籼粳交后代杂草稻棕色和红色果皮多样性形成的分子基础
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摘要
杂草稻最引人注目的特征之一是籽粒具有红色的果皮,并且颜色由浅至深具有多样性。然而,迄今对杂草稻果皮颜色变异成因的研究却鲜有报道。本研究以籼粳交后代衍生的42份棕色和红色果皮杂草稻株系(F9)及其白色果皮亲本为研究材料,鉴定其基因型并与表型比对;同时对Rc-bHLH基因和DFR基因序列进行测序比较分析。研究结果表明:42份杂草稻株系果皮颜色呈不同程度的棕色和红色具有多样性,其基因型与表型鉴定结果完全吻合;Rc-bHLH基因比较分析发现,杂草稻株系与亲本在452 bp处发生G/A替换;669～682 bp处亲本缺失14 bp,而杂草稻株系无缺失;DFR基因序列比较分析发现,红色与棕色果皮杂草稻株系之间存在22个突变位点,其中在DFR基因的外显子上有8个突变位点;亲本与棕色果皮杂草稻株系的DFR基因相同;杂草稻株系的DFR基因遗传多态性分析,发现Tajima'D值呈极显著性,说明杂草稻株系中的DFR基因是中性进化基因,受自然选择作用。根据Rc-b HLH基因序列的聚类分析,类群1主要是由籼型和粳型栽培稻组成,类群2主要是由棕/红色果皮的杂草稻株系和野生稻组成,表明杂草稻株系与野生稻遗传关系较近。该研究揭示了籼粳交可能导致后代Rc和Rd基因发生重组或突变从而产生不同颜色果皮,为阐明杂草稻棕色和红色果皮变异的分子基础提供了新的范例。
One of the most striking feature of weedy rice is the red pericarp of its grain, and a variety of colors from deep to shallow. Currently, only limited information was available on the origin of the red pericarp colour in weedy rice. This study took 42 strains of weedy rice having brown and red pericarp derived from indica-japonica hybridization and its white pericarp parent as research materials, which explored for their genotypes and compared with phenotypes. Meanwhile, the sequences of Rc-b HLH gene and DFR gene were sequenced and compared. The results showed that: The 42 selected weedy rice strains that vary in their pericarp colors phenotypes from brown to red. The results of genotypes and phenotypic identification were in perfect agreement. Comparing the sequence of Rc-bHLH genes, this study revealed that there was a G/A substitution at 452 bp in the weedy progenies, and a 14 bp parent deletion at 669～682 bp, while weedy rice strains without deletion. The comparative analysis of DFR gene sequence showed that there were 22 mutation sites between the red and brown pericarp weedy rice strains and 8 of them were in the exon of DFR gene, the DFR gene sequence of the parent was consistent with the brown pericarp weedy rice progenies. Genetic polymorphism analysis of DFR gene in weedy rice showed that the Tajima'D value was extremely significant, which indicated that DFR gene was a neutral evolutionary gene in weedy rice lines and was affected by natural selection. Cluster analysis of Rc-b HLH gene sequence showed that the first group composed of indica and japonica cultivars, the second group composed of brown/red pericarp weedy rice lines and wild rice, which also suggested that the weedy rice might have a closer relationship with wild rice. The results of this study concluded that crossing between the indica and japonica resulted in the recombination of mutations of Rc and Rd genes in their progenies due to which progenies acquired the diversity pericarp colours. The results of this study also would provid a new paradigm for elucidating the molecular basis of the colors variation of brown and red pericarp weedy rice.
One of the most striking feature of weedy rice is the red pericarp of its grain, and a variety of colors from deep to shallow. Currently, only limited information was available on the origin of the red pericarp colour in weedy rice. This study took 42 strains of weedy rice having brown and red pericarp derived from indica-japonica hybridization and its white pericarp parent as research materials, which explored for their genotypes and compared with phenotypes. Meanwhile, the sequences of Rc-b HLH gene and DFR gene were sequenced and compared. The results showed that: The 42 selected weedy rice strains that vary in their pericarp colors phenotypes from brown to red. The results of genotypes and phenotypic identification were in perfect agreement. Comparing the sequence of Rc-bHLH genes, this study revealed that there was a G/A substitution at 452 bp in the weedy progenies, and a 14 bp parent deletion at 669～682 bp, while weedy rice strains without deletion. The comparative analysis of DFR gene sequence showed that there were 22 mutation sites between the red and brown pericarp weedy rice strains and 8 of them were in the exon of DFR gene, the DFR gene sequence of the parent was consistent with the brown pericarp weedy rice progenies. Genetic polymorphism analysis of DFR gene in weedy rice showed that the Tajima'D value was extremely significant, which indicated that DFR gene was a neutral evolutionary gene in weedy rice lines and was affected by natural selection. Cluster analysis of Rc-b HLH gene sequence showed that the first group composed of indica and japonica cultivars, the second group composed of brown/red pericarp weedy rice lines and wild rice, which also suggested that the weedy rice might have a closer relationship with wild rice. The results of this study concluded that crossing between the indica and japonica resulted in the recombination of mutations of Rc and Rd genes in their progenies due to which progenies acquired the diversity pericarp colours. The results of this study also would provid a new paradigm for elucidating the molecular basis of the colors variation of brown and red pericarp weedy rice.
