小麦低分子量麦谷蛋白基因座位Glu-D3位点的分子进化
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摘要
小麦Glu-3位点含有低分子量麦谷蛋白(low-molecular-weight glutenin subunit, LMW-GS)基因、部分醇溶蛋白基因和抗病基因,其对品质改良和抗病育种具有重要意义。为了解析小麦Glu-D3位点和探讨其六倍体化,本研究从已发表的普通小麦基因组中截取了Glu-D3位点序列。该序列共7.51 Mb,包含49.07%的重复序列/元件。我们从中预测得到共163个基因,其中8个LMW-GS基因,6个醇溶蛋白基因和34个抗病基因。在整个位点,基因间的平均距离为46.07 kb。通过和普通小麦D基因组供体粗山羊草Glu-D3位点的共线性分析,我们发现六倍体化使得普通小麦的Glu-D3位点发生了两处片段倒置(0.91～3.12 Mb和3.97～5.14 Mb)和两处大片段(0.91～3.12 Mb和3.97～5.14 Mb)插入,但未对LMW-GS基因的编码区造成影响。进化树分析表明,普通小麦Glu-D3位点的基因可能来源于不同的粗山羊草品系。这项工作将有助于人们理解Glu-D3位点的组成和结构以及六倍体化对D基因组结构等方面的影响。
Wheat Glu-3 locus contains low-molecular-weight glutenin subunit(LMW-GS), partial gliadin and disease resistance genes, and it is of great significance to quality improvement and disease resistance breeding. In order to dissect Glu-D3 locus in wheat and explore its hexaploidization, the Glu-D3 locus sequence of common wheat was obtained from the published genome data in this study. The locus was 7.51 Mb with 49.07% repetitive DNA. In the locus, 163 genes were predicted with an average gene density of 46.07 kb/gene, among which there were eight LMW-GS genes, six gliadin g enes and 34 disease resistance genes. In the syntenic analysis with the progenitor locus in Aegilops tauschii, the Glu-D3 locus of common wheat comprised two large fragment inversions(at the positions 0.91～3.12 Mb and 3.97～5.14 Mb) and two huge insertions(at the positions 0.91～3.12 Mb and 3.97～5.14 Mb), which might be induced by wheat hexaploidiz ation. However, the coding sequences of homological LMW-GS genes between the two loci kept conserved. Phylogenetic analysis indicated that genes in the Glu-D3 locus of common wheat might originate from more than one Ae. tauschii genotypes. This work would undoubtedly facilitate elucidating not only the gene composition and structure of Glu-D3 locus but also the impact of hexaploidization on the structure of the D genome.
Wheat Glu-3 locus contains low-molecular-weight glutenin subunit(LMW-GS), partial gliadin and disease resistance genes, and it is of great significance to quality improvement and disease resistance breeding. In order to dissect Glu-D3 locus in wheat and explore its hexaploidization, the Glu-D3 locus sequence of common wheat was obtained from the published genome data in this study. The locus was 7.51 Mb with 49.07% repetitive DNA. In the locus, 163 genes were predicted with an average gene density of 46.07 kb/gene, among which there were eight LMW-GS genes, six gliadin g enes and 34 disease resistance genes. In the syntenic analysis with the progenitor locus in Aegilops tauschii, the Glu-D3 locus of common wheat comprised two large fragment inversions(at the positions 0.91～3.12 Mb and 3.97～5.14 Mb) and two huge insertions(at the positions 0.91～3.12 Mb and 3.97～5.14 Mb), which might be induced by wheat hexaploidiz ation. However, the coding sequences of homological LMW-GS genes between the two loci kept conserved. Phylogenetic analysis indicated that genes in the Glu-D3 locus of common wheat might originate from more than one Ae. tauschii genotypes. This work would undoubtedly facilitate elucidating not only the gene composition and structure of Glu-D3 locus but also the impact of hexaploidization on the structure of the D genome.
