杨梅基因组SSR引物的开发与应用
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摘要
基于杨梅(Myrica rubar Sieb. et Zucc.)基因组序列信息,研究了1 431条scaffold中SSR位点的分布特点。共发掘到二至六核苷酸SSR位点43842个,分布在623条scaffold中,共有194种重复单元。二核苷酸SSR位点有36 383个,占总SSR的82.99%;AG/CT的出现频率最高,为55.70%,占总SSR位点的46.23%。三核苷酸SSR位点有6 115个,占总SSR的13.95%。四核苷酸SSR位点有827个,占1.89%。五核苷酸SSR位点为245个,占0.56%。六核苷酸SSR位点为272个,占0.62%。设计合成了59对基因组SSR引物,多态性分析显示,高度多态性引物26对,中度多态性引物为33对;将其应用于杨梅优株早鲜856及其他13个主栽品种的聚类分析,结果表明,上述引物在相似系数0.56处将14份杨梅材料分为两个群体,早鲜856与其他13个主栽品种在DNA水平上均存在差异,且与对照品种‘早色’的相似系数为0.86。
The distribution of simple sequence repeat(SSR)was studied in 1 431 scaffolds of Chinese bayberry(Myrica rubar Sieb. et Zucc.)genome. There were 43 842 SSR loci identified totally. And 194 kinds of repeating motifs that distributed in 623 scaffolds were discovered. The number and frequency of dinucleotide SSR loci were 36 383 and 82.99%. The frequency of AG/CT in dinucleotide was 55.70%,and in all SSR loci was 46.23%. It was indicated that AG/CT was the most common repeat motifs in Chinese bayberry genome. The number of trinucleotide SSR loci was 6 115,accounting for 13.95%. The number of tetranucleotide,pentanucleotide and hexanucleotide were 827,245 and 272 with the frequency 1.89%,0.56% and 0.62%,respectively. Meanwhile,59 pairs of Genomic SSR markers(gSSRs)were developed. After polymorphism analysis,26 gSSRs were highly polymorphic markers and 33 gSSRs were moderatelypolymorphic markers. In this study,the clustering analysis among the advanced selection Zaoxian 856 and the other 13 main cultivars were identified by all 59 gSSRs. According to the result,14 Chinese bayberrymaterials were clustered into two groups at the similarity coefficient of 0.56. It was illustrated that Zaoxian 856 was different from the other 13 varieties at the DNA level,and the similarity coefficient between Zaoxian 856 and control‘Zaose'was 0.86.
The distribution of simple sequence repeat(SSR)was studied in 1 431 scaffolds of Chinese bayberry(Myrica rubar Sieb. et Zucc.)genome. There were 43 842 SSR loci identified totally. And 194 kinds of repeating motifs that distributed in 623 scaffolds were discovered. The number and frequency of dinucleotide SSR loci were 36 383 and 82.99%. The frequency of AG/CT in dinucleotide was 55.70%,and in all SSR loci was 46.23%. It was indicated that AG/CT was the most common repeat motifs in Chinese bayberry genome. The number of trinucleotide SSR loci was 6 115,accounting for 13.95%. The number of tetranucleotide,pentanucleotide and hexanucleotide were 827,245 and 272 with the frequency 1.89%,0.56% and 0.62%,respectively. Meanwhile,59 pairs of Genomic SSR markers(gSSRs)were developed. After polymorphism analysis,26 gSSRs were highly polymorphic markers and 33 gSSRs were moderatelypolymorphic markers. In this study,the clustering analysis among the advanced selection Zaoxian 856 and the other 13 main cultivars were identified by all 59 gSSRs. According to the result,14 Chinese bayberrymaterials were clustered into two groups at the similarity coefficient of 0.56. It was illustrated that Zaoxian 856 was different from the other 13 varieties at the DNA level,and the similarity coefficient between Zaoxian 856 and control‘Zaose'was 0.86.
