基于SSR标记的华南野生蓖麻遗传多样性分析
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摘要
国内外研究表明蓖麻是一个遗传多样性很低的物种,利用野生材料拓宽遗传基础对蓖麻育种至关重要。本研究用72对多态性SSR标记对从广东、广西和海南三省(区)收集的240份野生蓖麻材料进行了的遗传多样性分析。结果表明,平均每个SSR位点检测到等位基因4.819个、有效等位基因2.410个,平均多态性信息含量(PIC)为0.481,平均Shannon's信息指数(I)为1.007,平均期望杂合度(He)为0.525,均高于以往报道结果。按地理来源分析,来自广东的材料遗传多样性最高,广西的次之,海南的最低。群体遗传结构分析将240份材料划分为3个类群,每个类群遗传背景独特,与地理分布基本一致,类群间存在一定程度的基因交流。聚类分析在遗传相似系数为0.404时,将240份材料分为4个组,组间亲缘关系与地理分布没有直接联系,但随着遗传相似系数的增大,同一地区的材料有聚到一起的趋势。以上结果证明中国华南野生蓖麻材料遗传多样性较为丰富,是比较独特的一类蓖麻种质资源,应进一步加强保护、研究和利用。本研究对华南野生蓖麻的高效保护和研究利用提供了数据参考。
Studies at home and abroad have been proved that castor bean(Ricinus communis L.) is a species with low genetic diversity. It is very important to use wild materials to broaden genetic basis for castor breeding. In this study, the genetic diversity of 240 wild castor accessions, collected from Guangdong Province, Guangxi Zhuang Autonomous Region and Hainan Province, were analysed with 72 pairs of polymorphic SSR markers. The results showed that the average allele number per SSR locus was 4.819, the effective allele number per locus was 2.410,the average polymorphic information content(PIC) was 0.481, the average Shannon's information index(I) was1.007 and the average expected heterozygosity(He) was 0.525, all was higher than those of previous reports. According to the analysis of geographical sources, the genetic diversity of materials from Guangdong was the highest, that of Guangxi was the second, and that of Hainan was the lowest, 240 germplasm were divided into 3 groups by population genetic structure analysis. The genetic background of each group was unique and basically consistent with the geographical distribution. There was a certain degree of genetic communication between the two groups.In cluster analysis, 240 materials were divided into 4 groups when the genetic similarity coefficient was 0.404. The relationship between groups was not associated with the geographical distribution, but with the increase of genetic similarity coefficient, the materials in the same area tended to gather together. The above results indicated that the genetic diversity of wild castor in south China is richer, which can be regarded as a unique type of castor germplasm resources. The above results are of great significance to the efficient protection, research and utilization of wild castor in south China.
Studies at home and abroad have been proved that castor bean(Ricinus communis L.) is a species with low genetic diversity. It is very important to use wild materials to broaden genetic basis for castor breeding. In this study, the genetic diversity of 240 wild castor accessions, collected from Guangdong Province, Guangxi Zhuang Autonomous Region and Hainan Province, were analysed with 72 pairs of polymorphic SSR markers. The results showed that the average allele number per SSR locus was 4.819, the effective allele number per locus was 2.410,the average polymorphic information content(PIC) was 0.481, the average Shannon's information index(I) was1.007 and the average expected heterozygosity(He) was 0.525, all was higher than those of previous reports. According to the analysis of geographical sources, the genetic diversity of materials from Guangdong was the highest, that of Guangxi was the second, and that of Hainan was the lowest, 240 germplasm were divided into 3 groups by population genetic structure analysis. The genetic background of each group was unique and basically consistent with the geographical distribution. There was a certain degree of genetic communication between the two groups.In cluster analysis, 240 materials were divided into 4 groups when the genetic similarity coefficient was 0.404. The relationship between groups was not associated with the geographical distribution, but with the increase of genetic similarity coefficient, the materials in the same area tended to gather together. The above results indicated that the genetic diversity of wild castor in south China is richer, which can be regarded as a unique type of castor germplasm resources. The above results are of great significance to the efficient protection, research and utilization of wild castor in south China.
