基于ITS序列的百合属野生资源与栽培品种亲缘关系评价
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摘要
以野生百合资源和不同系列栽培品种为研究对象,利用ITS序列,构建最大简约法(maximum parsimony, MP)和最大似然法(maximum likelihood, ML)系统发育树,对其亲缘关系进行评价,为资源保护和可持续利用及育种亲本选配提供指导。系统发育树结果表明:轮叶组L. tsingtauense、L. martagon album (ML=67,MP=59)和L. distichum (ML=99, MP=96)单独聚在Group1。L. formosanum、L. longiflorum、L. brownii与LA(Longiflorum-Asiatic hybrids)系列的Bright Diamond聚在一起(ML=65, MP=50),可能是L (Longiflorum hybrids)系列的原生亲本。A (Asiatic hybrids)系列、LA系列和AZ.T (Asiatic-Trumpet Hybrid)系列的栽培品种亲缘关系很近,在Group 3中聚在同一个分支上。L. leichtlinii、L. lancifolium可能参与了A系列的品种育成。L.rubellum、L. speciosum var. gloriosoides和L. auratum与O (Oriental hybrids)系列的栽培品种的亲缘关系比较近,可能是O系列的原始亲本。TR (Trumpet hybrid)系列的栽培品种与喇叭组(Section leucolirion) L. leucanthum var. centifolium、L. regale和L. sulphureum (ML=98, MP=98)亲缘关系比较近,推测可能参与了栽培品种的育成。O系列与OT (Oriental-Trumpet hybrid)系列的栽培品种亲缘关系比较近,聚在同一个分支上。基于ITS序列的测定和系统发育树构建的分子生物学方法,能有效区分百合属野生种和不同系列栽培品种之间的亲缘关系,以及野生种之间、不同系列栽培品种之间的亲缘关系。利用中国丰富的百合属野生资源,构建系统发育树,提供可靠地亲缘关系图谱,为百合属资源品种的育成、分类以及野生资源的保护提供分子生物学根据。
Based on the wild Lilium resources and different series of cultivars, the ITS sequences were used to construct the Maximum Parsimony(MP) and Maximum Likelihood(ML) phylogenetic trees, and their genetic relationship was evaluated. Providing guidance for resource conservation and sustainable utilization and breeding parent selection. The results of phylogenetic tree showed that: species of sect. Martagon(L. tsingtauense, L. martagon album(ML=67, MP=59) and L. distichum(ML=99, MP=96)) were grouped together in Group1. L. formosanum, L.Longiflorum, L. brownii got together with LA(Longiflorum-Asiatic hybrids) series of Bright Diamonds(ML=65,MP=50), probably the original parent of the L(Longiflorum hybrids) series. The cultivated varieties of series A(Asiatic Hybrids), LA and AZ.T(Asiatic-Trumpet Hybrid) are closely related and clustered on the same branch in Group 3. L. leichtlinii and L. lancifolium may have been involved in the breeding of a series. L. rubellum, L. speciosum var. gloriosoides and L. auratum are closely related to the cultivated varieties of O(Oriental Hybrids) series, which may be the original parent of O series. TR(Trumpet Hybrid) series of cultivars are close to sect. Leucolirion group(L. leucanthum var. centifolium, L. regale and L. sulphureum(ML=98, MP=98)), that is speculated that it may be involved in the cultivation of varieties. The cultivars of the O series and the OT(Oriental-Trumpet hybrid) series are closely related gather on the same branch. The molecular biological method based on ITS sequence determination and phylogenetic tree construction could effectively distinguish the genetic relationship between wild species of Lilium wild and different series of varieties, as well as the relationship between Lilium wild species. Using the abundant wild resources of Lilium in China, we constructed phylogenetic trees, provided reliable atlas of relative genetic relationship, providing molecular biological basis for the breeding, classification and protection of wild resources of Lilium.
