谷子SSR标记在狗尾草中的有效性检测
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摘要
狗尾草(S. viridis (L.) Beauv.)为一年生草本植物,是谷子(S. italica (L.) P. Beauv.)的祖本植物。本研究采集赤峰地区狗尾草种质资源,随机挑选40份材料,利用种子发芽并提取叶片基因组DNA,构建混池。利用361对谷子SSR标记对狗尾草基因组DNA混池进行PCR检测,有311对(86.15%)标记能够扩增出目的片段。其中,1号～9号染色体SSR标记依次为38对、42对、43对、34对、42对、34对、8对、26对、44对,平均距离依次为1.11Mbp、1.17Mbp、1.18Mbp、1.19Mbp、1.13Mbp、1.06Mbp、4.50Mbp、1.57Mbp、1.34 Mbp。相比较而言,1号染色体上的SSR标记在检测狗尾草时有效性最高(100.00%),7号染色体上的有效性最低(24.24%),说明谷子不同染色体上的SSR标记在狗尾草中的有效性不同。这些有效的SSR标记可作为狗尾草遗传相关研究的核心引物。
Green foxtail(S.viridis(L.) Beauv.) as the annual herb,is the ancestral plant for foxtail millet(S.italica(L.) P.Beauv.).In this study,the germplasm resources of green foxtail in Chifeng region were collected at first,and 40 materials were randomly selected as materials.Then,genomic DNA of leaves was extracted by germination of seeds,and genomic DNA mixing pool was constructed.361 pairs SSR markers of foxtail millet were used for PCR detection of the green foxtail genomic DNA mixing pool,and 311 pairs(86.15%) SSR markers were able to amplify the target fragments in the genomic DNA mixing pool.There are38 pairs,42 pairs,43 pairs,34 pairs,42 pairs,34 pairs,8 pairs,26 pairs,and 44 pairs of SSR markers on chromosome 1 to 9,and the average genomic distance of markers in 9 chromosomes was 1.11 Mbp,1.17 Mbp,1.18 Mbp,1.19 Mbp,1.13 Mbp,1.06 Mbp,4.50 Mbp,1.57 Mbp,and 1.34 Mbp,Respectively.Compared among different chromosomes,the effectiveness of PCR detecting for green foxtail genomic DNA mixing pool of foxtail millet SSR markers which located in chromosome 1 was highest(100.00%),but which in chromosome 7 was lowest(24.24%).It means that the PCR detecting effectiveness of SSR markers from different chromosome is different.Those 311 pairs SSR markers can be used as mainly primers in genetic research of green foxtail.
Green foxtail(S.viridis(L.) Beauv.) as the annual herb,is the ancestral plant for foxtail millet(S.italica(L.) P.Beauv.).In this study,the germplasm resources of green foxtail in Chifeng region were collected at first,and 40 materials were randomly selected as materials.Then,genomic DNA of leaves was extracted by germination of seeds,and genomic DNA mixing pool was constructed.361 pairs SSR markers of foxtail millet were used for PCR detection of the green foxtail genomic DNA mixing pool,and 311 pairs(86.15%) SSR markers were able to amplify the target fragments in the genomic DNA mixing pool.There are38 pairs,42 pairs,43 pairs,34 pairs,42 pairs,34 pairs,8 pairs,26 pairs,and 44 pairs of SSR markers on chromosome 1 to 9,and the average genomic distance of markers in 9 chromosomes was 1.11 Mbp,1.17 Mbp,1.18 Mbp,1.19 Mbp,1.13 Mbp,1.06 Mbp,4.50 Mbp,1.57 Mbp,and 1.34 Mbp,Respectively.Compared among different chromosomes,the effectiveness of PCR detecting for green foxtail genomic DNA mixing pool of foxtail millet SSR markers which located in chromosome 1 was highest(100.00%),but which in chromosome 7 was lowest(24.24%).It means that the PCR detecting effectiveness of SSR markers from different chromosome is different.Those 311 pairs SSR markers can be used as mainly primers in genetic research of green foxtail.
引文
[1]李荫梅.谷子育种学[M].北京:中国农业出版社,1997.
[2]张恒庆,吴锦美,房孝迪,等.山东长岛南4岛狗尾草(Setaira Vividis(L.)Beauv)种群遗传多样性的ISSR分析[J].辽宁师范大学学报(自然科学版),2013(1):98-101.
[3]Li H W,Li CH,Pao WK.Cytogenetical and genetical studies of the interspecific cross between the cultivated foxtail millet,Setaria italica(L.)Beauv.and the green foxtail millet S.viridis L[J].J Am Soc Agron,1945,37:32-54.
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[5]Li CH,Pao WK,Li HW.Interspecific crosses in Setaria[J].J Hered,1942,33:351-355.
[6]Ayyangar GNR,Narayanan TR.The inheritance of characters in Setaria italica(Beauv.)the Italian millet,part I.Grain colours[J].Ind JArgic Sci,1931,1:586-608.
[7]MacVicar R M,Parnell HR.The inheritance of plant colour and the extent of natural crossing in foxtail millet[J].Sci Agric,1941,22:80-84.
