简单重复序列标记和序列相关扩增多态性标记在草莓遗传多样性分析中的比较
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摘要
利用简单重复序列(simple sequence repeat, SSR)和序列相关扩增多态性(sequence related amplified polymorphism, SRAP)标记分析了来自国内外43个草莓品种的遗传多样性,并比较了这2种分子标记的效果差异。结果表明:30对SSR引物平均多态性位点数为6.43个,每个位点的平均多态性信息含量(polymorphism information content, PIC)值为0.628 4;20个SRAP引物组合平均多态性位点数为14.30个,PIC值高达0.911 4。基于SSR标记的聚类结果与基于SRAP标记的聚类结果的相关系数为0.817,呈显著水平。而SSR标记、SRAP标记分别与SSR+SRAP联合标记的相关系数为0.938和0.966,都达到极显著水平。SSR和SRAP标记都能较好地分析草莓遗传多样性,其中SRAP标记的效果略优于SSR标记,而SSR+SRAP联合标记分析则能更好地评估种质的遗传多样性和亲缘关系。
Simple sequence repeat(SSR) and sequence related amplified polymorphism(SRAP) markers were applied to analyze genetic diversity among 43 strawberry(Fragaria×ananassa Duch.) cultivars and effectivenesses of these two kinds of molecular markers were also compared. The results showed that there were 6.43 polymorphic sites per primer pair of 30 SSR primers, and the average polymorphism information content(PIC) of each site was 0.628 4. While there were 14.30 polymorphic sites per primer pair of 20 SRAP primers,and the average PIC of each site was 0.911 4. The correlation coefficient between clustering results based on SSR markers and SRAP markers was 0.817, which was significant. The correlation coefficients between SSR markers, SRAP markers and SSR+SRAP joint markers were 0.938 and 0.966, respectively, which reached extremely significant levels. Both SSR and SRAP markers can be used to analyze the genetic diversity of strawberry, but the effect of SRAP marker is better than that of SSR marker. The analysis of SSR+SRAP joint markers can better evaluate the genetic diversity and genetic relationship of strawberry germplasm.
Simple sequence repeat(SSR) and sequence related amplified polymorphism(SRAP) markers were applied to analyze genetic diversity among 43 strawberry(Fragaria×ananassa Duch.) cultivars and effectivenesses of these two kinds of molecular markers were also compared. The results showed that there were 6.43 polymorphic sites per primer pair of 30 SSR primers, and the average polymorphism information content(PIC) of each site was 0.628 4. While there were 14.30 polymorphic sites per primer pair of 20 SRAP primers,and the average PIC of each site was 0.911 4. The correlation coefficient between clustering results based on SSR markers and SRAP markers was 0.817, which was significant. The correlation coefficients between SSR markers, SRAP markers and SSR+SRAP joint markers were 0.938 and 0.966, respectively, which reached extremely significant levels. Both SSR and SRAP markers can be used to analyze the genetic diversity of strawberry, but the effect of SRAP marker is better than that of SSR marker. The analysis of SSR+SRAP joint markers can better evaluate the genetic diversity and genetic relationship of strawberry germplasm.
引文
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[16]BUDAK H,SHEARMAN R C,PARMAKSIZ I,et al.Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs,SSRs,RAPDs and SRAPs.Theoretical and Applied Genetics,2004,109:280-288.
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[20]NEI M,LI W H.Mathematical model for studying genetic variation in terms of restriction endonucleases.Proceedings of the National Academy of Sciences of the USA,1979,76:5269-5273.
[21]BOTSTEIN D,WHITE R L,SKOLNICK M,et al.Construction of genetic linkage map in man using restriction fragment length polymorphisms.The American Journal of Human Genetics,1980,32:314-331.