Based on the wild Lilium resources and different series of cultivars, the ITS sequences were used to construct the Maximum Parsimony(MP) and Maximum Likelihood(ML) phylogenetic trees, and their genetic relationship was evaluated. Providing guidance for resource conservation and sustainable utilization and breeding parent selection. The results of phylogenetic tree showed that: species of sect. Martagon(L. tsingtauense, L. martagon album(ML=67, MP=59) and L. distichum(ML=99, MP=96)) were grouped together in Group1. L. formosanum, L.Longiflorum, L. brownii got together with LA(Longiflorum-Asiatic hybrids) series of Bright Diamonds(ML=65,MP=50), probably the original parent of the L(Longiflorum hybrids) series. The cultivated varieties of series A(Asiatic Hybrids), LA and AZ.T(Asiatic-Trumpet Hybrid) are closely related and clustered on the same branch in Group 3. L. leichtlinii and L. lancifolium may have been involved in the breeding of a series. L. rubellum, L. speciosum var. gloriosoides and L. auratum are closely related to the cultivated varieties of O(Oriental Hybrids) series, which may be the original parent of O series. TR(Trumpet Hybrid) series of cultivars are close to sect. Leucolirion group(L. leucanthum var. centifolium, L. regale and L. sulphureum(ML=98, MP=98)), that is speculated that it may be involved in the cultivation of varieties. The cultivars of the O series and the OT(Oriental-Trumpet hybrid) series are closely related gather on the same branch. The molecular biological method based on ITS sequence determination and phylogenetic tree construction could effectively distinguish the genetic relationship between wild species of Lilium wild and different series of varieties, as well as the relationship between Lilium wild species. Using the abundant wild resources of Lilium in China, we constructed phylogenetic trees, provided reliable atlas of relative genetic relationship, providing molecular biological basis for the breeding, classification and protection of wild resources of Lilium.
引文
Bald win B.G.,Sanderson M.J.,Porter J.M.,Wojciechowski M.,C ampbell C.S.,and Donoghue M.J.,1996,Erratum:The ITS region of nuclear ribosomal DNA:a valuable source of evidence on angiosperm phylogeny(Annals of the Missouri Botanical Garden(1995)82(247-277)),Annals of the Missouri Botanical Garden,83(1):151-181
Du Y.P.,2014,Collection and evaluation of Lilium spp.in China(Liliaceae)and research on resistance gene analog(RGA),Dissertation for Ph.D.,Beijing Forestry University,Supervisor:Jia G.X.,pp.Ⅰ-Ⅱ(杜运鹏,2014,我国百合属植物资源评价及抗病基因同源序列(RGA)的研究,博士学位论文,北京林业大学,导师:贾桂霞,pp.Ⅰ-Ⅱ)
Du Y.P.,He H.B.,Wang Z.X.,Li S.,Wei C.,Yuan X.N.,Cui Q.,and Jia G.X.,2014a,Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA,J.Plant Res.,127(2):249-263
Du Y.P.,He H.B.,Wang Z.X.,Wei C.,Li S.,and Jia G.X.,2014b,Investigation and evaluation of the genus Lilium,resources native to China,Genet.Resour.Crop Evol.,61(2):395-412
Hall T.A.,1999,BioEdit:a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT,Nucleic Acids Symposium Series,41(41):95-98
