基于SLAF＿seq的重组自交系群体定位水稻抽穗期QTLs
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摘要
抽穗期是水稻最重要的农艺性状之一,定位和克隆水稻抽穗期QTL具有重要意义。本研究利用早抽品种V20B和晚抽品种CPSLO17作为亲本,构建了150个重组自交系家系(RILs),结合SLAF_seq技术构建的水稻高密度遗传图谱,对水稻抽穗期进行QTL检测。利用MapQTL5进行区间作图,阈值设定为2.5,共检测到2个抽穗期QTL,分别命名为qHD1.1和qHD4.1,这2个QTL的LOD值分别为4.82和3.23,对表型变异的解释率分别为12.8%和8.2%,且增效位点均来自于V20B。本研究为克隆水稻抽穗期QTLs和阐明其分子调控机制提供了依据。
Heading date is one of the most important agronomic traits of rice, and mapping and clone the QTLs controlling the heading date of rice have vital significance. In this study, 150 recombinant inbred lines(RILs) derived from a cross between an earlier heading variety V20 B and a later heading variety CPSLO17 were used to detect rice heading date QTLs, combined with a rice high-density genetic linkage map constructed by SLAF_seq technology. MapQTL5 was used for interval mapping and the threshold was set to 2.5. Two QTLs at heading stage were detected, named qHD1.1 and qHD4.1, respectively. LOD of these two QTLs was 4.84 and 3.23, and the explanatory rates for phenotypic variation were 12.8% and 8.2%, respectively. Moreover, their effect-increasing loci were both originated from V20 B. This study could provide reference for the cloning of QTLs in heading date of rice and the clarification of their molecular regulation mechanism.
Heading date is one of the most important agronomic traits of rice, and mapping and clone the QTLs controlling the heading date of rice have vital significance. In this study, 150 recombinant inbred lines(RILs) derived from a cross between an earlier heading variety V20 B and a later heading variety CPSLO17 were used to detect rice heading date QTLs, combined with a rice high-density genetic linkage map constructed by SLAF_seq technology. MapQTL5 was used for interval mapping and the threshold was set to 2.5. Two QTLs at heading stage were detected, named qHD1.1 and qHD4.1, respectively. LOD of these two QTLs was 4.84 and 3.23, and the explanatory rates for phenotypic variation were 12.8% and 8.2%, respectively. Moreover, their effect-increasing loci were both originated from V20 B. This study could provide reference for the cloning of QTLs in heading date of rice and the clarification of their molecular regulation mechanism.
引文
Bian X.F.,Liu X.,Zhao Z.G.,Jiang L.,Gao H.,Zhang Y.H.Zheng M.,Chen L.M.,Liu S.J.,Zhai H.Q.,and Wan J.M.2011,Heading date gene,dth3 controlled late flowering in O.Glaberrima Steud.by down-regulating Ehd1,Plant Cel Rep.,30(12):2243-2254
Chen J.Y.,Guo L.,Ma H.,Chen Y.Y.,Zhang H.W.,Ying J.Z.and Zhuang J.Y.,2014,Fine mapping of qHd1,a minor heading date QTL with pleiotropism for yield traits in rice(Oryza sativa L.),Theor.Appl.Genet.,127(11):2515-2524
Chen L.N.,and Ma Q.G.,2015,Advances on association application of SSR and AFLP in plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(4):868-873(陈凌娜,马庆国,2015,SSR和AFLP在植物中联合应用的研究进展,基因组学与应用生物学,34(4):868-873)