引文
Allan G.,Williams A.,Rabinowicz P.D.,Chan A.P.,Ravel J.and Keim P.,2008,Worldwide genotyping of castor bean germplasm(Ricinus communis L.)using AFLPs and SSRs Genet.Resour.Crop Evol.,55(3):365-378
Bajay M.M.,Pinheiro J.B.,Batista C.E.A.,Nobrega M.B.M.,Zucchi M.I.,2009,Development and characterization of microsatellite markers for castor(Ricinus Communis L.),an important oleaginous species for biodiesel production,Conserv.Genet.Resour.,1(1):237-239
Bi C.,2010,studies on genetic relationship combining ability and genetic map in castor-oil plant,Thesis for M.S.,Guangdong Ocean University,Supervisor:Yin X.G.,pp.23-24(毕川,2010,蓖麻亲缘关系与配合力分析及遗传图谱构建,硕士学位论文,广东海洋大学,导师:殷学贵,pp.23-24)
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Evanno G.,Regnaut S.,and Goudet J.,2005,Detecting the number of clusters of individuals using the software STRUC-TURE:a simulation study,Mol.Ecol.,14(8):2611-2620
Fan W.Q.,Gai H.M.,Sun X.,Yang A.G.,Zhang Z.F.,Ren M.,2016,Data Formater,a softwar for SSR date formatting to population genetics analysis,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(1):265-270(樊文强,盖红梅,孙鑫,杨爱国,张忠锋,任民,2016,SSR数据格式转换软件Data Formater,分子植物育种,14(1):265-270)
Foster J.T.,Allan G.J.,Chan A.P.,Rabinowicz P.D.,Ravel J.,and Jackson P.J.,2010,Single nucleotide polymorphisms for assessing genetic diversity in castor bean(Ricinus communis),BMC Plant Biol.,10(1):13
Hong Q.B.,Hou L.,Luo X.Y.,Li D.M.,Xiao Y.H.,Yan Y.,Yang K.J.,and Jia C.,2001,Using RAPD for evaluating genetic background among naked barley varieties in Sichuan northwestern region,Zhongguo Nongye Kexue(Scientia A-gricultura Sinica),34(2):133-138(洪棋斌,侯磊,罗小英,李德谋,肖月华,裴炎,杨开俊,甲错,2001,应用RAPD分析川西北高原青稞的遗传背景,中国农业科学,34(2):133-138)
Kallamadi P.R.,Nadigatla V.P.R.G.R.,and Mulpuri S.,2015,Molecular diversity in castor(Ricinus communis L.),Ind.Crop.Prod.,66:271-281
Kashi Y.,King D.,and Soller M.,1997,Simple sequence repeats as a source of quantitative genetic variation,Trends Genet.,13(2):74-78
Kumar P.,Gupta V.K.,Misra A.K.,Modi D.R.,and Pandey B.K.,2009,Potential of molecular markers in plant biotechnology,Plant Omics,2(4):141-162
Senthilvel S.,Shaik M.,Anjani K.,Shaw R.K.,Kumari P.,Sarada C.,and Usha Kiran B.,2016,Genetic variability and population structure in a collection of inbred lines derived from a core germplasm of castor,J.Plant Biochem.Biot.,26(1):27-34
Seo K.I.,Lee G.A.,Ma K.H.,Hyun D.Y.,Park Y.J.,Jung J.W.Lee S.Y.,Gwag J.G.,Kim C.K.,and Lee M.C.,2011,Isolation and characterization of 28 polymorphic SSR loci from castor bean(Ricinus communis L.),J.Crop Sci.Biotechnol.14(2):97-103
Shi Y.T.,Bian H.W.,Han N.,Pan J.W.,Tong W.X.,and Zhu M.2004,Genetic variation analysis by RAPD of some barley cultivar in China,Zuowu Xuebao(Acta Agronomica Sinica)30(3):258-265(施永泰,边红武,韩凝,潘建伟,童微星,朱睦,2004,中国江、浙地区栽培大麦遗传资源的RAPD研究,作物学报,30(3):258-265)
Tan M.L.,Yan M.F.,Wang L.,Wang L.J.,and Yan X.C.,2012SSR identification and genetic variation analysis of castor hybrids,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),32(8):1539-1546(谭美莲,严明芳,汪磊王力军,严兴初,2012,蓖麻杂交种的SSR鉴定及遗传变异分析,西北植物学报,32(8):1539-1546)