引文
Chang J.,Chen T.,Hua ng T.D.,Huang H.S.,and Hua Y.W.,2016,Anthocyanin accumulation induced by MeJA in somatic embryo of rubber tree(Hevea brasiliensis),Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(11):3115-3121(畅姣,陈涛,黄天带,黄华孙,华玉伟,2016,茉莉酸诱导橡胶树体细胞胚花青素的累积,基因组学与应用生物学,35(11):3115-3121)
Chung J.W.,and Park Y.J.,2010,Population structure analysis reveals the maintenance of isolated sub-populations ofweedy rice,Weed Res.,50(6):606-620
Federici M.T.,Vaughan D.,Tomooka N.,Kaga A.,Wang W.X.,Doi K.,Francis M.,Zorrilla G.,and Saldain N.,2001,Analysis of Uruguayan weedy rice genetic diversity using AFLPmolecular markers,Electron.J.Biotechnol.,4(3):131-145
Furukawa T.,Maekawa M.,Oki T.,Suda I.,Lida S.,Shimada H.,Takamure I.,and Kadowaki K.I.,2007,The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp,Plant J.,49(1):91-102
Gealy D.R.,Mitten D.H.,and Rutger J.N.,2003,Gene flow between red rice(Oryza sativa)and herbicide-resistant rice(O.sativa):implications for weed management,Weed Technol.,17(3):627-645
Gressel J.,and Valverde B.E.,2009,A strategy to providelong-term control of weedy rice while mitigating herbicide resistance transgene flow,and its potential use for other crops with related weeds,Pest Manage.Sci.,65(7):723-731
Harborne J.B.,and Williams C.A.,2000,Advances in flavonoid research since 1992,Phytochemistry,55(6):481-504
Kinoshita T.,and Takahashi M.,1991,The one hundredth report of genetical studies on rice plant:linkage studies and future prospects,J.Fac.Agr.Hokkaido Univ.,65(1):1-61
Ling W.H.,Cheng Q.X.,Ma J.,and Wang T.,2001,Red and black rice decrease atherosclerotic plaque formation and increase antioxidant status in rabbits,J.Nutr.,131(5):1421-1426
Nadir S.,Xiong H.B.,Zhu Q.,Zhang X.L.,Xu H.Y.,Li J.,Dongchen W.H.,Henry D.,Guo X.Q.,Khan S.,Suh H.S.,Lee D.S.,and Chen L.J.,2017,Weedy rice in sustainable rice production a review,Agron.Sustain.Dev.,37(5):46
Oki T.,Masuda M.,Kobayashi M.,Nishiba Y.,Furuta S.,Suda I.,and Sato T.,2002,Polymeric procyanidins as radical-scavenging components in red-hulled rice,J.Agric.Food Chem.,50(26):7524-7529
Prathepha P.,2009,Seed morphological traits and genotypic diversity of weedy rice(Oryza sativa f.spontanea)populations found in the thai hom mali rice fields of north-eastern Thailand,Weed Biol.Manag.,9(1):1-9
Reddy V.,Dash S.,and Reddy A.,1995,Anthocyanin pathway in rice(Oryza sativa L.):identification of a mutant showing dominant inhibition of anthocyanins in leaf and accumulation of proanthocyanidins in pericarp,Theor.Appl.Genet.,91(2):301-312
Rozas J.,Snchez-DelBarrio J.C.,Messeguer X.,and Rozas R.,2003,DnaSP DNA polymorphism analyses by the coalescent and other methods,Bioinformatics,19(18):2496-2497
Shivrain V.K.,Burgos N.R.,Gealy D.R.,Smith K.L.,Scott R.C.,and Mauromoustakos A.,2009,Red rice(Oryza sativa L.)emergence characteristics and influence on rice(O.sativa)yieldat different planting dates,Weed Sci.,57(1):94-102
Song Z.P.,Xu X.,Wang B.,Chen J.K.,and Lu B.R.,2003,Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers,Theor.Appl.Genet.,107(8):1492
Sun X.M.,Zhang Z.Y.,Chen C.,Wu W.,Ren N.N.,Jiang C.H.,Yu J.P.,Zhao Y.,Zheng X.M.,Yang Q.W.,Zhang H.L.,Li J.J.,and Li Z.C.,2017,The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice,J.Exp.Bot.,69(7):1485-1498