[22]陈伦林,邹小云,李书宇,等.SSR和SRAP标记揭示甘蓝型油菜遗传多样性的差异分析.分子植物育种,2008,6(3):511-516.CHEN L L,ZOU X Y,LI S Y,et al.Analysis of the genetic diversity of rapeseed by SSR and SRAP with emphasis on the difference of this two kinds of markers.Molecular Plant Breeding,2008,6(3):511-516.(in Chinese with English abstract)
[23]谭祖猛,李云昌,胡琼,等.通过分子标记估算遗传距离预测甘蓝型油菜的杂种优势.中国油料作物学报,2007,29(2):126-132.TAN Z M,LI Y C,HU Q,et al.Heterosis prediction based on genetic distance estimated by molecular markers in rapeseed.Chinese Journal of Oil Crop Sciences,2007,29(2):126-132.(in Chinese with English abstract)
[24]甘晓燕,程永芳,巩檑,等.SRAP和SSR标记对马铃薯遗传多样性的差异分析.中国农学通报,2015,31(30):225-230.GAN X Y,CHENG Y F,GONG L,et al.Variance analysis of genetic diversity of potato with SRAP and SSR markers.Chinese Agricultural Science Bulletin,2015,31(30):225-230.(in Chinese with English abstract)
[25]刘通,邓崇岭,程玉芳,等.利用SSR和SRAP技术分析广西柑橘种质遗传多样性.华中农业大学学报,2016(2):23-29.LIU T,DENG C L,CHENG Y F,et al.Analyzing genetic diversity of citrus germplasm in Guangxi Province with SSRand SRAP markers.Journal of Huazhong Agricultural University,2016(2):23-29.(in Chinese with English abstract)
[26]班骞,谢彩云,范国华,等.基于EST-SSR及SRAP标记构建苦荬菜品种(系)DNA指纹图谱.草业学报,2018,27(4):111-122.BAN Q,XIE C Y,FAN G H,et al.DNA fingerprinting of Ixeris polycephala varieties based on EST-SSR and SRAPmarkers.Acta Prataculturae Sinica,2018,27(4):111-122.(in Chinese with English abstract)
[27]王国莉,徐毓璇,黄梅花.基于SSR和SRAP标记的苦瓜品种鉴定及亲缘关系分析.分子植物育种,2016(2):501-510.WANG G L,XU Y X,HUANG M H.Identification and genetic relationship analysis of bitter gourd varieties based on SSR and SPAP.Molecular Plant Breeding,2016(2):501-510.(in Chinese with English abstract)
[28]延娜,李巧丽,郭军战.果桑遗传差异的SRAP和EST-SSR分析.西北农业学报,2015,24(9):91-97.YAN N,LI Q L,GUO J Z.SRAP and EST-SSR analysis of genetic differences in fruit mulberry(Morus spp.).Acta Agriculturae Boreali-Occidentalis Sinica,2015,24(9):91-97.(in Chinese with English abstract)
[29]邹自征,陈建华,栾明宝,等.应用RSAP、SRAP和SSR分析苎麻种质亲缘关系.作物学报,2012,38(5):840-847.ZHOU Z Z,CHEN J H,LUAN M B,et al.Genetic relationship of ramie germplasm revealed by RSAP,SRAPand SSR markers.Acta Agronomica Sinica,2012,38(5):840-847.(in Chinese with English abstract)
[30]董静,张运涛,王桂霞,等.五叶草莓与凤梨草莓种间杂交F1代的形态学及SSR标记鉴定.西北农业学报,2010,19(11):145-148.DONG J,ZHANG Y T,WANG G X,et al.Identification of F1interspecies hybrids between fragaria pentaphylla and F.ananassa by morphological and SSR markers.Acta Agriculturae Boreali-Occidentalis Sinica,2010,19(11):145-148.(in Chinese with English abstract)
[31]史芳芳,汪泉,赵密珍,等.凤梨草莓与绿色草莓种间杂种一代的形态学观察及SSR分析.果树学报,2017(2):175-185.SHI F F,WANG Q,ZHAO M Z,et al.Identification of interspecific hybrids derived from Fragaria×ananassa×F.viridis by morphological features and SSR markers.Journal of Fruit Science,2017(2):175-185.(in Chinese with English abstract)
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[33]黄志城,石敬韡,庞夫花,等.基于SSR标记的草莓品种DNA指纹图谱的构建及应用.分子植物育种,2017,15(8):3097-3116.HUANG Z C,SHI J W,PANG F H,et al.Construction and application of DNA fingerprinting of strawberry(Fragaria ananassa Duch.)varieties based on SSR markers.Molecular Plant Breeding,2017,15(8):3097-3116.(in Chinese with English abstract)
[2]常琳琳,董静,钟传飞,等.中国育成草莓品种的系谱分析.果树学报,2018,35(2):158-167.CHANG L L,DONG J,ZHONG C F,et al.Pedigree analysis of strawberry cultivars released in China.Journal of Fruit Science,2018,35(2):158-167.(in Chinese with English abstract)
[3]马鸿翔,盛炳成,戴子林,等.草莓品种的遗传距离研究.江苏农业学报,1995,11(3):41-45.MA H X,SHENG B C,DAI Z L,et al.Studies on genetic distances among strawberry varieties.Jiangsu Journal of Agricultural Sciences,1995,11(3):41-45.(in Chinese with English abstract)
[4]陈琼娥,钟凤林,潘东明,等.草莓分子标记技术研究进展.亚热带农业研究,2011,7(1):64-67.CHEN Q E,ZHONG F L,PAN D M,et al.Progress of molecular mark on genetic research of strawberry.Subtropical Agriculture Research,2011,7(1):64-67.(in Chinese with English abstract)
[5]WHITAKER V M.Applications of molecular markers in strawberry.Journal of Berry Research,2011,1(3):115-127.