引文
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He Ping,Li Lin-guang,Wang Hai-bo,Li Hui-feng,Chang Yuan-sheng.2016.Analysis on SSR information in transcriptome and development of molecular markers in peach(Prunus persica[L.]Batsch).Molecular Plant Breeding,14(11):3130-3135.(in Chinese)何平,李林光,王海波,李慧峰,常源升.2016.桃(Prunus persica[L.]Batsch)转录组SSR信息分析及其分子标记开发.分子植物育种,14(11):3130-3135.
Jia H M,Jiao Y,Wang G Y,Li Y,Jia H J,Wu H X,Chai C Y,Dong X,Guo Y P,Zhang L P,Gao Q K,Chen W,Song L J,Weg E,Gao Z S.2015.Genetic diversity of male and female Chinese bayberry(Myrica rubra)populations and identification of sex-associated markers.BMC Genomics,16:394.
Jiao Y,Jia H M,Li X W,Chai M L,Jia H J,Chen Z,Wang G Y,Chai CY,Weg E,Gao Z S.2012.Development of simple sequence repeat(SSR)markers from a genome survey of Chinese bayberry(Myrica rubra).BMC Genomics,13:201.
Li Yong-ping,Liu Jian-ting,Chen Min-dong,Zhang Qian-rong,Zhu Hai-sheng,Wen Qing-fang.2018.SSR markers excavation and germplasm analysis using the transcriptome information of Hibiscus esculentus.Acta Horticulturae Sinica,45(3):579-590.(in Chinese)李永平,刘建汀,陈敏氡,张前荣,朱海生,温庆放.2018.利用黄秋葵转录组信息挖掘SSR标记及用于种质分析.园艺学报,45(3):579-590.
Lin Kai-qin,Li Yan,Zhao De-gang.2016.SSR mining and marker development in Eucommia ulmoides oliver transcriptome.Molecular Plant Breeding,14(6):1548-1558.(in Chinese)林开勤,李岩,赵德刚.2016.杜仲转录组SSR发掘及标记开发.分子植物育种,14(6):1548-1558.
Liu Zhen,Wang Xin-chao,Zhao Li-ping,Yao Ming-zhe,Wang Ping-shen,Xu Mei,Tang Yi-chun,Chen Liang.2008.Genetic diversity and relationship analysis of tea germplasms originated from south western China based on EST-SSR.Molecular Plant Breeding,6(1):100-110.(in Chinese)刘振,王新超,赵丽萍,姚明哲,王平盛,许玫,唐一春,陈亮.2008.基于EST-SSR的西南茶区茶树资源遗传多样性和亲缘关系分析.分子植物育种,6(1):100-110.
Lu Yu-sheng,Chen Zhe,Chang Xiao-xiao,Qiu Ji-shui,Lin Zhi-xiong,Pan Jian-ping.2018.Excavation and usability analysis of SSR from transcriptome of Clausena lansium.Acta Horticulturae Sinica,45(1):149-158.(in Chinese)陆育生,陈喆,常晓晓,邱继水,林志雄,潘建平.2018.黄皮转录组SSR挖掘及其可用性分析.园艺学报,45(1):149-158.
McCouch S R,Cho Y G,Ishii T,Temnykh S,Chen X,Lipovich L,Park W D,Ayres N,Cartinhour S.2000.Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice(Oryza sativa L.).Theoretical and Applied Genetics,100(5):713-722.
Paterson A H,Brubaker C,Wendel J F.2003.A rapid method for extraction of cotton(Gossypium spp.)genomic DNA suitable for AFLP or PCRanalysis.Plant Molecular Biology,11:122-127.
Qi Xing-jiang,Ren Hai-ying,Liang Sen-miao,Zheng Xi-liang,Wu Yang-chun.2015.Preliminary report on whole genome sequencing of Chinese bayberry.Journal of Zhejiang Agricultural Sciences,56(10):1564-1566.(in Chinese)戚行江,任海英,梁森苗,郑锡良,吴阳春.2015.杨梅全基因组测序结果初报.浙江农业科学,56(10):1564-1566.