引文
Bottley A.,Xia G.M.,and Koebner R.M.D.,2006,Homoeologous gene silencing in hexaploid wheat,Plant J.,47(6):897-906
Caldwell K.S.,Dvorak J.,Lagudah E.S.,Akhunov E.,Luo M.C.,Wolters P.,and Powell W.,2004,Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor,Genetics,167(2):941-947
Chantret N.,Salse J.,Sabot F.,Rahman S.,Bellec A.,Laubin B.,Dubois I.,Dossat C.,Sourdille P.,Joudrier P.,Gautier M.F.,Cattolico L.,Beckert M.,Aubourg S.,Weissenbach J.,Caboche M.,Bernard M.,Leroy P.,and Chalhoub B.,2005,Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species(Triticum and Aegilops),Plant Cell,17(4):1033-1045
Dong L.L.,Huo N.X.,Wang Y.,Deal K.,Wang D.W.,Hu T.Z.,Dvoraw J.,Anderson O.D.,Luo M.C.,and Gu Y.Q.,2016,Rapid evolutionary dynamics in a 2.8 Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii,Plant J.,87(5):495-506
D'Ovidio R.,and Masci S.,2004,The low-molecular-weight glutenin subunits of wheat gluten,J.Cereal Sci.,39(3):321-339
Faris J.D.,2014,Wheat domestication:key to agricultural revolutions past and future,In:Tuberosa R.,Graner A.,and Frison E.(eds.),Genomics of plant genetic resources,Springer Science and Business Media,Springer,Dordrecht,Netherlands,pp.439-464
He P.,Friebe B.R.,Gill B.S.,and Zhou J.M.,2003,Allopolyploidy alters gene expression in the highly stable hexaploid wheat,Plant Mol.Biol.,52(2):401-414
Huang L.,Brooks S.A.,Li W.L.,Fellers J.P.,Trick H.N.,and Gill B.S.,2003,Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat,Genetics,164(2):655-664
Huang S.,Sirikhachornkit A.,Su X.J.,Faris J.,Gill B.,Haselkorn R.,and Gornicki P.,2002,Genes encoding plastid acetylCoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat,Proc.Natl.Acad.Sci.USA,99(12):8133-8138
International Wheat Genome Sequencing Consortium,2014,Achromosome-based draft sequence of the hexaploid bread wheat(Triticum aestivum)genome,Science,345(6194):1251788
Jia J.Z.,Zhao S.C.,Kong X.Y.,Li Y.R.,Zhao G.Y.,He W.M.,Appels R.,Pfeifer M.,Tao Y.,Zhang X.Y.,Jing R.L.,Zhang C.,Ma Y.Z.,Gao L.F.,Gao C.,Spannagl M.,Mayer K.F.X.,Li D.,Pan S.K.,Zheng F.Y.,Hu Q.,Xia X.C.,Li J.W.,Liang Q.S.,Chen J.,Wicker T.,Gou C.Y.,Kuang H.H.,He G.Y.,Luo Y.D.,Keller B.,Xia Q.J.,Lu P.,Wang J.Y.,Zou H.F.,Zhang R.Z.,Xu J.Y.,Gao J.L.,Middleton C.,Quan Z.W.,Liu G.M.,Wang J.,Yang H.M.,Liu X.,He Z.H.,Mao L.,and Wang J.,2013,Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation,Nature,496(7443):91-95
Kashkush K.,Feldman M.,and Levy A.A.,2002,Gene loss,silencing and activation in a newly synthesized wheat allotetraploid,Genetics,160(4):1651-1659
Luo M.C.,Gu Y.Q.,Puiu D.,Wang H.,Twardziok S.O.,Deal K.R.,Huo N.X.,Zhu T.T.,Wang L.,Wang Y.,McGuire P.E.,Liu S.Y.,Long H.,Ramasamy R.K.,Rodriguez J.C.,Van.SL.,Yuan L.,Wang Z.Z.,Xia Z.Q.,Xiao L.C.,Anderson O.D.,Ouyang S.H.,Liang Y.,Zimin A.V.,Pertea G.,Qi P.,Bennetzen J.L.,Dai X.T.,Dawson M.W.,Muller H.G.,Kugler K.,Rivarola-Duarte L.,Spannagl M.,Mayer K.F.X.,Lu F.H.,Bevan M.W.,Leroy P.,Li P.C.,You F.M.,Sun Q.X,Liu Z.Y.,Lyons E.,Wicker T.,Salzberg S.L.,Devos K.M.,and Dvorak J.,2017,Genome sequence of the progenitor of the wheat D genome Aegilops tauschii,Nature,551(7681):498-502