[6]张运涛,冯志广,李天忠,等.草莓品种亲缘关系的AFLP分子标记分析.园艺学报,2006,33(6):1199-1202.ZHANG Y T,FENG Z G,LI T Z,et al.Genetic relationships of strawberry cultivars by AFLP analysis.Acta Horticulturae Sinica,2006,33(6):1199-1202.(in Chinese with English abstract)
[7]何淑娟.利用AFLP分子标记分析草莓的遗传多样性.河北,保定:河北农业大学,2007.HE S J.Using AFLP molecular markers to analyse genetic diversity in strawberry.Baoding,Hebei:Hebei Agricultural University,2007.(in Chinese with English abstract)
[8]王志刚,张志宏,李贺,等.利用RAPD和SCAR标记鉴定草莓品种.园艺学报,2007,34(3):591-596.WANG Z G,ZHANG Z H,LI H,et al.Identification of strawberry cultivars by RAPD and SCAR markers.Acta Horticulturae Sinica,2007,34(3):591-596.(in Chinese with English abstract)
[9]闫玉华,马鸿翔,雷家军,等.红花草莓红花基因RAPD标记转化为SCAR标记.分子植物育种,2006,4(5):690-694.YAN Y H,MA H X,LEI J J,et al.Conversion of RAPDmarker linked to red-flowered gene of red-flowered strawberry to SCAR marker.Molecular Plant Breeding,2006,4(5):690-694.(in Chinese with English abstract)
[10]董清华,王西成,赵密珍,等.草莓EST-SSR标记开发及在品种遗传多样性分析中的应用.中国农业科学,2011,44(17):3603-3612.DONG Q H,WANG X C,ZHAO M Z,et al.Development of EST-derived SSR markers and their application in strawberry genetic diversity analysis.Scientia Agricultura Sinica,2011,44(17):3603-3612.(in Chinese with English abstract)
[11]韩柏明,赵密珍,王静,等.草莓属种质资源亲缘关系的SSR标记分析.园艺学报,2012,39(12):2352-2360.HAN B M,ZHAO M Z,WANG J,et al.Phylogenetic relationships among Fragaria germplasm by SSR markers.Acta Horticulturae Sinica,2012,39(12):2352-2360.(in Chinese with English abstract)
[12]忻雅,阮松林,马华升,等.基于SSR和SCAR标记的草莓主栽品种指纹图谱构建及亲缘关系分析.江西农业大学学报,2013,35(2):307-312.XIN Y,RUAN S L,MA H S,et al.Establishment of DNAfingerprinting and analysis of genetic relationship among main strawberry cultivars in southern China.Acta Agriculturae Universitis Jiangxiensis,2013,35(2):307-312.(in Chinese with English abstract)
[13]LI G,QUIROS C F.Sequence-related amplified polymorphism(SRAP),a new marker system based on a simple PCR reaction:its application to mapping and gene tagging in Brassica.Theoretical&Applied Genetics,2001,103(2/3):455-461.
[14]ANEJA B,YADAV N R,CHAWLA V,et al.Sequencerelated amplified polymorphism(SRAP)molecular marker system and its applications in crop improvement.Molecular Breeding,2012,30(4):1635-1648.
[15]FERRIOL M,PICO B,NUEZ F.Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers.Theoretical and Applied Genetics,2003,107(2):271-282.
[16]BUDAK H,SHEARMAN R C,PARMAKSIZ I,et al.Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs,SSRs,RAPDs and SRAPs.Theoretical and Applied Genetics,2004,109:280-288.