Librado P.,and Rozas J.,2009,DnaSP v5:a software for comprehensive analysis of DNA polymorphism data,Bioinformatics,25(11):1451-1452
Lim K.B.,Ramanna M.S,and van Tuyl J.M.,2003,Homoeologous recombination in interspecific hybrids of Lilium,Korean Journal of Breeding,35:8-12
Liu H.B.,Gu X.L.,Zhang H.H.,and Zhang D.S.,2013,Phylogenetic analysis of Schizonepeta tenuifolia from different producing areas based on ITS sequences,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),13(6):1073-1077(刘红彬,顾小龙,张海红,张丹参,2012,基于ITS序列的不同产地裂叶荆芥系统发育分析,植物遗传资源学报,13(6):1073-1077)
Liu Y.L.,Xu L.M.,and Cheng Z.P.,2007,Phylogenetic analysis of stone fruits such as peach,plum,apricot,mume and cherry based on ITS sequences,Yuanyi Xuebao(Acta Horti Culturae Sinica),34(1):23-28(刘艳玲,徐立铭,程中平,2007,基于ITS序列探讨核果类果树桃、李、杏、梅、樱的系统发育关系,园艺学报,34(1):23-28)
Lohse M.,Drechsel O.,Kahlau S.,and Bock R.,2013,OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets,Nucleic Acids Res.,41(W):575-581
Long Y.Y.,and Zhang J.Z.,1998,Protection and utilization of Lilium resources,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),(1):40-44(龙雅宜,张金政,1998,百合属植物资源的保护与利用,植物资源与环境学报,(1):40-44)
Ngan F.,Shaw P.,But P.,and Wang J.P.,1999,Molecular authentication of Panax species,Phytochemistry,50(5):787-791
Patterson T.B.,and Givnish T.J.,2002,Phylogeny,concerted convergence,and phylogenetic niche conservatism in the core Liliales:insights from rbcL and ndhF sequence data,Evolution,56(2):233-252
Qiu R.,Cheng Z.P.,and Wang Z.L.,2012,Studies on genetic relationship and evolutionary path of subgenus Amygdalus in China,Yuanyi Xuebao(Acta Horticulturae Sinica),39(2):205-214(邱蓉,程中平,王章利,2012,中国扁桃亚属植物亲缘关系及其演化途径研究,园艺学报,39(2):205-214)
Schattner P.,Brooks A.N.,and Lowe T.M.,2005,The t RNAscanSE,snoscan and snoGPS web servers for the detection of t RNAs and snoRNAs,Nucleic Acids Res.,33(W):686-689
Tamura K.,Stecher G.,Peterson D.,Filipskj A.,and Kumar S.,2013,MEGA6:Molecular evolutionary genetics analysis version 6.0,Mol.Biol.Evol.,30(12):2725-2729
Tian M.,Li J.Y.,Ni S.,Fan Z.Q.,and Li X.L.,2008,Phylogenetic study on section Camellia based on ITS sequences data,Yuanyi Xuebao(Acta Horticulturae Sinica),35(11):1685-1688(田敏,李纪元,倪穗,范正琪,李辛雷,2008,基于ITS序列的红山茶组植物系统发育关系的研究,园艺学报,35(11):1685-1688)
Tu W.F.,Zhang Z.L.,Wang Y.C.,Duan Z.Z.,Wu Y.C.,Jia G.H.,Wang W.H.,He Z.Q.,and Yao W.,2017,ITS sequence analysis and identification of wild ancient Malus hupehensis in Dajiuhu wetland area of Shennongjia,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(4):1484-1491(涂万富,张志麒,汪迎春,段真珍,吴运才,贾国华,王文华,何正权,姚伟,2017,神农架大九湖湿地古野生湖北海棠ITS序列分析及鉴定,基因组学与应用生物学,36(4):1484-1491)
Wang H.K.,Tao J.M.,Qu S.C.,Fang J.G.,Ma R.J.,Zhang Z.,and Lou X.M.,2010,Molecular evolution and phylogeny of stone fruit trees based on sequences of the internal transcribed spacers(ITS)of nuclear ribosomal DNA,Yuanyi Xuebao(Acta Horticulturae Sinica),37(3):363-374(王化坤,陶建敏,渠慎春,房经贵,马瑞娟,章镇,娄晓鸣,2010,核果类果树ITS序列分子进化及系统发育关系研究,园艺学报,37(3):363-374)
