东乡野生稻与日本晴多态性标记的开发
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摘要
东乡野生稻是分布于全球最北端的一种普通野生稻,与亚洲栽培稻基因组差异较大,目前缺少覆盖其全基因组的分子标记。本文以东乡野生稻和日本晴为材料,通过筛选已有的1017个标记,并利用东乡野生稻基因组重测序信息设计的217个InDel标记,共检测出203个标记在东乡野生稻与日本晴间呈现多态性。这些标记均匀分布于12条染色体,平均间隔1.9 Mb,基本覆盖东乡野生稻全基因组区域。通过对籼粳亚种的检验分析,发现该套多态性分子标记在东乡野生稻与粳稻杂交后代群体基因型分析上具有较高的应用价值。本研究结果为发掘东乡野生稻的有利基因以及分子标记辅助选择育种提供了有力的工具。
Dongxiang wild rice is a type of common wild rice(Oryza rufipogon) that has the northernmost natural distribution of any wild rice species. The genome of Dongxiang wild rice differs from that of modern cultivated rice varieties(Oryza sativa). At present, a set of molecular markers that covers the entire genome of Dongxiang wild rice is lacking. In this study, we used Dongxiang wild rice and the Geng rice variety "Nipponbare" as research materials. By screening the existing collection of 1017 SSR and InDel markers and the 217 InDel markers which were designed using Dongxiang wild rice genome resequencing information, we obtained a set of 203 markers polymorphic between Dongxiang wild rice and ‘Nipponbare', which were relatively uniformly distributed on the 12 rice chromosomes, and basically covered the entire genome, with an average inter-locus distance of 1.9 Mb. Through the genotyping of five Xian and five Geng varieties, we concluded that those 203 polymorphic molecular markers have a high application value in genotype analysis of Dongxiang wild rice and Geng rice offspring population. These results provide a powerful tool for exploring beneficial genes from Dongxiang wild rice as well as marker-assisted breeding and selection.
Dongxiang wild rice is a type of common wild rice(Oryza rufipogon) that has the northernmost natural distribution of any wild rice species. The genome of Dongxiang wild rice differs from that of modern cultivated rice varieties(Oryza sativa). At present, a set of molecular markers that covers the entire genome of Dongxiang wild rice is lacking. In this study, we used Dongxiang wild rice and the Geng rice variety "Nipponbare" as research materials. By screening the existing collection of 1017 SSR and InDel markers and the 217 InDel markers which were designed using Dongxiang wild rice genome resequencing information, we obtained a set of 203 markers polymorphic between Dongxiang wild rice and ‘Nipponbare', which were relatively uniformly distributed on the 12 rice chromosomes, and basically covered the entire genome, with an average inter-locus distance of 1.9 Mb. Through the genotyping of five Xian and five Geng varieties, we concluded that those 203 polymorphic molecular markers have a high application value in genotype analysis of Dongxiang wild rice and Geng rice offspring population. These results provide a powerful tool for exploring beneficial genes from Dongxiang wild rice as well as marker-assisted breeding and selection.
引文
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[10]Yu H H,Xie W B,Wang J,Xing Y Z,Xu C G,Li X H,Xiao J H,Zhang Q F.Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.PLoS One,2011,6:e17595.
[11]Abyzov A,Urban A E,Snyder M,Gerstein M.CNVnator:an approach to discover,genotype,and characterize typical and atypical CNVs from family and population genome sequencing.Genome Res,2011,21:974-984.
[12]李德军.江西东乡普通野生稻渗入系的构建及高产QTL定位.中国农业大学博士学位论文,北京,2003.Li D J.Development of Introgression Lines of Common Wild Rice(O.rufipogon Griff.)from Dongxiang in Jiangxi Province and Mapping QTLs for Improving Yield.PhD Dissertation of China Agricultural University,Beijing,China,2003(in Chinese with English abstract).
[13]Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics,2009,25:1754-1760.
[14]Li H,Handsaker B,Wysoker A,Fennell T,Ruan J,Homer N,Marth G,Abecasis G,Durbin R.The Sequence Alignment/Map format and SAMtools.Bioinformatics,2009,25:2078-2079.
[15]Wang K,Li M,Hakonarson H.ANNOVAR:functional annotation of genetic variants from high-throughput sequencing data.Nucl Acids Res,2010,38:e164.
[16]Murray M G,Thompson W F.Rapid isolation of high molecular weight plant DNA.Nucl Acids Res,1980,8:4321-4325.