Doi K.,Izawa T.,Fuse T.,Yamanouchi U.,Kubo T.,Shimatan Z.,Yano M.,and Yoshimura A.,2004,Ehd1,aβ-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1,Genes Dev.,18(8):926-936
Gao H.,Jin M.N.,Zheng X.M.,Chen J.,Yuan D.Y.,Xin Y.Y.Wang M.Q.,Huang D.Y.,Zhang Z.,Zhou K.N,Sheng P.K.Ma J.,Deng H.F.,Jiang L.,Liu S.J.,Wang H.Y.,Wu C.Y.Yuan L.P.,and Wan J.M.,2014,Days to heading 7,a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice,Proc.Natl.Acad.Sci.USA,111(46):16337-16342
Gao H.,Zheng X.M.,Fei G.L.,Chen J.,Jin M.N.,Ren Y.L.,Wu W.X.,Zhou K.N.,Sheng P.K.,Zhou F.,Jiang L.,Wang J.Zhang X.,Guo X.P.,Wang J.L.,Cheng Z.J.,Wu C.Y.,Wang H.Y.,and Wan J.M.,2013,Ehd4 encodes a novel and O-ryza-genus-specific regulator of photoperiodi c flowering in rice,PLoS Genet.,9(2):e1003281
Hori K.,Ogiso-Tanaka E.,Matsubara K.,Yamanouchi U.,Ebana K.,and Yano M.,2013,Hd16,a gene for casein kinase I,is involved in the control of rice flowering time by modulating the day-length response,Plant J.Cell Mol.Biol.,76(1):36-46
Hu M.,Sun Z.Z.,Sun X.W.,Tan Y.N.,Yu D.,Liu R.F.,Yuan G.L.,Ding J.,Yuan D.Y.,and Duan M.J.,2015,Mapping of rice grain shape relevant QTLs using high-density SNPmarkers,Zajiao Shuidao(Hybrid Rice),30(5):54-58(胡苗,孙志忠,孙学武,谭炎宁,余东,刘瑞芬,袁贵龙,丁佳,袁定阳,段美娟,2015,利用高密度SNP标记定位水稻粒形相关QTL,杂交水稻,30(5):54-58)
Kojima S.,Takahashi Y.J.,Yasushi K.,Lisa M.,Sasaki T.,Araki T.,and Yano M.,2002,Hd3a,a rice ortholog of the Arabidopsis FT gene,promotes transition to flowering downstream of Hd1 under short-day conditions,Plant Cell Physiol.,43(10):1096-1105
Li Z.K.,Pinson S.R.M.,Stansel J.W.,and Park W.D.,1995,Identification of quantitative trait loci(QTLs)for heading date and plant height in cultivated rice(Oryza sativa L.),Theor.Appl.Genet.,91(2):374-381
Lin H.X.,Qian H.R.,Xiong Z.M.,Min S.K.,and Zheng K.L.,1996,Mapping of major genes and minor genes for heading date in several rice varieties(Oryza sativa L.),Yichuan Xuebao(Acta Genetica Sinica),23(3):205-213(林鸿宣,钱惠荣,熊振民,闵绍楷,郑康乐,1996,几个水稻品种抽穗期主效基因与微效基因的定位研究,遗传学报,23(3):205-213)
Lin S.Y.,Sasaki T.,and Yano M.,1998,Mapping quantitative trait loci controlling seed dormancy and heading date in rice,Oryza sativa L.,using backcross inbred lines,Theor.Appl.Genet.,96(8):997-1003
Liu G.L.,Luo Q.C.,Chen Y.M.,Chen C.H.,and Jiang X.B.,2013,Analysis and evaluation on cold tolerance for rice germplasm resources at flowering stage,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),26(2):395-398(刘广林,罗群昌,陈远孟,陈传华,蒋县斌,2013,水稻种质资源抽穗扬花期耐冷性鉴定评价,西南农业学报,26(2):395-398)
Lu B.Y.,Ma M.L.,Jiang L.,Li C.Y.,Su Y.L.,and Liu Y.H.,2015,QTL mapping and genetic analysis of heading date in rice,Xinan Nongye Xuebao(Southwest China Journal of A-gricultural Sciences),28(2):453-456(卢丙越,马孟莉,江玲,李春燕,苏一兰,刘艳红,2015,水稻抽穗期QTL定位及遗传分析,西南农业学报,28(2):453-456)