Rohlf F J.2005.NTSYSpc:Numerical Taxonomy System ver.2.20d,Exeter Publishing,Ltd.Setauket,NY.http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html.
Sneath P H,Sokal R R.1973.Numerical taxonomy.San Francisco:W H Freeman and Company:573.
Wang W T,Feng C,Zhang Z H,Yan L J,Ding M M,Xu C J,Chen K S.2016.Development of highly polymorphic expressed sequence tags-simple sequence repeat markers and their application in analysis of genetic diversity of Chinese bayberry(Morella rubra).HortScience,51(3):227-231.
Wang Yun-sheng,Nie Fei,Lin Shun-quan.2015.The latest research progress in high-throughput sequencing of fruit tree.Genomics and Applied Biology,34(9):2034-2043.(in Chinese)王云生,聂飞,林顺权.2015.果树高通量测序的最新研究进展.基因组学与应用生物学,34(9):2034-2043.
Wei Xiu-qing,Xu Ling,Zhang Xi-juan,Yu Dong,Chen Zhi-feng,Zhang Li-mei,Chen Chang-zhong,Xu Jia-hui.2018.Analysis on SSR information in transcriptome and development of molecular markers in wax apple.Acta Horticulturae Sinica,45(3):541-551.(in Chinese)魏秀清,许玲,章希娟,余东,陈志峰,张丽梅,陈长忠,许家辉.2018.莲雾转录组SSR信息分析及其分子标记开发.园艺学报,45(3):541-551.
Xie W G,Zhang X Q,Cai H W,Liu H W,Liu W,Peng Y.2010.Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass(Dactylis glomerata L.).Biochemical Systematics and Ecology,38:740-749.
Zhang Hua-li,Cong Ri-chen,Wang Mao-liang,Dong Ai-xiang,Xin Hai-bo,Yi Ming-fang,Guo Hua.2018.Development of SSR molecular markers based on transcriptome sequencing of Tagetes erecta.Acta Horticulturae Sinica,45(1):159-167.(in Chinese)张华丽,丛日晨,王茂良,董爱香,辛海波,义鸣放,郭华.2018.基于万寿菊转录组测序的SSR标记开发.园艺学报,45(1):159-167.
Zhang J,Guo W Z,Zhang T Z.2002.Molecular linkage map of allotetraploid cotton(Gossypium hirsutum L.×Gossypium barbadense L.)with a haploid population.Theoretical and Applied Genetics,105:1166-1174.
Zhang S Y,Li X,Feng C,Zhu C Q,Grierson D,Xu C J,Chen K S.2012.Development and characterization of 109 polymorphic EST-SSRs derived from the Chinese bayberry(Myrica rubra,Myricaceae)transcriptome.American Journal of Botany,99(12):e501-e507.
Zhang Yan-yan,Qi Hong,Guo Qing-mei,Sun Zhi-ying,Zhou Feng-qin,Li Sheng-bo.2016.Analysis of genetic diversity in Chaenomeles using apple EST-SSRs.Biotechnology Bulletin,32(7):93-98.(in Chinese)张艳艳,齐红,郭庆梅,孙稚颖,周凤琴,李圣波.2016.利用苹果EST-SSR分析木瓜属种质遗传多样性.生物技术通报,32(7):93-98.
Zhou R,Wu Z,Jiang F L,Liang M.2015.Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars(Solanum lycopersicum L.).Genetics and Molecular Research,14(4):13184-13194.
Zhu Ting-ting,Liang Sen-miao,Zhang Shu-wen,Zheng Xi-liang,Ren Hai-ying,Qi Xing-jiang.2018.Study on fruit development and quality formation of(Myrica rubra)cv.Zaoxian.Acta Agriculturae Zhejiangensis,30(5):764-770.(in Chinese)朱婷婷,梁森苗,张淑文,郑锡良,任海英,戚行江.2018.早鲜杨梅果实发育和品质形成规律的研究.浙江农业学报,30(5):764-770.
