民猪全基因组序列测定与分析
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摘要
民猪是我国优良地方猪品种,具有高繁殖、耐粗饲、抗逆和肉质优良等特性,但遗传背景模糊。为合理保护和利用民猪资源,利用Illumina Hiseq2000测序平台,采用双末端测序方法,测定10头民猪和4头东北野猪全基因组序列,统计分析SNPs和InDel标记信息,利用NCBI数据库中已知的50个不同个体的SNPs信息作主成分分析并构建分子进化树,使用θπ和Fst两个参数筛选民猪和东北野猪基因组内受选择基因。结果表明,民猪基因组内检测8 255 874个SNPs,大量的SNPs发生在基因间区及内含子区;与猪dbSNP数据库相比,新发现7 739 173个SNPs;检测到739 647个InDel位点,其中纯合多于杂合位点。民猪在遗传距离上介于亚洲猪种和欧洲猪种之间,说明民猪在品种形成过程中,曾引入欧洲猪血统,东北野猪则与亚洲家猪和亚洲野猪聚为一类,符合其地理分布。民猪基因组内共181个基因受到选择,涉及能量代谢、脂质转运、脊椎及视神经发育等。东北野猪基因组内共411个基因受到选择,涉及神经系统、免疫应答、繁殖、线粒体能量代谢等。
Min pig is a famous indigenous pig breed in China. It has the characteristics of high reproduction, rough feeding, good resistance and meat quality. But, its genetic background is fuzzy. In order to protect and utilize the Min pig resources more reasonably in the future, the Illumina Hiseq2000 sequencing platform and the dual terminal sequencing method were used to determine the complete genome sequences of 10 Min pigs and four northeast wild boars. SNPs and InDel marker information were analyzed. SNPs information of Min pig, Northeast wild boar and 50 different individuals which came from NCBI database were analyzed together by principal component analysis. The phylogenetic tree was constructed, too. Using two parameters of θπ and Fst, the selected genes were screened in the genome of Min pig and Northeast wild boar. The results showed that there were 8 255 874 SNPs in Min pig genome and a large number of SNPs were occurred in the intergenic region and intron region. 7739 173 were newly discovered SNPs comparing with dbSNP database of pigs. At the same time, 739647 InDel loci were detected. Homozygous InDel loci were more than hetero-zygous InDel loci. Min pig was existed between the Asian pig breeds and the European pig breeds in the genetic distance. It meaned that the Min pig had been introduced into the European pig breeds in the course of breed formation, while the northeast wild boar was clustered with the Asian pig and the Asian wild boar,conforming to its geographical distribution. 181 candidate genes were selected from the Min pig genome, which involved energy metabolism, lipid transport, spine and optic nerve development. 411 candidate genes were selected from northeast wild boar genome, including nervous system, immune response, reproduction, mitochondrial energy metabolism and so on.
Min pig is a famous indigenous pig breed in China. It has the characteristics of high reproduction, rough feeding, good resistance and meat quality. But, its genetic background is fuzzy. In order to protect and utilize the Min pig resources more reasonably in the future, the Illumina Hiseq2000 sequencing platform and the dual terminal sequencing method were used to determine the complete genome sequences of 10 Min pigs and four northeast wild boars. SNPs and InDel marker information were analyzed. SNPs information of Min pig, Northeast wild boar and 50 different individuals which came from NCBI database were analyzed together by principal component analysis. The phylogenetic tree was constructed, too. Using two parameters of θπ and Fst, the selected genes were screened in the genome of Min pig and Northeast wild boar. The results showed that there were 8 255 874 SNPs in Min pig genome and a large number of SNPs were occurred in the intergenic region and intron region. 7739 173 were newly discovered SNPs comparing with dbSNP database of pigs. At the same time, 739647 InDel loci were detected. Homozygous InDel loci were more than hetero-zygous InDel loci. Min pig was existed between the Asian pig breeds and the European pig breeds in the genetic distance. It meaned that the Min pig had been introduced into the European pig breeds in the course of breed formation, while the northeast wild boar was clustered with the Asian pig and the Asian wild boar,conforming to its geographical distribution. 181 candidate genes were selected from the Min pig genome, which involved energy metabolism, lipid transport, spine and optic nerve development. 411 candidate genes were selected from northeast wild boar genome, including nervous system, immune response, reproduction, mitochondrial energy metabolism and so on.
引文
[1]国家畜禽遗传资源委员会组编.中国畜禽遗传资源志·猪志[M].北京:中国农业出版社,2011.
[2]张太湘,朱国忱,杨虎.黑龙江宁安县莺歌岭遗址[J].考古,1981(6):481-491,577-578.
[3]汪文强,赵生国,马利青,等.动物基因组学重测序的应用研究进展[J].畜牧兽医学报,2016,47(10):1947-1953.
[4]Li M,Tian S,Jin L,et al.Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars[J].Nature Genetics,2013,45(12):1431-1438.
[5]Ma Y,Wei J,Zhang Q,et al.A genome scan for selection signatures in pigs[J].Plos One,2015,10(3):e0116850.