Wyman S.K.,Jansen R.K.,and Boore J.L.,2004,Automatic annotation of organellar genomes with DOGMA,Bioinformatics,20(17):3252-3255
Xi M.,Tuyl J.M.V.,and Arens P.,2015,GISH analyzed progenies generated from allotriploid lilies as female parent,Sci.Hortic.,183:130-135
Yuan B.,Yan J.J.,Ke L.N.,Zhang Z.H.,and Lai B.M.,2018,I-dentification of wild Ganoderma spp.strains based on ITSseries analysis,Zhongguo Shiyongjun(Mycological Research Center),37(2):62-66(袁滨,严俊杰,柯丽娜,张志鸿,赖碧梅,2018,基于ITS系列分析鉴定野生灵芝属菌种,中国食用菌,37(2):62-66)
Zhang X.L.,and Zhou H.G.,1999,Advances in the research of hybridization between distantly related species of Lilium,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),18(2):157-160(张西丽,周厚高,1999,百合远缘杂交育种研究现状,基因组学与应用生物学,18(2):157-160)
Zhou S.L.,Zou X.H.,Zhou Z.Q.,Liu J.,Xu C.,Yu J.,Wang Q.,Zhang D.M.,Wang X.Q.,Ge S.,Sang T.,Pan K.Y.,and Hong D.Y.,2014,Multiple species of wild tree peonies gave rise to the'king of flowers',Paeonia suffruticosa Andrews,Proc.Biol.Sci.,281(1797):20141687
Zufall R.A.,and Rausher M.D.,2004,Genetic changes associated with floral adaptation restrict future evolutionary potential,Nature,428(6985):847-850
Du Y.P.,2014,Collection and evaluation of Lilium spp.in China(Liliaceae)and research on resistance gene analog(RGA),Dissertation for Ph.D.,Beijing Forestry University,Supervisor:Jia G.X.,pp.Ⅰ-Ⅱ(杜运鹏,2014,我国百合属植物资源评价及抗病基因同源序列(RGA)的研究,博士学位论文,北京林业大学,导师:贾桂霞,pp.Ⅰ-Ⅱ)
Du Y.P.,He H.B.,Wang Z.X.,Li S.,Wei C.,Yuan X.N.,Cui Q.,and Jia G.X.,2014a,Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA,J.Plant Res.,127(2):249-263
Du Y.P.,He H.B.,Wang Z.X.,Wei C.,Li S.,and Jia G.X.,2014b,Investigation and evaluation of the genus Lilium,resources native to China,Genet.Resour.Crop Evol.,61(2):395-412
Hall T.A.,1999,BioEdit:a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT,Nucleic Acids Symposium Series,41(41):95-98
Librado P.,and Rozas J.,2009,DnaSP v5:a software for comprehensive analysis of DNA polymorphism data,Bioinformatics,25(11):1451-1452
Lim K.B.,Ramanna M.S,and van Tuyl J.M.,2003,Homoeologous recombination in interspecific hybrids of Lilium,Korean Journal of Breeding,35:8-12
Liu H.B.,Gu X.L.,Zhang H.H.,and Zhang D.S.,2013,Phylogenetic analysis of Schizonepeta tenuifolia from different producing areas based on ITS sequences,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),13(6):1073-1077(刘红彬,顾小龙,张海红,张丹参,2012,基于ITS序列的不同产地裂叶荆芥系统发育分析,植物遗传资源学报,13(6):1073-1077)
Liu Y.L.,Xu L.M.,and Cheng Z.P.,2007,Phylogenetic analysis of stone fruits such as peach,plum,apricot,mume and cherry based on ITS sequences,Yuanyi Xuebao(Acta Horti Culturae Sinica),34(1):23-28(刘艳玲,徐立铭,程中平,2007,基于ITS序列探讨核果类果树桃、李、杏、梅、樱的系统发育关系,园艺学报,34(1):23-28)
Lohse M.,Drechsel O.,Kahlau S.,and Bock R.,2013,OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets,Nucleic Acids Res.,41(W):575-581
Long Y.Y.,and Zhang J.Z.,1998,Protection and utilization of Lilium resources,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),(1):40-44(龙雅宜,张金政,1998,百合属植物资源的保护与利用,植物资源与环境学报,(1):40-44)