He Ping,Li Lin-guang,Wang Hai-bo,Li Hui-feng,Chang Yuan-sheng.2016.Analysis on SSR information in transcriptome and development of molecular markers in peach(Prunus persica[L.]Batsch).Molecular Plant Breeding,14(11):3130-3135.(in Chinese)何平,李林光,王海波,李慧峰,常源升.2016.桃(Prunus persica[L.]Batsch)转录组SSR信息分析及其分子标记开发.分子植物育种,14(11):3130-3135.
Jia H M,Jiao Y,Wang G Y,Li Y,Jia H J,Wu H X,Chai C Y,Dong X,Guo Y P,Zhang L P,Gao Q K,Chen W,Song L J,Weg E,Gao Z S.2015.Genetic diversity of male and female Chinese bayberry(Myrica rubra)populations and identification of sex-associated markers.BMC Genomics,16:394.
Jiao Y,Jia H M,Li X W,Chai M L,Jia H J,Chen Z,Wang G Y,Chai CY,Weg E,Gao Z S.2012.Development of simple sequence repeat(SSR)markers from a genome survey of Chinese bayberry(Myrica rubra).BMC Genomics,13:201.
Li Yong-ping,Liu Jian-ting,Chen Min-dong,Zhang Qian-rong,Zhu Hai-sheng,Wen Qing-fang.2018.SSR markers excavation and germplasm analysis using the transcriptome information of Hibiscus esculentus.Acta Horticulturae Sinica,45(3):579-590.(in Chinese)李永平,刘建汀,陈敏氡,张前荣,朱海生,温庆放.2018.利用黄秋葵转录组信息挖掘SSR标记及用于种质分析.园艺学报,45(3):579-590.
Lin Kai-qin,Li Yan,Zhao De-gang.2016.SSR mining and marker development in Eucommia ulmoides oliver transcriptome.Molecular Plant Breeding,14(6):1548-1558.(in Chinese)林开勤,李岩,赵德刚.2016.杜仲转录组SSR发掘及标记开发.分子植物育种,14(6):1548-1558.
Liu Zhen,Wang Xin-chao,Zhao Li-ping,Yao Ming-zhe,Wang Ping-shen,Xu Mei,Tang Yi-chun,Chen Liang.2008.Genetic diversity and relationship analysis of tea germplasms originated from south western China based on EST-SSR.Molecular Plant Breeding,6(1):100-110.(in Chinese)刘振,王新超,赵丽萍,姚明哲,王平盛,许玫,唐一春,陈亮.2008.基于EST-SSR的西南茶区茶树资源遗传多样性和亲缘关系分析.分子植物育种,6(1):100-110.
Lu Yu-sheng,Chen Zhe,Chang Xiao-xiao,Qiu Ji-shui,Lin Zhi-xiong,Pan Jian-ping.2018.Excavation and usability analysis of SSR from transcriptome of Clausena lansium.Acta Horticulturae Sinica,45(1):149-158.(in Chinese)陆育生,陈喆,常晓晓,邱继水,林志雄,潘建平.2018.黄皮转录组SSR挖掘及其可用性分析.园艺学报,45(1):149-158.
McCouch S R,Cho Y G,Ishii T,Temnykh S,Chen X,Lipovich L,Park W D,Ayres N,Cartinhour S.2000.Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice(Oryza sativa L.).Theoretical and Applied Genetics,100(5):713-722.
Paterson A H,Brubaker C,Wendel J F.2003.A rapid method for extraction of cotton(Gossypium spp.)genomic DNA suitable for AFLP or PCRanalysis.Plant Molecular Biology,11:122-127.
Qi Xing-jiang,Ren Hai-ying,Liang Sen-miao,Zheng Xi-liang,Wu Yang-chun.2015.Preliminary report on whole genome sequencing of Chinese bayberry.Journal of Zhejiang Agricultural Sciences,56(10):1564-1566.(in Chinese)戚行江,任海英,梁森苗,郑锡良,吴阳春.2015.杨梅全基因组测序结果初报.浙江农业科学,56(10):1564-1566.