[8]Jusuf M,Pernes J.Genetic variability of foxtail millet(Setaria italica Beauv.),electrophoretic studies of five isozyme systems[J].Theor Appl Genet,1985,71:385-391.
[9]Gale MD,Devos KM.Comparative genetics in the grasses[J].Proc Natl Acad Sci USA,1998,95:1971-1974.
[10]Moore G,Devos KM,Wang Z,et al.Cereal genome evolution[J].Curr Biol,1995,5:737-739.
[11]Wang Z,Devos KM,Liu C,et al.Construction of R FLP based maps of foxtail millet,Setaria italica[J].Theor Appl Genet,1998,96:31-36.
[12]Doust AN,Devos KM,Gadberry M,et al.Genetic control of branching in the foxtail millet[J].Proc Natl Acad Sci USA,2004,101:9045-9050.
[13]Jia X,Zhang Z,Liu Y,et al.Development and genetic mapping of SSR markers in foxtail millet[Setaria italica(L.)P.Beauv.][J].Theor Appl Genet,2009,118:821-829.
[14]Zhang S,Tang C,Zhao Q,et al.Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet[Setaria italica(L.)P.Beauv][J].BMC Genomics,2014,15:78 http://www.biomedcentral.com/1471-2164/15/78.
[15]李伟,智慧,王永芳,等.适合于狗尾草属遗传分析的ISSR标记筛选及反应体系优化研究[J].华北农学报,2007,22(4):141-145.
[16]张恒庆,吴锦美,房孝迪,等.山东长岛南4岛狗尾草(Setaira viridis(L.)Beauv)种群遗传多样性的ISSR分析[J].辽宁师范大学学报(自然科学版),2013(1):98-101.
[17]Murray M G,Thompson W F.R apid isolation of high molecular weight plant DNA[J].Nucl Acids R es,1980,8:4321-4325.
[18]Sanguinetti C J,Dias N E,Simpson A J.R apid silver staining and recovery of PCR products separated on polyacrylamide gels[J].Biotechniques,1994,17:914-921.
[19]张耀元,任彦鑫,禾璐,等.基于表型性状和SSR标记的山西省青狗尾草资源遗传多样性分析[J].中国农业大学学报,2016,21(10):11-22.
[20]Jia G Q,Shi S K,Wang C F,et al.Molecular diversity and population structure of Chinese green foxtail[Setaria viridis(L.)Beauv.]revealed by microsatellite analysis[J].Journal of Experimental Botany,2013,64(12):3645-3656.
[21]Wang R L,Wendel J F,Dekker J H.Weedy adaptation in Setaria Spp.1.isozyme analysis of genetic diversity and population genetic structure in Setaria viridis[J].Am J Bot,1995,82:308-317.
[22]d'Ennequin M L,Panaud O,Toupance B,et al.Assessment of genetic relationships between Setaria italica and its wild relative S.viridis using AFLP markers[J].Theor Appl Genet,2000,100:1061-1066.
[23]阎洪波,黎裕,王天宇,等.中国谷子主产区谷子近缘种狗尾草的遗传多样性[J].西北植物学报,2003,23(6):926-932.
[24]秦岭,于淑婷,杨延兵,等.1980s-2010s华北夏谷区主栽谷子品种SSR遗传多样性分析[J].植物遗传资源学报,2019,20(01):225-232.
[25]丁银灯,胡相伟,聂石辉,等.谷子种质资源表型及SSR遗传多样性分析[J].植物遗传资源学报,2018,19(06):196-207.
[26]杨天育,牟平,孙万仓,等.中国北部高原地区谷子品种遗传差异的SSR分析[J].西北植物学报,2010,30(9):1786-1791.
[27]朱学海,张艳红,宋燕春,等.基于SSR标记的谷子遗传多样性研究[J].植物遗传资源学报,2010,11(6):698-702.
[28]Kim E J,Sa K J,Park K C,et al.Study of genetic diversity and relationships among accessions of foxtail millet[Setaria italica(L.)P.Beauv.]in Korea,China,and Pakistan using SSR markers[J].Genes&Genomics,2012,34(5):529-538.
[29]Wang C,Chen J,Zhi H,et al.Population genetics of foxtail millet and its wild ancestor[J].BMC Genetics,2010,11:90.
[30]Zhu Q,Zheng X,Luo J,et al.Multilocus analysis of nucleotide variation of O ryza sativa and its wild relatives:severe bottleneck during domestication of rice[J].Mol Biol Evol,2007,24:875-888.
[2]张恒庆,吴锦美,房孝迪,等.山东长岛南4岛狗尾草(Setaira Vividis(L.)Beauv)种群遗传多样性的ISSR分析[J].辽宁师范大学学报(自然科学版),2013(1):98-101.
[3]Li H W,Li CH,Pao WK.Cytogenetical and genetical studies of the interspecific cross between the cultivated foxtail millet,Setaria italica(L.)Beauv.and the green foxtail millet S.viridis L[J].J Am Soc Agron,1945,37:32-54.