Ngan F.,Shaw P.,But P.,and Wang J.P.,1999,Molecular authentication of Panax species,Phytochemistry,50(5):787-791
Patterson T.B.,and Givnish T.J.,2002,Phylogeny,concerted convergence,and phylogenetic niche conservatism in the core Liliales:insights from rbcL and ndhF sequence data,Evolution,56(2):233-252
Qiu R.,Cheng Z.P.,and Wang Z.L.,2012,Studies on genetic relationship and evolutionary path of subgenus Amygdalus in China,Yuanyi Xuebao(Acta Horticulturae Sinica),39(2):205-214(邱蓉,程中平,王章利,2012,中国扁桃亚属植物亲缘关系及其演化途径研究,园艺学报,39(2):205-214)
Schattner P.,Brooks A.N.,and Lowe T.M.,2005,The t RNAscanSE,snoscan and snoGPS web servers for the detection of t RNAs and snoRNAs,Nucleic Acids Res.,33(W):686-689
Tamura K.,Stecher G.,Peterson D.,Filipskj A.,and Kumar S.,2013,MEGA6:Molecular evolutionary genetics analysis version 6.0,Mol.Biol.Evol.,30(12):2725-2729
Tian M.,Li J.Y.,Ni S.,Fan Z.Q.,and Li X.L.,2008,Phylogenetic study on section Camellia based on ITS sequences data,Yuanyi Xuebao(Acta Horticulturae Sinica),35(11):1685-1688(田敏,李纪元,倪穗,范正琪,李辛雷,2008,基于ITS序列的红山茶组植物系统发育关系的研究,园艺学报,35(11):1685-1688)
Tu W.F.,Zhang Z.L.,Wang Y.C.,Duan Z.Z.,Wu Y.C.,Jia G.H.,Wang W.H.,He Z.Q.,and Yao W.,2017,ITS sequence analysis and identification of wild ancient Malus hupehensis in Dajiuhu wetland area of Shennongjia,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),36(4):1484-1491(涂万富,张志麒,汪迎春,段真珍,吴运才,贾国华,王文华,何正权,姚伟,2017,神农架大九湖湿地古野生湖北海棠ITS序列分析及鉴定,基因组学与应用生物学,36(4):1484-1491)
Wang H.K.,Tao J.M.,Qu S.C.,Fang J.G.,Ma R.J.,Zhang Z.,and Lou X.M.,2010,Molecular evolution and phylogeny of stone fruit trees based on sequences of the internal transcribed spacers(ITS)of nuclear ribosomal DNA,Yuanyi Xuebao(Acta Horticulturae Sinica),37(3):363-374(王化坤,陶建敏,渠慎春,房经贵,马瑞娟,章镇,娄晓鸣,2010,核果类果树ITS序列分子进化及系统发育关系研究,园艺学报,37(3):363-374)
Wyman S.K.,Jansen R.K.,and Boore J.L.,2004,Automatic annotation of organellar genomes with DOGMA,Bioinformatics,20(17):3252-3255
Xi M.,Tuyl J.M.V.,and Arens P.,2015,GISH analyzed progenies generated from allotriploid lilies as female parent,Sci.Hortic.,183:130-135
Yuan B.,Yan J.J.,Ke L.N.,Zhang Z.H.,and Lai B.M.,2018,I-dentification of wild Ganoderma spp.strains based on ITSseries analysis,Zhongguo Shiyongjun(Mycological Research Center),37(2):62-66(袁滨,严俊杰,柯丽娜,张志鸿,赖碧梅,2018,基于ITS系列分析鉴定野生灵芝属菌种,中国食用菌,37(2):62-66)
Zhang X.L.,and Zhou H.G.,1999,Advances in the research of hybridization between distantly related species of Lilium,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),18(2):157-160(张西丽,周厚高,1999,百合远缘杂交育种研究现状,基因组学与应用生物学,18(2):157-160)
Zhou S.L.,Zou X.H.,Zhou Z.Q.,Liu J.,Xu C.,Yu J.,Wang Q.,Zhang D.M.,Wang X.Q.,Ge S.,Sang T.,Pan K.Y.,and Hong D.Y.,2014,Multiple species of wild tree peonies gave rise to the'king of flowers',Paeonia suffruticosa Andrews,Proc.Biol.Sci.,281(1797):20141687
Zufall R.A.,and Rausher M.D.,2004,Genetic changes associated with floral adaptation restrict future evolutionary potential,Nature,428(6985):847-850
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