Rohlf F J.2005.NTSYSpc:Numerical Taxonomy System ver.2.20d,Exeter Publishing,Ltd.Setauket,NY.http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html.
Sneath P H,Sokal R R.1973.Numerical taxonomy.San Francisco:W H Freeman and Company:573.
Wang W T,Feng C,Zhang Z H,Yan L J,Ding M M,Xu C J,Chen K S.2016.Development of highly polymorphic expressed sequence tags-simple sequence repeat markers and their application in analysis of genetic diversity of Chinese bayberry(Morella rubra).HortScience,51(3):227-231.
Wang Yun-sheng,Nie Fei,Lin Shun-quan.2015.The latest research progress in high-throughput sequencing of fruit tree.Genomics and Applied Biology,34(9):2034-2043.(in Chinese)王云生,聂飞,林顺权.2015.果树高通量测序的最新研究进展.基因组学与应用生物学,34(9):2034-2043.
Wei Xiu-qing,Xu Ling,Zhang Xi-juan,Yu Dong,Chen Zhi-feng,Zhang Li-mei,Chen Chang-zhong,Xu Jia-hui.2018.Analysis on SSR information in transcriptome and development of molecular markers in wax apple.Acta Horticulturae Sinica,45(3):541-551.(in Chinese)魏秀清,许玲,章希娟,余东,陈志峰,张丽梅,陈长忠,许家辉.2018.莲雾转录组SSR信息分析及其分子标记开发.园艺学报,45(3):541-551.
Xie W G,Zhang X Q,Cai H W,Liu H W,Liu W,Peng Y.2010.Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass(Dactylis glomerata L.).Biochemical Systematics and Ecology,38:740-749.
Zhang Hua-li,Cong Ri-chen,Wang Mao-liang,Dong Ai-xiang,Xin Hai-bo,Yi Ming-fang,Guo Hua.2018.Development of SSR molecular markers based on transcriptome sequencing of Tagetes erecta.Acta Horticulturae Sinica,45(1):159-167.(in Chinese)张华丽,丛日晨,王茂良,董爱香,辛海波,义鸣放,郭华.2018.基于万寿菊转录组测序的SSR标记开发.园艺学报,45(1):159-167.
Zhang J,Guo W Z,Zhang T Z.2002.Molecular linkage map of allotetraploid cotton(Gossypium hirsutum L.×Gossypium barbadense L.)with a haploid population.Theoretical and Applied Genetics,105:1166-1174.
Zhang S Y,Li X,Feng C,Zhu C Q,Grierson D,Xu C J,Chen K S.2012.Development and characterization of 109 polymorphic EST-SSRs derived from the Chinese bayberry(Myrica rubra,Myricaceae)transcriptome.American Journal of Botany,99(12):e501-e507.
Zhang Yan-yan,Qi Hong,Guo Qing-mei,Sun Zhi-ying,Zhou Feng-qin,Li Sheng-bo.2016.Analysis of genetic diversity in Chaenomeles using apple EST-SSRs.Biotechnology Bulletin,32(7):93-98.(in Chinese)张艳艳,齐红,郭庆梅,孙稚颖,周凤琴,李圣波.2016.利用苹果EST-SSR分析木瓜属种质遗传多样性.生物技术通报,32(7):93-98.
Zhou R,Wu Z,Jiang F L,Liang M.2015.Comparison of gSSR and EST-SSR markers for analyzing genetic variability among tomato cultivars(Solanum lycopersicum L.).Genetics and Molecular Research,14(4):13184-13194.
Zhu Ting-ting,Liang Sen-miao,Zhang Shu-wen,Zheng Xi-liang,Ren Hai-ying,Qi Xing-jiang.2018.Study on fruit development and quality formation of(Myrica rubra)cv.Zaoxian.Acta Agriculturae Zhejiangensis,30(5):764-770.(in Chinese)朱婷婷,梁森苗,张淑文,郑锡良,任海英,戚行江.2018.早鲜杨梅果实发育和品质形成规律的研究.浙江农业学报,30(5):764-770.