[4]K.E.Prasada R ao,J.M.J.de Wet,D.E.Brink,et al.Infraspecific variation and systematics of cultivated Setaria italica,foxtail millet(Poaceae)[J].Economic Botany,1987,January,Volume 41(1):108-116.
[5]Li CH,Pao WK,Li HW.Interspecific crosses in Setaria[J].J Hered,1942,33:351-355.
[6]Ayyangar GNR,Narayanan TR.The inheritance of characters in Setaria italica(Beauv.)the Italian millet,part I.Grain colours[J].Ind JArgic Sci,1931,1:586-608.
[7]MacVicar R M,Parnell HR.The inheritance of plant colour and the extent of natural crossing in foxtail millet[J].Sci Agric,1941,22:80-84.
[8]Jusuf M,Pernes J.Genetic variability of foxtail millet(Setaria italica Beauv.),electrophoretic studies of five isozyme systems[J].Theor Appl Genet,1985,71:385-391.
[9]Gale MD,Devos KM.Comparative genetics in the grasses[J].Proc Natl Acad Sci USA,1998,95:1971-1974.
[10]Moore G,Devos KM,Wang Z,et al.Cereal genome evolution[J].Curr Biol,1995,5:737-739.
[11]Wang Z,Devos KM,Liu C,et al.Construction of R FLP based maps of foxtail millet,Setaria italica[J].Theor Appl Genet,1998,96:31-36.
[12]Doust AN,Devos KM,Gadberry M,et al.Genetic control of branching in the foxtail millet[J].Proc Natl Acad Sci USA,2004,101:9045-9050.
[13]Jia X,Zhang Z,Liu Y,et al.Development and genetic mapping of SSR markers in foxtail millet[Setaria italica(L.)P.Beauv.][J].Theor Appl Genet,2009,118:821-829.
[14]Zhang S,Tang C,Zhao Q,et al.Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet[Setaria italica(L.)P.Beauv][J].BMC Genomics,2014,15:78 http://www.biomedcentral.com/1471-2164/15/78.
[15]李伟,智慧,王永芳,等.适合于狗尾草属遗传分析的ISSR标记筛选及反应体系优化研究[J].华北农学报,2007,22(4):141-145.
[16]张恒庆,吴锦美,房孝迪,等.山东长岛南4岛狗尾草(Setaira viridis(L.)Beauv)种群遗传多样性的ISSR分析[J].辽宁师范大学学报(自然科学版),2013(1):98-101.
[17]Murray M G,Thompson W F.R apid isolation of high molecular weight plant DNA[J].Nucl Acids R es,1980,8:4321-4325.
[18]Sanguinetti C J,Dias N E,Simpson A J.R apid silver staining and recovery of PCR products separated on polyacrylamide gels[J].Biotechniques,1994,17:914-921.
[19]张耀元,任彦鑫,禾璐,等.基于表型性状和SSR标记的山西省青狗尾草资源遗传多样性分析[J].中国农业大学学报,2016,21(10):11-22.
[20]Jia G Q,Shi S K,Wang C F,et al.Molecular diversity and population structure of Chinese green foxtail[Setaria viridis(L.)Beauv.]revealed by microsatellite analysis[J].Journal of Experimental Botany,2013,64(12):3645-3656.
[21]Wang R L,Wendel J F,Dekker J H.Weedy adaptation in Setaria Spp.1.isozyme analysis of genetic diversity and population genetic structure in Setaria viridis[J].Am J Bot,1995,82:308-317.
[22]d'Ennequin M L,Panaud O,Toupance B,et al.Assessment of genetic relationships between Setaria italica and its wild relative S.viridis using AFLP markers[J].Theor Appl Genet,2000,100:1061-1066.
[23]阎洪波,黎裕,王天宇,等.中国谷子主产区谷子近缘种狗尾草的遗传多样性[J].西北植物学报,2003,23(6):926-932.
[24]秦岭,于淑婷,杨延兵,等.1980s-2010s华北夏谷区主栽谷子品种SSR遗传多样性分析[J].植物遗传资源学报,2019,20(01):225-232.
[25]丁银灯,胡相伟,聂石辉,等.谷子种质资源表型及SSR遗传多样性分析[J].植物遗传资源学报,2018,19(06):196-207.
[26]杨天育,牟平,孙万仓,等.中国北部高原地区谷子品种遗传差异的SSR分析[J].西北植物学报,2010,30(9):1786-1791.
[27]朱学海,张艳红,宋燕春,等.基于SSR标记的谷子遗传多样性研究[J].植物遗传资源学报,2010,11(6):698-702.
[28]Kim E J,Sa K J,Park K C,et al.Study of genetic diversity and relationships among accessions of foxtail millet[Setaria italica(L.)P.Beauv.]in Korea,China,and Pakistan using SSR markers[J].Genes&Genomics,2012,34(5):529-538.
[29]Wang C,Chen J,Zhi H,et al.Population genetics of foxtail millet and its wild ancestor[J].BMC Genetics,2010,11:90.
[30]Zhu Q,Zheng X,Luo J,et al.Multilocus analysis of nucleotide variation of O ryza sativa and its wild relatives:severe bottleneck during domestication of rice[J].Mol Biol Evol,2007,24:875-888.