Sweeney M.T.,Thomson M.J.,Pfeil B.E.,and McCouch S.R.,2006,Caught red-handed:encodes a basic helix-loop-helix protein conditioning red pericarp in rice,Plant Cell,18(2):283-294
Tajima F.,1983,Evolutionary relationship of DNA sequences infinite populations,Genetics,105(2):437-460
Tajima F.,1989,Statistical method for testing the neutral mutation hypothesis by DNA polymorphism,Genetics,123(2):585-595
Thompson J.D.,Gibson T.J.,Plewniak F.,Jeanmougin F.,and Higgins D.G.,1997,The Clustal X windows interface:flexible strategies for multiplesequence alignment aided by quality analysis tools,Nucleic Acids Res.,25(24):4876-4882
Tian M.L.,Huang Y.B.,Tan G.X.,Liu Y.J.,and Rong T.Z.,2008,Sequence polymorphism of waxy genes in landraces of waxy maize from southwest China,Zuowu Xuebao(Acta Agronomica Sinica),34(5):729-736(田孟良,黄玉碧,谭功燮,刘永建,荣廷昭,2008,西南糯玉米地方品种waxy基因序列多态性分析,作物学报,34(5):729-736)
Xiong H.B.,Bai H.J.,Dongchen W.H.,Li J.,Wen J.C.,Xu H.Y.,Zhu Q.,Zhang X.L.,Zhang H.X.,Wang K.B.,Liu S.Q.,Guo X.Q.,Nadir S.,Lee D.S.,and Chen L.J.,2017,Origin and characterization of weedy rice in japonica rice regions of northern Henan along Yellow River,China,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(8):3351-3357(熊海波,白怀瑾,董陈文华,李娟,文建成,许红云,朱骞,张小玲,张慧鑫,汪琨璧,刘思琪,付亚雄,郭效琼,Nadir S.,李东宣,陈丽娟,2017,黄河流域豫北粳稻区杂草稻特性及其发生机制分析,分子植物育种,16(8):3351-3357)
Zhang S.L.,Li J.,Dongchen W.H.,Xiong H.B.,Zhang L.D.,Zhu Q.,Zhang X.L.,Wu T.F.,Lee D.S.,and Chen L.J.,2015,Molecular identification of red pericarp and variation analysis of Rc-bHLH sequence in Asian weedy rice,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(1):51-60(张树林,李娟,董陈文华,熊海波,张利东,朱骞,张小玲,伍腾飞,李东宣,陈丽娟,2015,亚洲杂草稻红色果皮分子鉴定及其Rc-bHLH序列多态性分析,分子植物育种,13(1):51-60)
Chung J.W.,and Park Y.J.,2010,Population structure analysis reveals the maintenance of isolated sub-populations ofweedy rice,Weed Res.,50(6):606-620
Federici M.T.,Vaughan D.,Tomooka N.,Kaga A.,Wang W.X.,Doi K.,Francis M.,Zorrilla G.,and Saldain N.,2001,Analysis of Uruguayan weedy rice genetic diversity using AFLPmolecular markers,Electron.J.Biotechnol.,4(3):131-145
Furukawa T.,Maekawa M.,Oki T.,Suda I.,Lida S.,Shimada H.,Takamure I.,and Kadowaki K.I.,2007,The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp,Plant J.,49(1):91-102
Gealy D.R.,Mitten D.H.,and Rutger J.N.,2003,Gene flow between red rice(Oryza sativa)and herbicide-resistant rice(O.sativa):implications for weed management,Weed Technol.,17(3):627-645
Gressel J.,and Valverde B.E.,2009,A strategy to providelong-term control of weedy rice while mitigating herbicide resistance transgene flow,and its potential use for other crops with related weeds,Pest Manage.Sci.,65(7):723-731
Harborne J.B.,and Williams C.A.,2000,Advances in flavonoid research since 1992,Phytochemistry,55(6):481-504
Kinoshita T.,and Takahashi M.,1991,The one hundredth report of genetical studies on rice plant:linkage studies and future prospects,J.Fac.Agr.Hokkaido Univ.,65(1):1-61
Ling W.H.,Cheng Q.X.,Ma J.,and Wang T.,2001,Red and black rice decrease atherosclerotic plaque formation and increase antioxidant status in rabbits,J.Nutr.,131(5):1421-1426