Shewry P.R.,Halford N.G.,and Lafiandra D.,2003,Genetics of wheat gluten proteins,Adv.Genet.,49(49):111-184
Shewry P.R.,Napier J.A.,and Tatham A.S.,1995,Seed storage proteins:structures and biosynthesis,Plant Cell,7(7):945-956
Singh N.K.,and Shepherd K.W.,1988,Linkage mapping of genes controlling endosperm storage proteins in wheat,1.genes on the short arms of group1 chromosomes,Theor.Appl.Genet.,75(4):628-641
Spielmeyer W.,and Lagudah E.S.,2003,Homoeologous set of NBS-LRR genes located at leaf and stripe rust resistance loci on short arms of chromosome 1 of wheat,Funct.Integr.Genomics,3(1-2):86-90
Talbert L.E.,Smith L.Y.,and Blake N.K.,1998,More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA,Genome,41(3):402-407
Yahiaoui N.,Srichumpa P.,Dudler R.,and Keller B.,2004,Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat,Plant J.,37(4):528-538
Zhang H.K.,Bian Y.,Gou X.W.,Zhu B.,Xu C.M.,Qi B.,Li N.,Rustgi S.,Zhou H.,Han F.P.,Jiang J.M.,Von Wettstein D.,and Liu B.,2013,Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat,Proc.Natl.Acad.Sci.USA,110(9):3447-3452
Zhao G.Y.,Zou C.,Li K.,Wang K.,Li T.B.,Gao L.F.,Zhang X.X.,Wang H.J.,Yang Z.J.,Liu X.,Jiang W.K.,Mao L.,Kong X.Y.,Jiao Y.N.,and Jia J.Z.,2017,The Aegilops tauschii genome reveals multiple impacts of transposons,Nat.Plants,3(12):946-955
Zhao N.,Zhu B.,Li M.J.,Wang L.,Xu L.Y.,Zhang H.K.,Zheng S.S.,Qi B.,Han F.P.,and Liu B.,2011,Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat,Genetics,188(3):499-509
Caldwell K.S.,Dvorak J.,Lagudah E.S.,Akhunov E.,Luo M.C.,Wolters P.,and Powell W.,2004,Sequence polymorphism in polyploid wheat and their D-genome diploid ancestor,Genetics,167(2):941-947
Chantret N.,Salse J.,Sabot F.,Rahman S.,Bellec A.,Laubin B.,Dubois I.,Dossat C.,Sourdille P.,Joudrier P.,Gautier M.F.,Cattolico L.,Beckert M.,Aubourg S.,Weissenbach J.,Caboche M.,Bernard M.,Leroy P.,and Chalhoub B.,2005,Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species(Triticum and Aegilops),Plant Cell,17(4):1033-1045
Dong L.L.,Huo N.X.,Wang Y.,Deal K.,Wang D.W.,Hu T.Z.,Dvoraw J.,Anderson O.D.,Luo M.C.,and Gu Y.Q.,2016,Rapid evolutionary dynamics in a 2.8 Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii,Plant J.,87(5):495-506
D'Ovidio R.,and Masci S.,2004,The low-molecular-weight glutenin subunits of wheat gluten,J.Cereal Sci.,39(3):321-339
Faris J.D.,2014,Wheat domestication:key to agricultural revolutions past and future,In:Tuberosa R.,Graner A.,and Frison E.(eds.),Genomics of plant genetic resources,Springer Science and Business Media,Springer,Dordrecht,Netherlands,pp.439-464
He P.,Friebe B.R.,Gill B.S.,and Zhou J.M.,2003,Allopolyploidy alters gene expression in the highly stable hexaploid wheat,Plant Mol.Biol.,52(2):401-414
Huang L.,Brooks S.A.,Li W.L.,Fellers J.P.,Trick H.N.,and Gill B.S.,2003,Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat,Genetics,164(2):655-664