Lu B.Y.,Ma M.L.,Jiang L.,Meng H.L.,Lei E.,and Liu Y.H.,2014,QTL mapping and genetic effects of main loci controlling rice heading date using a BIL population in rice,Xibei Nongye Xuebao(Acta Agriculturae Boreali-occidentalis Sinica),23(7):51-54(卢丙越,马孟莉,江玲,孟衡玲,雷恩,刘艳红,2014,利用BIL群体定位水稻抽穗期QTL及主效位点遗传效应分析,西北农业学报,23(7):51-54)
Matsubara K.,Ogiso-Tanaka E.,Hori K.,Ebana K.,Ando T.,and Yano M.,2012,Natural variation in Hd17,a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering,Plant Cell Physiol.,53(4):709-716
Ogiso-Tanaka E.,Matsubara K.,Yamamoto S.,Nonoue Y.,Wu J.Z.,Fujisawa H.,Ishikubo H.,Tanaka T.,Ando T.,Matsumoto T.,and Yano M.,2013,Natural variation of the RICE Flowering Locus T1 contributes to flowering time divergence in rice,PLoS One,8(10):e75959
Peng Q.,Ye S.X.,Huang L.,Zhang D.S.,Liu Y.,Wu J.Q.,Zhang Y.S.,and Zhu S.S.,2016,Construction of a high-density genetic map in rice by using specific-length amplified fragment sequencing(SLAF-seq)technology,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):2127-2132(彭强叶圣鑫,黄龙,张大双,刘颖,吴健强,张玉珊,朱速松2016,运用SLAF-seq技术构建水稻高密度遗传图谱,分子植物育种,14(8):2127-2132)
Takahashi Y.,Shomura A.,Sasaki T.,and Yano M.,2001,Hd6,a rice quantitative trait locus involved in photoperiod sensitivity,encodes the alpha subunit of protein kinase CK2,Proc Natl.Acad.Sci.USA,98(14):7922-7927
Wei X.J.,Xu J.F.,Guo H.N.,Jiang L.,Chen S.H.,Yu C.Y.,Zhou Z.L.,Hu P.S.,Zhai H.Q.,and Wan J.M.,2010,DTH8 suppresses flowering in rice,influencing plant height and yield potential simultaneously,Plant Physiol.,153(4):1747-1758
Wu W.X.,Zheng X.M.,Lu G.W.,Zhong Z.Z.,Gao H.,Chen L.P.,Wu C.Y.,Wang H.J.,Wang Q.,Zhou K.N.,Wang J.L.,Wu F.Q.,Zhang X.,Guo X.P.,Cheng Z.J.,Lei C.L.,Lin Q.B.,Jiang L.,Wang H.Y.,Ge S.,and Wan J.M.,2013,Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia,Proc.Natl.Acad.Sci.USA,110(8):2775-2780
Xue W.Y.,Xing Y.Z.,Weng X.Y.,Zhao Y,Tang W.J.,Wang L.,Zhou H.J.,Yu S.B.,Xu C.G.,Li X.H.,and Zhang Q.F.,2008,Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice,Nat.Genet.,40(6):761-767
Yang Y.,Fu D.B.,Zhu C.M.,He Y.H.,Zhang H.J.,Liu T.,Li X.H.,and Wu C.Y.,2015,The RING-Finger ubiquitin ligase HAF1 mediates heading date 1 degradation during photoperiodic flowering in rice,Plant Cell,27(9):2455-2468
Yano M.,Katayose Y.,Ashikari M.,Yamanouchi U.,Monna L.,Fuse T.,Baba T.,Yamamoto K.,Umehara Y.,Nagamura Y.,and Sasaki T.,2000,Hd1,a major photoperiod sensitivity quantitative trait locus in rice,is closely related to the Arabidopsis flowering time gene Constans,Plant Cell,12(12):2473-2483
Zhou Y.,Cui G.K.,Zhang Y.Z.,Guan C.R.,Chang S.Y.,Gu M.H.,and Liang G.H.,2012,Fine mapping of a major QTLqHd8.1 for heading date in rice,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),26(1):43-48(周勇,崔国昆,张言周,关成冉,常思源,顾铭洪,梁国华,2012,水稻抽穗期主效QTL qHd8.1的精细定位,中国水稻科学,26(1):43-48)
Chen J.Y.,Guo L.,Ma H.,Chen Y.Y.,Zhang H.W.,Ying J.Z.and Zhuang J.Y.,2014,Fine mapping of qHd1,a minor heading date QTL with pleiotropism for yield traits in rice(Oryza sativa L.),Theor.Appl.Genet.,127(11):2515-2524