[17]Bassam B J,Caetano-Anollés G,Gresshoff P M.Fast and sensitive silver staining of DNA in polyacrylamide gels.Anal Biochem,1991,196:80-83.
[2]潘熙淦,饶宪章.东乡野生稻观察及特征鉴定报告.江西农业科技,1982,(7):5-9.Pan X G,Rao X Z.Report of Dongxiang wild rice observation and characterization.Jiangxi Agric Sci&Technol,1982,(7):5-9(in Chinese with English abstract).
[3]黄依南,黄国勤.东乡野生稻的发现、价值与保护.农业资源与环境学报,2012,29:13-15.Huang Y N,Huang G Q.The discovery,value and protection of Dongxiang wild rice.J Agric Resour Environ,2012,29:13-15(in Chinese with English abstract).
[4]刘丹,孙玉友,魏才强,解忠,李洪亮,张巍巍,程杜娟,孙国宏,徐德海.InDel分子标记及其在水稻研究中的应用.种子,2017,(9):47-52.Liu D,Sun Y Y,Wei C Q,Xie Z,Li H L,Zhang W W,Cheng D J,Sun G H,Xu D H.InDel molecular marker and its application in rice(Oryza sativa)research.Seed,2017,(9):47-52(in Chinese with English abstract).
[5]Shen Y J,Jiang H,Jin J P,Zhang Z B,Xi B,He Y Y,Wang G,Qian L L,Li X,Yu Q B,Liu H J,Chen D H,Gao J H,Huang H,Shi T L,Yang Z N.Development of genome-wide DNA polymorphism database for map-based cloning of rice genes.Plant Physiol,2004,135:1198-1205.
[6]冯芳君,罗利军,李荧,周立国,徐小艳,吴金,陈宏伟,陈亮,梅捍卫.水稻InDel和SSR标记多态性的比较分析.分子植物育种,2005,3:725-730.Feng F J,Luo L J,Li Y,Zhou L G,Xu X Y,Wu J,Chen H W,Chen L,Mei H W.Comparative analysis of polymorphism of InDel and SSR markers in rice.Mol Plant Breed,2005,3:725-730(in Chinese with English abstract).
[7]初志战,郭海滨,曾栋昌,刘耀光.籼粳稻基因组295个InDel标记的开发.作物学报,2016,42:932-941.Chu Z Z,Guo H B,Zeng D C,Liu Y G.Development of 295 InDel markers for indica and japonica rice.Acta Agron Sin,2016,42:932-941(in Chinese with English abstract).
[8]Taillon-Miller P,Gu Z J,Li Q,Hillier L,Kwok P Y.Overlapping genomic sequences:a treasure trove of single nucleotide polymorphisms.Genome Res,1998,8:748-754.
[9]唐立群,肖层林,王伟平.SNP分子标记的研究及其应用进展.中国农学通报,2012,28(12):154-158.Tang L Q,Xiao C L,Wang W P.Research and application progress of SNP markers.Chin Agric Sci Bull,2012,28(12):154-158(in Chinese with English abstract).
[10]Yu H H,Xie W B,Wang J,Xing Y Z,Xu C G,Li X H,Xiao J H,Zhang Q F.Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers.PLoS One,2011,6:e17595.
[11]Abyzov A,Urban A E,Snyder M,Gerstein M.CNVnator:an approach to discover,genotype,and characterize typical and atypical CNVs from family and population genome sequencing.Genome Res,2011,21:974-984.
[12]李德军.江西东乡普通野生稻渗入系的构建及高产QTL定位.中国农业大学博士学位论文,北京,2003.Li D J.Development of Introgression Lines of Common Wild Rice(O.rufipogon Griff.)from Dongxiang in Jiangxi Province and Mapping QTLs for Improving Yield.PhD Dissertation of China Agricultural University,Beijing,China,2003(in Chinese with English abstract).
[13]Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics,2009,25:1754-1760.
[14]Li H,Handsaker B,Wysoker A,Fennell T,Ruan J,Homer N,Marth G,Abecasis G,Durbin R.The Sequence Alignment/Map format and SAMtools.Bioinformatics,2009,25:2078-2079.
[15]Wang K,Li M,Hakonarson H.ANNOVAR:functional annotation of genetic variants from high-throughput sequencing data.Nucl Acids Res,2010,38:e164.
[16]Murray M G,Thompson W F.Rapid isolation of high molecular weight plant DNA.Nucl Acids Res,1980,8:4321-4325.
[17]Bassam B J,Caetano-Anollés G,Gresshoff P M.Fast and sensitive silver staining of DNA in polyacrylamide gels.Anal Biochem,1991,196:80-83.