[17]魏丽丽,朱世东,贾庆美,等.草莓SRAP反应体系优化及引物筛选.中国农学通报,2014,30(25):159-165.WEI L L,ZHU S D,JIA Q M,et al.Optimization of SRAPreaction system and selection of primers for strawberry.Chinese Agricultural Science Bulletin,2014,30(25):159-165.(in Chinese with English abstract)
[18]黄璐琦,钱丹,邓超.双分子标记法的构建及在中药研究中的应用.中国中药杂志,2015,40(2):165-168.HUANG L Q,QIAN D,DENG C.Hypothesis and application of bimolecular marking methods in Chinese materia medica.China Journal of Chinese Materia Medica,2015,40(2):165-168.(in Chinese with English abstract)
[19]ISOBE S N,HIDEKI H,SHUSEI S,et al.Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry(Fragaria×ananassa)and its applicability.DNA Research,2012,20(1):79-92.
[20]NEI M,LI W H.Mathematical model for studying genetic variation in terms of restriction endonucleases.Proceedings of the National Academy of Sciences of the USA,1979,76:5269-5273.
[21]BOTSTEIN D,WHITE R L,SKOLNICK M,et al.Construction of genetic linkage map in man using restriction fragment length polymorphisms.The American Journal of Human Genetics,1980,32:314-331.
[22]陈伦林,邹小云,李书宇,等.SSR和SRAP标记揭示甘蓝型油菜遗传多样性的差异分析.分子植物育种,2008,6(3):511-516.CHEN L L,ZOU X Y,LI S Y,et al.Analysis of the genetic diversity of rapeseed by SSR and SRAP with emphasis on the difference of this two kinds of markers.Molecular Plant Breeding,2008,6(3):511-516.(in Chinese with English abstract)
[23]谭祖猛,李云昌,胡琼,等.通过分子标记估算遗传距离预测甘蓝型油菜的杂种优势.中国油料作物学报,2007,29(2):126-132.TAN Z M,LI Y C,HU Q,et al.Heterosis prediction based on genetic distance estimated by molecular markers in rapeseed.Chinese Journal of Oil Crop Sciences,2007,29(2):126-132.(in Chinese with English abstract)
[24]甘晓燕,程永芳,巩檑,等.SRAP和SSR标记对马铃薯遗传多样性的差异分析.中国农学通报,2015,31(30):225-230.GAN X Y,CHENG Y F,GONG L,et al.Variance analysis of genetic diversity of potato with SRAP and SSR markers.Chinese Agricultural Science Bulletin,2015,31(30):225-230.(in Chinese with English abstract)
[25]刘通,邓崇岭,程玉芳,等.利用SSR和SRAP技术分析广西柑橘种质遗传多样性.华中农业大学学报,2016(2):23-29.LIU T,DENG C L,CHENG Y F,et al.Analyzing genetic diversity of citrus germplasm in Guangxi Province with SSRand SRAP markers.Journal of Huazhong Agricultural University,2016(2):23-29.(in Chinese with English abstract)
[26]班骞,谢彩云,范国华,等.基于EST-SSR及SRAP标记构建苦荬菜品种(系)DNA指纹图谱.草业学报,2018,27(4):111-122.BAN Q,XIE C Y,FAN G H,et al.DNA fingerprinting of Ixeris polycephala varieties based on EST-SSR and SRAPmarkers.Acta Prataculturae Sinica,2018,27(4):111-122.(in Chinese with English abstract)
[27]王国莉,徐毓璇,黄梅花.基于SSR和SRAP标记的苦瓜品种鉴定及亲缘关系分析.分子植物育种,2016(2):501-510.WANG G L,XU Y X,HUANG M H.Identification and genetic relationship analysis of bitter gourd varieties based on SSR and SPAP.Molecular Plant Breeding,2016(2):501-510.(in Chinese with English abstract)
[28]延娜,李巧丽,郭军战.果桑遗传差异的SRAP和EST-SSR分析.西北农业学报,2015,24(9):91-97.YAN N,LI Q L,GUO J Z.SRAP and EST-SSR analysis of genetic differences in fruit mulberry(Morus spp.).Acta Agriculturae Boreali-Occidentalis Sinica,2015,24(9):91-97.(in Chinese with English abstract)
[29]邹自征,陈建华,栾明宝,等.应用RSAP、SRAP和SSR分析苎麻种质亲缘关系.作物学报,2012,38(5):840-847.ZHOU Z Z,CHEN J H,LUAN M B,et al.Genetic relationship of ramie germplasm revealed by RSAP,SRAPand SSR markers.Acta Agronomica Sinica,2012,38(5):840-847.(in Chinese with English abstract)
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