Nadir S.,Xiong H.B.,Zhu Q.,Zhang X.L.,Xu H.Y.,Li J.,Dongchen W.H.,Henry D.,Guo X.Q.,Khan S.,Suh H.S.,Lee D.S.,and Chen L.J.,2017,Weedy rice in sustainable rice production a review,Agron.Sustain.Dev.,37(5):46
Oki T.,Masuda M.,Kobayashi M.,Nishiba Y.,Furuta S.,Suda I.,and Sato T.,2002,Polymeric procyanidins as radical-scavenging components in red-hulled rice,J.Agric.Food Chem.,50(26):7524-7529
Prathepha P.,2009,Seed morphological traits and genotypic diversity of weedy rice(Oryza sativa f.spontanea)populations found in the thai hom mali rice fields of north-eastern Thailand,Weed Biol.Manag.,9(1):1-9
Reddy V.,Dash S.,and Reddy A.,1995,Anthocyanin pathway in rice(Oryza sativa L.):identification of a mutant showing dominant inhibition of anthocyanins in leaf and accumulation of proanthocyanidins in pericarp,Theor.Appl.Genet.,91(2):301-312
Rozas J.,Snchez-DelBarrio J.C.,Messeguer X.,and Rozas R.,2003,DnaSP DNA polymorphism analyses by the coalescent and other methods,Bioinformatics,19(18):2496-2497
Shivrain V.K.,Burgos N.R.,Gealy D.R.,Smith K.L.,Scott R.C.,and Mauromoustakos A.,2009,Red rice(Oryza sativa L.)emergence characteristics and influence on rice(O.sativa)yieldat different planting dates,Weed Sci.,57(1):94-102
Song Z.P.,Xu X.,Wang B.,Chen J.K.,and Lu B.R.,2003,Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers,Theor.Appl.Genet.,107(8):1492
Sun X.M.,Zhang Z.Y.,Chen C.,Wu W.,Ren N.N.,Jiang C.H.,Yu J.P.,Zhao Y.,Zheng X.M.,Yang Q.W.,Zhang H.L.,Li J.J.,and Li Z.C.,2017,The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice,J.Exp.Bot.,69(7):1485-1498
Sweeney M.T.,Thomson M.J.,Pfeil B.E.,and McCouch S.R.,2006,Caught red-handed:encodes a basic helix-loop-helix protein conditioning red pericarp in rice,Plant Cell,18(2):283-294
Tajima F.,1983,Evolutionary relationship of DNA sequences infinite populations,Genetics,105(2):437-460
Tajima F.,1989,Statistical method for testing the neutral mutation hypothesis by DNA polymorphism,Genetics,123(2):585-595
Thompson J.D.,Gibson T.J.,Plewniak F.,Jeanmougin F.,and Higgins D.G.,1997,The Clustal X windows interface:flexible strategies for multiplesequence alignment aided by quality analysis tools,Nucleic Acids Res.,25(24):4876-4882
Tian M.L.,Huang Y.B.,Tan G.X.,Liu Y.J.,and Rong T.Z.,2008,Sequence polymorphism of waxy genes in landraces of waxy maize from southwest China,Zuowu Xuebao(Acta Agronomica Sinica),34(5):729-736(田孟良,黄玉碧,谭功燮,刘永建,荣廷昭,2008,西南糯玉米地方品种waxy基因序列多态性分析,作物学报,34(5):729-736)
Xiong H.B.,Bai H.J.,Dongchen W.H.,Li J.,Wen J.C.,Xu H.Y.,Zhu Q.,Zhang X.L.,Zhang H.X.,Wang K.B.,Liu S.Q.,Guo X.Q.,Nadir S.,Lee D.S.,and Chen L.J.,2017,Origin and characterization of weedy rice in japonica rice regions of northern Henan along Yellow River,China,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(8):3351-3357(熊海波,白怀瑾,董陈文华,李娟,文建成,许红云,朱骞,张小玲,张慧鑫,汪琨璧,刘思琪,付亚雄,郭效琼,Nadir S.,李东宣,陈丽娟,2017,黄河流域豫北粳稻区杂草稻特性及其发生机制分析,分子植物育种,16(8):3351-3357)
Zhang S.L.,Li J.,Dongchen W.H.,Xiong H.B.,Zhang L.D.,Zhu Q.,Zhang X.L.,Wu T.F.,Lee D.S.,and Chen L.J.,2015,Molecular identification of red pericarp and variation analysis of Rc-bHLH sequence in Asian weedy rice,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(1):51-60(张树林,李娟,董陈文华,熊海波,张利东,朱骞,张小玲,伍腾飞,李东宣,陈丽娟,2015,亚洲杂草稻红色果皮分子鉴定及其Rc-bHLH序列多态性分析,分子植物育种,13(1):51-60)