Chen L.N.,and Ma Q.G.,2015,Advances on association application of SSR and AFLP in plants,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),34(4):868-873(陈凌娜,马庆国,2015,SSR和AFLP在植物中联合应用的研究进展,基因组学与应用生物学,34(4):868-873)
Doi K.,Izawa T.,Fuse T.,Yamanouchi U.,Kubo T.,Shimatan Z.,Yano M.,and Yoshimura A.,2004,Ehd1,aβ-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1,Genes Dev.,18(8):926-936
Gao H.,Jin M.N.,Zheng X.M.,Chen J.,Yuan D.Y.,Xin Y.Y.Wang M.Q.,Huang D.Y.,Zhang Z.,Zhou K.N,Sheng P.K.Ma J.,Deng H.F.,Jiang L.,Liu S.J.,Wang H.Y.,Wu C.Y.Yuan L.P.,and Wan J.M.,2014,Days to heading 7,a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice,Proc.Natl.Acad.Sci.USA,111(46):16337-16342
Gao H.,Zheng X.M.,Fei G.L.,Chen J.,Jin M.N.,Ren Y.L.,Wu W.X.,Zhou K.N.,Sheng P.K.,Zhou F.,Jiang L.,Wang J.Zhang X.,Guo X.P.,Wang J.L.,Cheng Z.J.,Wu C.Y.,Wang H.Y.,and Wan J.M.,2013,Ehd4 encodes a novel and O-ryza-genus-specific regulator of photoperiodi c flowering in rice,PLoS Genet.,9(2):e1003281
Hori K.,Ogiso-Tanaka E.,Matsubara K.,Yamanouchi U.,Ebana K.,and Yano M.,2013,Hd16,a gene for casein kinase I,is involved in the control of rice flowering time by modulating the day-length response,Plant J.Cell Mol.Biol.,76(1):36-46
Hu M.,Sun Z.Z.,Sun X.W.,Tan Y.N.,Yu D.,Liu R.F.,Yuan G.L.,Ding J.,Yuan D.Y.,and Duan M.J.,2015,Mapping of rice grain shape relevant QTLs using high-density SNPmarkers,Zajiao Shuidao(Hybrid Rice),30(5):54-58(胡苗,孙志忠,孙学武,谭炎宁,余东,刘瑞芬,袁贵龙,丁佳,袁定阳,段美娟,2015,利用高密度SNP标记定位水稻粒形相关QTL,杂交水稻,30(5):54-58)
Kojima S.,Takahashi Y.J.,Yasushi K.,Lisa M.,Sasaki T.,Araki T.,and Yano M.,2002,Hd3a,a rice ortholog of the Arabidopsis FT gene,promotes transition to flowering downstream of Hd1 under short-day conditions,Plant Cell Physiol.,43(10):1096-1105
Li Z.K.,Pinson S.R.M.,Stansel J.W.,and Park W.D.,1995,Identification of quantitative trait loci(QTLs)for heading date and plant height in cultivated rice(Oryza sativa L.),Theor.Appl.Genet.,91(2):374-381
Lin H.X.,Qian H.R.,Xiong Z.M.,Min S.K.,and Zheng K.L.,1996,Mapping of major genes and minor genes for heading date in several rice varieties(Oryza sativa L.),Yichuan Xuebao(Acta Genetica Sinica),23(3):205-213(林鸿宣,钱惠荣,熊振民,闵绍楷,郑康乐,1996,几个水稻品种抽穗期主效基因与微效基因的定位研究,遗传学报,23(3):205-213)
Lin S.Y.,Sasaki T.,and Yano M.,1998,Mapping quantitative trait loci controlling seed dormancy and heading date in rice,Oryza sativa L.,using backcross inbred lines,Theor.Appl.Genet.,96(8):997-1003
Liu G.L.,Luo Q.C.,Chen Y.M.,Chen C.H.,and Jiang X.B.,2013,Analysis and evaluation on cold tolerance for rice germplasm resources at flowering stage,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),26(2):395-398(刘广林,罗群昌,陈远孟,陈传华,蒋县斌,2013,水稻种质资源抽穗扬花期耐冷性鉴定评价,西南农业学报,26(2):395-398)
Lu B.Y.,Ma M.L.,Jiang L.,Li C.Y.,Su Y.L.,and Liu Y.H.,2015,QTL mapping and genetic analysis of heading date in rice,Xinan Nongye Xuebao(Southwest China Journal of A-gricultural Sciences),28(2):453-456(卢丙越,马孟莉,江玲,李春燕,苏一兰,刘艳红,2015,水稻抽穗期QTL定位及遗传分析,西南农业学报,28(2):453-456)
