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Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (11): 1853-1863.doi: 10.3724/SP.J.1006.2010.01853

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Phylogenetic Relationships of Sugarcane Related Genera and Species Based on ITS Sequences of Nuclear Ribosomal DNA

LIU Xin-Long1,SU Huo-Sheng1,MA Li1,LU Xin1,YING Xiong-Mei1,CAI Qing1,2,FAN Yuan-Hong1,*   

  1. 1 Yunnan Key Laboratory of Sugarcane Genetic Improvement / Sugarcane Research Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan 661600, China; 2 Biotechnology & Genetic Germplasm Institute, Yunnan Academy of Agricultural Sciences, Kunming 650223, China
  • Received:2010-03-16 Revised:2010-06-27 Online:2010-11-12 Published:2010-08-30
  • Contact: FAN Hong-Li,E-mail:fyhysri@vip.sohu.com

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Abstract: Sugarcane related genera and species are important germplasm resources for sugarcane breeding and germplasm innovation. To effectively collect these wild resources and utilize them, ITS (Internal Transcribed Spacer) sequence of 120 accessions which belong to eight genera and thirty seven species were used to analyze their genetic relationships and construct phylogentic relationships with P. purpureum as an outgroup. The results showed the sequence lengths of ITS1, ITS2 and 5.8sDNA of all accessions were 204–208 bp, 215–220 bp, and 164 bp respectively, and their variable sites were 91, 93, and 18, the informative sites were 70, 68, and 9, the GC content was 60.4%–69.1%, 66.1%–73.4% and 54.1%–58.0%. According to the ratio of the variable sites and informative sites to all sites, ITS sequence was richer in variances than 5.8sDNA sequence, and the variances of ITS1 sequence were richer than those of ITS2’s. The genetic distance analysis between sugarcane related genera and species indicated that Miscanthus and Triarrhena were the closest to Saccharum, and the closer ones were Erianthus and Narenga, so the species from these genera should be more considered on collecting sugarcane wild resources in the future; Microstegium, Spodiopogon and Imperata represented farther relationships with Saccharum. The sugarcane related genera and species were separated into ten groups according to the phylogenetic tree of neighbor-joining and maximum parsimony. According to their phylogenetic relationships, E. arundinaceus should be separated from Saccharum and clastified as Erianthus species; Triarrhena shoud be included in Miscanthus; the two species of Narenga did not remain in the same group, but N. porphyrocoma and E. rockii were clustered into the same group, and N. fallax did not belong to any groups, so further researches are needed in identifying the two species. These species from Erianthus and Miscanthus were put in different groups, indicating the very complex genetic relationships within Erianthus and Miscanthus, their species possess big genetic differences. Four samples were found error in classifying species, so the application of their ITS sequences should be avoided. 