Thatikunta R.,Sankar A.S.,Sreelakshmi J.,Palle G.,Leela C.and Rani C.V.D.,2016,Utilization of in silico EST-SSRmarkers for diversity studies in castor(Ricinus Communis L.),Physiol.Mol.Biol.Plants,22(4):535-545
Wang M.L.,Dzievit M.,Chen Z.,Morris J.B.,Norris J.E.Barkley N.A.,Tonnis B.,Pederson G.A.,and Yu J.,2016Genetic diversity and population structure of castor(Ricinus communis L.)germplasm within the us collection assessed with EST-SSR markers,Genome,60(3):193-200
Xue J.F.,Tan M.L.,Yan M.F.,Wang L.,Fu C.,Wang L.J.,and Yan X.C.,2015,Genetic diversity and DNA fingerprints of castor bean cultivars based on SSR markers,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(1):48-54(薛建峰,谭美莲,严明芳,汪磊,傅春玲,王力军,严兴初,2015,我国部分蓖麻品种遗传资源SSR分析及DNA指纹图谱,中国油料作物学报,37(1):48-54)
Yan X.C.,Wang L.J.,2007,The status in quo and foreground of exploiting castor-oil plant as energy sources,Anhui Nongye Kexue(Journal of Anhui Agricultural Sciences),35(34):11165,11167(严兴初,王力军,2007,蓖麻作为能源开发的现状与前景,安徽农业科学,35(34):11165,11167)
Yang J.B.,Tian B.,Yang C.,Qiu L.,and Liu A.,2010,Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean(Ricinus communis L.),BMC Plant Biol.,10:278
Yao Y.,Li F.S.,Chen Y.S.,Li J.Q.,Huang F.L.,and Wang Y.J.,2009,Research progress on castor,Neimenggu Minzu Dax ue Xuebao(Journal of Inner Mongolia University for Nationalities(Natural Science Edition)),24(2):172-175(姚远,李凤山,陈永胜,李金琴,黄凤兰,王永佳,2009,国内外蓖麻研究进展,内蒙古民族大学学报(自然科学版),24(2):172-175)
Zhang D.,2010,Genetic diversity and core collection of wild castor-oil plant in south China,Thesis for M.S.,Guangdong Ocean University,Supervisor:Yin X.G.,pp.30-32(张丹,2010,华南野生蓖麻遗传多样性分析与核心种质构建,硕士学位论文,广东海洋大学,导师:殷学贵,pp.30-32)
Bajay M.M.,Pinheiro J.B.,Batista C.E.A.,Nobrega M.B.M.,Zucchi M.I.,2009,Development and characterization of microsatellite markers for castor(Ricinus Communis L.),an important oleaginous species for biodiesel production,Conserv.Genet.Resour.,1(1):237-239
Bi C.,2010,studies on genetic relationship combining ability and genetic map in castor-oil plant,Thesis for M.S.,Guangdong Ocean University,Supervisor:Yin X.G.,pp.23-24(毕川,2010,蓖麻亲缘关系与配合力分析及遗传图谱构建,硕士学位论文,广东海洋大学,导师:殷学贵,pp.23-24)
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Evanno G.,Regnaut S.,and Goudet J.,2005,Detecting the number of clusters of individuals using the software STRUC-TURE:a simulation study,Mol.Ecol.,14(8):2611-2620
Fan W.Q.,Gai H.M.,Sun X.,Yang A.G.,Zhang Z.F.,Ren M.,2016,Data Formater,a softwar for SSR date formatting to population genetics analysis,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(1):265-270(樊文强,盖红梅,孙鑫,杨爱国,张忠锋,任民,2016,SSR数据格式转换软件Data Formater,分子植物育种,14(1):265-270)
Foster J.T.,Allan G.J.,Chan A.P.,Rabinowicz P.D.,Ravel J.,and Jackson P.J.,2010,Single nucleotide polymorphisms for assessing genetic diversity in castor bean(Ricinus communis),BMC Plant Biol.,10(1):13
Hong Q.B.,Hou L.,Luo X.Y.,Li D.M.,Xiao Y.H.,Yan Y.,Yang K.J.,and Jia C.,2001,Using RAPD for evaluating genetic background among naked barley varieties in Sichuan northwestern region,Zhongguo Nongye Kexue(Scientia A-gricultura Sinica),34(2):133-138(洪棋斌,侯磊,罗小英,李德谋,肖月华,裴炎,杨开俊,甲错,2001,应用RAPD分析川西北高原青稞的遗传背景,中国农业科学,34(2):133-138)