Lu B.Y.,Ma M.L.,Jiang L.,Meng H.L.,Lei E.,and Liu Y.H.,2014,QTL mapping and genetic effects of main loci controlling rice heading date using a BIL population in rice,Xibei Nongye Xuebao(Acta Agriculturae Boreali-occidentalis Sinica),23(7):51-54(卢丙越,马孟莉,江玲,孟衡玲,雷恩,刘艳红,2014,利用BIL群体定位水稻抽穗期QTL及主效位点遗传效应分析,西北农业学报,23(7):51-54)
Matsubara K.,Ogiso-Tanaka E.,Hori K.,Ebana K.,Ando T.,and Yano M.,2012,Natural variation in Hd17,a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering,Plant Cell Physiol.,53(4):709-716
Ogiso-Tanaka E.,Matsubara K.,Yamamoto S.,Nonoue Y.,Wu J.Z.,Fujisawa H.,Ishikubo H.,Tanaka T.,Ando T.,Matsumoto T.,and Yano M.,2013,Natural variation of the RICE Flowering Locus T1 contributes to flowering time divergence in rice,PLoS One,8(10):e75959
Peng Q.,Ye S.X.,Huang L.,Zhang D.S.,Liu Y.,Wu J.Q.,Zhang Y.S.,and Zhu S.S.,2016,Construction of a high-density genetic map in rice by using specific-length amplified fragment sequencing(SLAF-seq)technology,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),14(8):2127-2132(彭强叶圣鑫,黄龙,张大双,刘颖,吴健强,张玉珊,朱速松2016,运用SLAF-seq技术构建水稻高密度遗传图谱,分子植物育种,14(8):2127-2132)
Takahashi Y.,Shomura A.,Sasaki T.,and Yano M.,2001,Hd6,a rice quantitative trait locus involved in photoperiod sensitivity,encodes the alpha subunit of protein kinase CK2,Proc Natl.Acad.Sci.USA,98(14):7922-7927
Wei X.J.,Xu J.F.,Guo H.N.,Jiang L.,Chen S.H.,Yu C.Y.,Zhou Z.L.,Hu P.S.,Zhai H.Q.,and Wan J.M.,2010,DTH8 suppresses flowering in rice,influencing plant height and yield potential simultaneously,Plant Physiol.,153(4):1747-1758
Wu W.X.,Zheng X.M.,Lu G.W.,Zhong Z.Z.,Gao H.,Chen L.P.,Wu C.Y.,Wang H.J.,Wang Q.,Zhou K.N.,Wang J.L.,Wu F.Q.,Zhang X.,Guo X.P.,Cheng Z.J.,Lei C.L.,Lin Q.B.,Jiang L.,Wang H.Y.,Ge S.,and Wan J.M.,2013,Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia,Proc.Natl.Acad.Sci.USA,110(8):2775-2780
Xue W.Y.,Xing Y.Z.,Weng X.Y.,Zhao Y,Tang W.J.,Wang L.,Zhou H.J.,Yu S.B.,Xu C.G.,Li X.H.,and Zhang Q.F.,2008,Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice,Nat.Genet.,40(6):761-767
Yang Y.,Fu D.B.,Zhu C.M.,He Y.H.,Zhang H.J.,Liu T.,Li X.H.,and Wu C.Y.,2015,The RING-Finger ubiquitin ligase HAF1 mediates heading date 1 degradation during photoperiodic flowering in rice,Plant Cell,27(9):2455-2468
Yano M.,Katayose Y.,Ashikari M.,Yamanouchi U.,Monna L.,Fuse T.,Baba T.,Yamamoto K.,Umehara Y.,Nagamura Y.,and Sasaki T.,2000,Hd1,a major photoperiod sensitivity quantitative trait locus in rice,is closely related to the Arabidopsis flowering time gene Constans,Plant Cell,12(12):2473-2483
Zhou Y.,Cui G.K.,Zhang Y.Z.,Guan C.R.,Chang S.Y.,Gu M.H.,and Liang G.H.,2012,Fine mapping of a major QTLqHd8.1 for heading date in rice,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),26(1):43-48(周勇,崔国昆,张言周,关成冉,常思源,顾铭洪,梁国华,2012,水稻抽穗期主效QTL qHd8.1的精细定位,中国水稻科学,26(1):43-48)