Key words: Sugarcane, ITS, Phylogeny, Saccharinae

[1]Yu H(于慧), Zhao N-X(赵南先). Geographical distribution of Saccharinae (Gramineae). J Trop Subtrop Bot (热带亚热带植物学报), 2004, 12(1): 29–35 (in Chinese with English abstract)
[2]Brown J S, Schnell R J, Power E J, Douglas S L, Kuhn D N. Analysis of clonal germplasm from five Saccharum species: S. barberi, S. robustum, S. officinarum, S. sinense and S. spontaneum. A study of inter- and intra species relationships using microsatellite markers. Genet Resour Crop Evol, 2007, 54: 627–648
[3]Mukherjce S K. Origin and distribution of Sacharum. Bot Gaz, 1957, 119: 55–61
[4]Daniels J, Daniels C A. Geographical, historical and cultural aspects of the origin of the Indian and Chinese sugarcanes S. barberi and S. sinense. Sugarcane Breed Newslett, 1975, 36: 4–23
[5]Wen Y(文颖). Intergenetic crossing between Saccharum and related plants and their chromosome behavior. Sugarcane Canesugar (甘蔗糖业), 1998, 3: 1–7 (in Chinese with English abstract)
[6]Coto O, Cornide M T, Calvo D, Canales E, D’Hont A, de Prada F. Genetic diversity among wild sugarcane germplasm from Laos revealed with markers. Euphytica, 2002, 123: 121–130
[7]Chen H(陈辉), Fan Y-H(范源洪), Xiang-Yu J-G(向余颈攻), Cai Q(蔡青), Zhang Y-P(张亚平). Phylogenetic relationships of saccharum and related species inferred from sequence analysis of the nrDNA ITS region. Acta Agron Sin (作物学报), 2003, 29(3): 379–385 (in Chinese with English abstract)
[8]Cai Q(蔡青), Fan Y-H(范源洪), Aitken K, Piperidis G, McIntyre C L, Jackson P. Assessment of the phylogenetic relationships within the “Saccharum complex” using AFLP markers. Acta Agron Sin (作物学报), 2005, 31(5): 551–559 (in Chinese with English abstract)
[9]Selvi A, Nair N V, Noyer J L, Singh N K, Balasundaram N, Bansal K C, Koundal K R, Mohapatra T. AFLP analysis of the phenetic organization and genetic diversity in the sugarcane complex. Saccharum Erianthus. Genet Resour Crop Evol, 2006, 53: 831–842
[10]Nakayama S. Intra-species diversity of interspersed sequences in polyploid cultivated Saccharum species. Genes & Genetic Systems, 2006, 81: 418–418
[11]Besse P, McIntyre C L, Berding N. Ribosomal DNA variations in Erianthus, a wild sugarcane relative ( Andropogoneae-Saccharinae). Theor Appl Genet, 1996, 92: 733–743
[12]Besse P, McIntyre C L, Berding N. Characterisation of Erianthus sect. Ripidium and Saccharum germplasm (Andropogoneae-Saccharinae ) using RFLP markers. Euphytica, 1997, 93: 283–292
[13]Nair N V, Nair S, Sreenivasan T V, Mohan M. Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genet Res Crop Evol, 1999, 46: 73–79
[14]Pan Y B, Burner D M, Legendre B L. An assessment of the phylogenetic relationship among sugarcane and related taxa based on the nucleotide sequence of 5S rRNA intergenic spacers. Genetica, 2000, 108: 285–295
[15]Zhang Y-W(张云武), Long H-S(龙火生), Fan Y-H(范源洪), Yao Y-G(姚永刚), Cai Q(蔡青), Zhang Y-P(张亚平). Sequence variation of rbcl gene and evolution of Saccharum and related species. Acta Bot Yunnan (云南植物研究), 2002, 24(1): 29–36 (in Chinese with English abstract)
[16]Chen S-F(陈少风), Dong S-S(董穗穗), Wu W(吴伟), Shi S-H(施苏华), Zhou P-H(周朴华). Phylogenetics of Triarrhena and related genera based on ITS sequence data. J Wuhan Bot Res (武汉植物学研究), 2007, 25(3): 239–244 (in Chinese with English abstract)
[17]Kumar S, Nei M, Dudley J, Tamura K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 2008, 9: 299–306
[18]Editorial Board of the Flora of China (中国植物志编辑部委员会). Flora of China, Vol. 10, No. 2 (中国植物志第十卷第二分册). Beijing: Science Press, 1997. pp 4–46 (in Chinese)
[19]Heinz K J. Report of the Standing Committee on Germplasm and Breeding. In: Proc. of the XVII Congress of the ISSCT. Philippines, 1980. LIV–LVI
[20]Liu X-L(刘新龙), Cai Q(蔡青), Wang L-P(王丽萍), Ma L(马丽), Lu X(陆鑫), Ying X-M(应雄美), Mao J(毛钧). The advance of sugarcane germplasm resource in genetic diversity and crossing utilization. Sugar Crops China (中国糖料), 2007, (1): 46–49 (in Chinese with English abstract)
[21]Emily A H,  Stephen P L, Thomas B V, Michael B J, John C B. Miscanthus for renewable energy generation: european union experience and projections for Illinois. Mitigation Adapt Strategies Global Change, 2004, 9: 433–451
[22]Wilfred Vermerris. Genetic Improvement of Bioenergy Crops. New York: Springer Press, 2008. pp 295–308
[23]Lao Z-Z(廖兆周), Lao F-Y(劳方业), Zhou Y-H(周耀辉), Li Q-W(李奇伟), Deng H-H(邓海华), Huang H-N(黄鸿能), Fu C(符城), Hu H-X(胡后祥), Yang Y-H(杨业后), Chen X-W(陈西文). Breeding of drought-tolerant sugarcane lines with E. arundinaceus germplasm. Acta Agron Sin (作物学报), 2002, 28(6): 841–846 (in Chinese with English abstract)
[24]Wang L-P(王丽萍), Cai Q(蔡青), Fan Y-H(范源洪), Lu X(陆鑫), Aiken K, Ma L(马丽), Liu X-L(刘新龙), Xia H-M(夏红明). Study on the distant hybrid utilization between Saccharum and Erianthus arundinanceus. Southwest China J Agric Sci (西南农业学报), 2007, 20(4): 721–726 (in Chinese with English abstract)
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