Kallamadi P.R.,Nadigatla V.P.R.G.R.,and Mulpuri S.,2015,Molecular diversity in castor(Ricinus communis L.),Ind.Crop.Prod.,66:271-281
Kashi Y.,King D.,and Soller M.,1997,Simple sequence repeats as a source of quantitative genetic variation,Trends Genet.,13(2):74-78
Kumar P.,Gupta V.K.,Misra A.K.,Modi D.R.,and Pandey B.K.,2009,Potential of molecular markers in plant biotechnology,Plant Omics,2(4):141-162
Senthilvel S.,Shaik M.,Anjani K.,Shaw R.K.,Kumari P.,Sarada C.,and Usha Kiran B.,2016,Genetic variability and population structure in a collection of inbred lines derived from a core germplasm of castor,J.Plant Biochem.Biot.,26(1):27-34
Seo K.I.,Lee G.A.,Ma K.H.,Hyun D.Y.,Park Y.J.,Jung J.W.Lee S.Y.,Gwag J.G.,Kim C.K.,and Lee M.C.,2011,Isolation and characterization of 28 polymorphic SSR loci from castor bean(Ricinus communis L.),J.Crop Sci.Biotechnol.14(2):97-103
Shi Y.T.,Bian H.W.,Han N.,Pan J.W.,Tong W.X.,and Zhu M.2004,Genetic variation analysis by RAPD of some barley cultivar in China,Zuowu Xuebao(Acta Agronomica Sinica)30(3):258-265(施永泰,边红武,韩凝,潘建伟,童微星,朱睦,2004,中国江、浙地区栽培大麦遗传资源的RAPD研究,作物学报,30(3):258-265)
Tan M.L.,Yan M.F.,Wang L.,Wang L.J.,and Yan X.C.,2012SSR identification and genetic variation analysis of castor hybrids,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),32(8):1539-1546(谭美莲,严明芳,汪磊王力军,严兴初,2012,蓖麻杂交种的SSR鉴定及遗传变异分析,西北植物学报,32(8):1539-1546)
Thatikunta R.,Sankar A.S.,Sreelakshmi J.,Palle G.,Leela C.and Rani C.V.D.,2016,Utilization of in silico EST-SSRmarkers for diversity studies in castor(Ricinus Communis L.),Physiol.Mol.Biol.Plants,22(4):535-545
Wang M.L.,Dzievit M.,Chen Z.,Morris J.B.,Norris J.E.Barkley N.A.,Tonnis B.,Pederson G.A.,and Yu J.,2016Genetic diversity and population structure of castor(Ricinus communis L.)germplasm within the us collection assessed with EST-SSR markers,Genome,60(3):193-200
Xue J.F.,Tan M.L.,Yan M.F.,Wang L.,Fu C.,Wang L.J.,and Yan X.C.,2015,Genetic diversity and DNA fingerprints of castor bean cultivars based on SSR markers,Zhongguo Youliao Zuowu Xuebao(Chinese Journal of Oil Crop Sciences),37(1):48-54(薛建峰,谭美莲,严明芳,汪磊,傅春玲,王力军,严兴初,2015,我国部分蓖麻品种遗传资源SSR分析及DNA指纹图谱,中国油料作物学报,37(1):48-54)
Yan X.C.,Wang L.J.,2007,The status in quo and foreground of exploiting castor-oil plant as energy sources,Anhui Nongye Kexue(Journal of Anhui Agricultural Sciences),35(34):11165,11167(严兴初,王力军,2007,蓖麻作为能源开发的现状与前景,安徽农业科学,35(34):11165,11167)
Yang J.B.,Tian B.,Yang C.,Qiu L.,and Liu A.,2010,Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean(Ricinus communis L.),BMC Plant Biol.,10:278
Yao Y.,Li F.S.,Chen Y.S.,Li J.Q.,Huang F.L.,and Wang Y.J.,2009,Research progress on castor,Neimenggu Minzu Dax ue Xuebao(Journal of Inner Mongolia University for Nationalities(Natural Science Edition)),24(2):172-175(姚远,李凤山,陈永胜,李金琴,黄凤兰,王永佳,2009,国内外蓖麻研究进展,内蒙古民族大学学报(自然科学版),24(2):172-175)
Zhang D.,2010,Genetic diversity and core collection of wild castor-oil plant in south China,Thesis for M.S.,Guangdong Ocean University,Supervisor:Yin X.G.,pp.30-32(张丹,2010,华南野生蓖麻遗传多样性分析与核心种质构建,硕士学位论文,广东海洋大学,导师:殷学贵,pp.30-32)