Hadonou A M,Sargent D J,Wi lson F,et al.Development of microsatell ite markers in Fragaria,their use in genetic diversity analysis,and their potential for genetic linkage mapping[J].Genome,2004,47(3):429-438.
[3]Staten R,Schully S D,Noor M A.A microsatellite linkage map of Drosophila mojavensis[J].BMC Genetics,2004,5(1):1-12.
[4]Romero C,Pedryc A,Munoz V,et al.Genetic diversity of different apricot geographical groups det-ermined by SSR markers[J].Genome,2003,46(2):244-252.
[5]Sakurai K,Horiuchi Y,Ikeda H,et al.A novel susceptibility locus for moyamoya disease on chromosome8 q23[J].Journal of Human Genetics,2004,49(5):278-281.
[6]王曦,李红霞,许尚忠,等.中国西门塔尔牛产奶性状与微卫星标记相关分析[J].畜牧兽医学报,2004,35(4):372-374.
[7]Ritz L R,Glowatzki-Mullis M L,MacHugh D E,et al.Phylogenetic analysis of the tribe Bovini using microsatellites[J].Animal Genetics,2000,31(3):178-185.
[8]李铎,柴志欣,姬秋梅,等.西藏牦牛微卫星DNA的遗传多样性[J].遗传,2013,35(2):175-184.
[9]Li Q,Wan J M.SSRHunter:Development of a local searching software for SSR sites[J].Yi Chuan,2005,27(5):808-810.
[10]李红梅.基于基因组信息的大黄鱼(Pseudosciaena crocea)微卫星标记开发及应用[D].舟山:浙江海洋学院,2014.
[11]Müllenbach R,Lagoda P J,Welter C.An efficient salt-chloroform extraction of DNA from blood and tissues[J].Trends in Genetics,1989,5(12):391.
[12]Kalinowski S T,Taper M L,Marshall T C.Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment[J].Molecular Ecology,2007,16(5):1099-1106.
[13]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data[J].Genetics,2000,155(2):945-959.
[14]戚文华,蒋雪梅,肖国生,等.牛和绵羊全基因组微卫星序列的搜索及其生物信息学分析[J].畜牧兽医学报,2013,44(11):1724-1733.
[15]闫秋良,张英汉,李宏滨,等.从绵羊UniGene数据库中筛选微卫星标记的初步研究[J].西北农林科大学学报(自然科学版),2007,11:15-18.
[16]戚文华,蒋雪梅,肖国生,等.猪全基因组中微卫星分布规律[J].畜牧与兽医,2014,8:9-13.
[17]黄杰,杜联明,李玉芝,等.红原鸡全基因组中微卫星分布规律研究[J].四川动物,2012,3:358-363.
[18]Cai X,Mipam T,Zhao F,et al.Isolation and characterization of polymorphic microsatellites in the genome of yak(Bos grunniens)[J].Molecular Biology Reports,2014,41(6):3829-3837.
[19]Li Q F,Zhao Z B,Li Y H,et al.Construction of microsatellite-enriched library of yak and phylogenetic study of six Chinese yak populations using yak-specific microsatellites[A].In:Proceedings of the Fourth International Congress on Yak[C].2004.
[2]Hadonou A M,Sargent D J,Wi lson F,et al.Development of microsatell ite markers in Fragaria,their use in genetic diversity analysis,and their potential for genetic linkage mapping[J].Genome,2004,47(3):429-438.
[3]Staten R,Schully S D,Noor M A.A microsatellite linkage map of Drosophila mojavensis[J].BMC Genetics,2004,5(1):1-12.
[4]Romero C,Pedryc A,Munoz V,et al.Genetic diversity of different apricot geographical groups det-ermined by SSR markers[J].Genome,2003,46(2):244-252.
[5]Sakurai K,Horiuchi Y,Ikeda H,et al.A novel susceptibility locus for moyamoya disease on chromosome8 q23[J].Journal of Human Genetics,2004,49(5):278-281.
[6]王曦,李红霞,许尚忠,等.中国西门塔尔牛产奶性状与微卫星标记相关分析[J].畜牧兽医学报,2004,35(4):372-374.
[7]Ritz L R,Glowatzki-Mullis M L,MacHugh D E,et al.Phylogenetic analysis of the tribe Bovini using microsatellites[J].Animal Genetics,2000,31(3):178-185.
[8]李铎,柴志欣,姬秋梅,等.西藏牦牛微卫星DNA的遗传多样性[J].遗传,2013,35(2):175-184.
[9]Li Q,Wan J M.SSRHunter:Development of a local searching software for SSR sites[J].Yi Chuan,2005,27(5):808-810.
[10]李红梅.基于基因组信息的大黄鱼(Pseudosciaena crocea)微卫星标记开发及应用[D].舟山:浙江海洋学院,2014.
[11]Müllenbach R,Lagoda P J,Welter C.An efficient salt-chloroform extraction of DNA from blood and tissues[J].Trends in Genetics,1989,5(12):391.
[12]Kalinowski S T,Taper M L,Marshall T C.Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment[J].Molecular Ecology,2007,16(5):1099-1106.
[13]Pritchard J K,Stephens M,Donnelly P.Inference of population structure using multilocus genotype data[J].Genetics,2000,155(2):945-959.
[14]戚文华,蒋雪梅,肖国生,等.牛和绵羊全基因组微卫星序列的搜索及其生物信息学分析[J].畜牧兽医学报,2013,44(11):1724-1733.
[15]闫秋良,张英汉,李宏滨,等.从绵羊UniGene数据库中筛选微卫星标记的初步研究[J].西北农林科大学学报(自然科学版),2007,11:15-18.
[16]戚文华,蒋雪梅,肖国生,等.猪全基因组中微卫星分布规律[J].畜牧与兽医,2014,8:9-13.
[17]黄杰,杜联明,李玉芝,等.红原鸡全基因组中微卫星分布规律研究[J].四川动物,2012,3:358-363.
[18]Cai X,Mipam T,Zhao F,et al.Isolation and characterization of polymorphic microsatellites in the genome of yak(Bos grunniens)[J].Molecular Biology Reports,2014,41(6):3829-3837.
[19]Li Q F,Zhao Z B,Li Y H,et al.Construction of microsatellite-enriched library of yak and phylogenetic study of six Chinese yak populations using yak-specific microsatellites[A].In:Proceedings of the Fourth International Congress on Yak[C].2004.