Huang S.,Sirikhachornkit A.,Su X.J.,Faris J.,Gill B.,Haselkorn R.,and Gornicki P.,2002,Genes encoding plastid acetylCoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat,Proc.Natl.Acad.Sci.USA,99(12):8133-8138
International Wheat Genome Sequencing Consortium,2014,Achromosome-based draft sequence of the hexaploid bread wheat(Triticum aestivum)genome,Science,345(6194):1251788
Jia J.Z.,Zhao S.C.,Kong X.Y.,Li Y.R.,Zhao G.Y.,He W.M.,Appels R.,Pfeifer M.,Tao Y.,Zhang X.Y.,Jing R.L.,Zhang C.,Ma Y.Z.,Gao L.F.,Gao C.,Spannagl M.,Mayer K.F.X.,Li D.,Pan S.K.,Zheng F.Y.,Hu Q.,Xia X.C.,Li J.W.,Liang Q.S.,Chen J.,Wicker T.,Gou C.Y.,Kuang H.H.,He G.Y.,Luo Y.D.,Keller B.,Xia Q.J.,Lu P.,Wang J.Y.,Zou H.F.,Zhang R.Z.,Xu J.Y.,Gao J.L.,Middleton C.,Quan Z.W.,Liu G.M.,Wang J.,Yang H.M.,Liu X.,He Z.H.,Mao L.,and Wang J.,2013,Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation,Nature,496(7443):91-95
Kashkush K.,Feldman M.,and Levy A.A.,2002,Gene loss,silencing and activation in a newly synthesized wheat allotetraploid,Genetics,160(4):1651-1659
Luo M.C.,Gu Y.Q.,Puiu D.,Wang H.,Twardziok S.O.,Deal K.R.,Huo N.X.,Zhu T.T.,Wang L.,Wang Y.,McGuire P.E.,Liu S.Y.,Long H.,Ramasamy R.K.,Rodriguez J.C.,Van.SL.,Yuan L.,Wang Z.Z.,Xia Z.Q.,Xiao L.C.,Anderson O.D.,Ouyang S.H.,Liang Y.,Zimin A.V.,Pertea G.,Qi P.,Bennetzen J.L.,Dai X.T.,Dawson M.W.,Muller H.G.,Kugler K.,Rivarola-Duarte L.,Spannagl M.,Mayer K.F.X.,Lu F.H.,Bevan M.W.,Leroy P.,Li P.C.,You F.M.,Sun Q.X,Liu Z.Y.,Lyons E.,Wicker T.,Salzberg S.L.,Devos K.M.,and Dvorak J.,2017,Genome sequence of the progenitor of the wheat D genome Aegilops tauschii,Nature,551(7681):498-502
Shewry P.R.,Halford N.G.,and Lafiandra D.,2003,Genetics of wheat gluten proteins,Adv.Genet.,49(49):111-184
Shewry P.R.,Napier J.A.,and Tatham A.S.,1995,Seed storage proteins:structures and biosynthesis,Plant Cell,7(7):945-956
Singh N.K.,and Shepherd K.W.,1988,Linkage mapping of genes controlling endosperm storage proteins in wheat,1.genes on the short arms of group1 chromosomes,Theor.Appl.Genet.,75(4):628-641
Spielmeyer W.,and Lagudah E.S.,2003,Homoeologous set of NBS-LRR genes located at leaf and stripe rust resistance loci on short arms of chromosome 1 of wheat,Funct.Integr.Genomics,3(1-2):86-90
Talbert L.E.,Smith L.Y.,and Blake N.K.,1998,More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA,Genome,41(3):402-407
Yahiaoui N.,Srichumpa P.,Dudler R.,and Keller B.,2004,Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat,Plant J.,37(4):528-538
Zhang H.K.,Bian Y.,Gou X.W.,Zhu B.,Xu C.M.,Qi B.,Li N.,Rustgi S.,Zhou H.,Han F.P.,Jiang J.M.,Von Wettstein D.,and Liu B.,2013,Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat,Proc.Natl.Acad.Sci.USA,110(9):3447-3452
Zhao G.Y.,Zou C.,Li K.,Wang K.,Li T.B.,Gao L.F.,Zhang X.X.,Wang H.J.,Yang Z.J.,Liu X.,Jiang W.K.,Mao L.,Kong X.Y.,Jiao Y.N.,and Jia J.Z.,2017,The Aegilops tauschii genome reveals multiple impacts of transposons,Nat.Plants,3(12):946-955
Zhao N.,Zhu B.,Li M.J.,Wang L.,Xu L.Y.,Zhang H.K.,Zheng S.S.,Qi B.,Han F.P.,and Liu B.,2011,Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat,Genetics,188(3):499-509