[6]Wang K,Wu P,Yang Q,et al.Detection of selection signatures in Chinese Landrace and Yorkshire pigs based on genotyping-bysequencing data[J].Frontiers in Genetics,2018,9:119.
[7]Zhang Y.Smart PCA Proceedings of the international joint conference on Artificial Intelligence[C].Pasadena,2009.
[8]Tamura K,Peterson D,Peterson N,et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[9]Groenen M A,Archibald A L,Uenishi H,et al.Analyses of pig genomes provide insight into porcine demography and evolution[J].Nature,2012,491(7424):393-398.
[10]Xiang H,Gao J Q,Cai D W,et al.Origin and dispersal of early domestic pigs in northern China[J].Scientific Reports,2017,7:5602.
[11]Hudson N J,Naval-Sánchez M,Porto-Neto L,et al.Rapid communication:a haplotype information theory method reveals genes of evolutionary interest in European vs.Asian Pigs[J].Journal of Animal Science.2018,96(8):3064-3069.
[12]欧阳依娜,江炎庭,孙利民,等.10个云南地方猪种微卫星遗传多样性分析[J].中国畜牧兽医,2018,45(4):992-1001.
[13]盛中华,陈国宏,潘玉春,等.上海白猪(上系)基因组遗传变异检测与功能注释分析[J].畜牧兽医学报,2018,49(5):887-896.
[14]陈治伟,李晓琴.基于全基因组结构域信息的进化树构建[J].生物信息学,2012,10:31-36.
[15]Ai H,Fang X,Yang B,et al.Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J].Nature Genetics,2015,47(3):217-25.
[16]Wang Z,Chen Q,Yang Y,et al.A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data[J].Animal Genetics,2014,45(6):808-816.
[17]吴一尘,杜星,李平华,等.苏淮猪VRTN基因克隆、组织表达特征与多态性分析[J].中国农业科学,2016,49(18):3639-3648.
[18]Pretegiani E,Rosini F,Rufa A,et al.Genotype-phenotype and OCT correlations in autosomal dominant optic atrophy related to OPA1 gene mutations:Report of 13 Italian families[J].Journal of the Neurological Sciences,2017,382:29.
[2]张太湘,朱国忱,杨虎.黑龙江宁安县莺歌岭遗址[J].考古,1981(6):481-491,577-578.
[3]汪文强,赵生国,马利青,等.动物基因组学重测序的应用研究进展[J].畜牧兽医学报,2016,47(10):1947-1953.
[4]Li M,Tian S,Jin L,et al.Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars[J].Nature Genetics,2013,45(12):1431-1438.
[5]Ma Y,Wei J,Zhang Q,et al.A genome scan for selection signatures in pigs[J].Plos One,2015,10(3):e0116850.
[6]Wang K,Wu P,Yang Q,et al.Detection of selection signatures in Chinese Landrace and Yorkshire pigs based on genotyping-bysequencing data[J].Frontiers in Genetics,2018,9:119.
[7]Zhang Y.Smart PCA Proceedings of the international joint conference on Artificial Intelligence[C].Pasadena,2009.
[8]Tamura K,Peterson D,Peterson N,et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.
[9]Groenen M A,Archibald A L,Uenishi H,et al.Analyses of pig genomes provide insight into porcine demography and evolution[J].Nature,2012,491(7424):393-398.
[10]Xiang H,Gao J Q,Cai D W,et al.Origin and dispersal of early domestic pigs in northern China[J].Scientific Reports,2017,7:5602.
[11]Hudson N J,Naval-Sánchez M,Porto-Neto L,et al.Rapid communication:a haplotype information theory method reveals genes of evolutionary interest in European vs.Asian Pigs[J].Journal of Animal Science.2018,96(8):3064-3069.
[12]欧阳依娜,江炎庭,孙利民,等.10个云南地方猪种微卫星遗传多样性分析[J].中国畜牧兽医,2018,45(4):992-1001.
[13]盛中华,陈国宏,潘玉春,等.上海白猪(上系)基因组遗传变异检测与功能注释分析[J].畜牧兽医学报,2018,49(5):887-896.
[14]陈治伟,李晓琴.基于全基因组结构域信息的进化树构建[J].生物信息学,2012,10:31-36.
[15]Ai H,Fang X,Yang B,et al.Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J].Nature Genetics,2015,47(3):217-25.
[16]Wang Z,Chen Q,Yang Y,et al.A genome-wide scan for selection signatures in Yorkshire and Landrace pigs based on sequencing data[J].Animal Genetics,2014,45(6):808-816.
[17]吴一尘,杜星,李平华,等.苏淮猪VRTN基因克隆、组织表达特征与多态性分析[J].中国农业科学,2016,49(18):3639-3648.
[18]Pretegiani E,Rosini F,Rufa A,et al.Genotype-phenotype and OCT correlations in autosomal dominant optic atrophy related to OPA1 gene mutations:Report of 13 Italian families[J].Journal of the Neurological Sciences,2017,382:29.
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