Welcome to Acta Agronomica Sinica，

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

PDF

1770

Cited

7

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)
[1] HU Wen-Jing, LI Dong-Sheng, YI Xin, ZHANG Chun-Mei, ZHANG Yong. Molecular mapping and validation of quantitative trait loci for spike-related traits and plant height in wheat [J]. Acta Agronomica Sinica, 2022, 48(6): 1346-1356.
[2] XIAO Jian, CHEN Si-Yu, SUN Yan, YANG Shang-Dong, TAN Hong-Wei. Characteristics of endophytic bacterial community structure in roots of sugarcane under different fertilizer applications [J]. Acta Agronomica Sinica, 2022, 48(5): 1222-1234.
[3] ZHOU Hui-Wen, QIU Li-Hang, HUANG Xing, LI Qiang, CHEN Rong-Fa, FAN Ye-Geng, LUO Han-Min, YAN Hai-Feng, WENG Meng-Ling, ZHOU Zhong-Feng, WU Jian-Ming. Cloning and functional analysis of ScGA20ox1 gibberellin oxidase gene in sugarcane [J]. Acta Agronomica Sinica, 2022, 48(4): 1017-1026.
[4] KONG Chui-Bao, PANG Zi-Qin, ZHANG Cai-Fang, LIU Qiang, HU Chao-Hua, XIAO Yi-Jie, YUAN Zhao-Nian. Effects of arbuscular mycorrhizal fungi on sugarcane growth and nutrient- related gene co-expression network under different fertilization levels [J]. Acta Agronomica Sinica, 2022, 48(4): 860-872.
[5] YANG Zong-Tao, LIU Shu-Xian, CHENG Guang-Yuan, ZHANG Hai, ZHOU Ying-Shuan, SHANG He-Yang, HUANG Guo-Qiang, XU Jing-Sheng. Sugarcane ubiquitin-like protein UBL5 responses to SCMV infection and interacts with SCMV-6K2 [J]. Acta Agronomica Sinica, 2022, 48(2): 332-341.
[6] XU De-Rong, SUN Chao, BI Zhen-Zhen, QIN Tian-Yuan, WANG Yi-Hao, LI Cheng-Ju, FAN You-Fang, LIU Yin-Du, ZHANG Jun-Lian, BAI Jiang-Ping. Identification of StDRO1 gene polymorphism and association analysis with root traits in potato [J]. Acta Agronomica Sinica, 2022, 48(1): 76-85.
[7] ZHAO Xue, ZHOU Shun-Li. Research progress on traits and assessment methods of stalk lodging resistance in maize [J]. Acta Agronomica Sinica, 2022, 48(1): 15-26.
[8] ZHAO Jing, MENG Fan-Gang, YU De-Bin, QIU Qiang, ZHANG Ming-Hao, RAO De-Min, CONG Bo-Tao, ZHANG Wei, YAN Xiao-Yan. Response of agronomic traits and P/Fe utilization efficiency to P application with different P efficiency in soybean [J]. Acta Agronomica Sinica, 2021, 47(9): 1824-1833.
[9] ZHANG Hai, CHENG Guang-Yuan, YANG Zong-Tao, LIU Shu-Xian, SHANG He-Yang, HUANG Guo-Qiang, XU Jing-Sheng. Sugarcane PsbR subunit response to SCMV infection and its interaction with SCMV-6K2 [J]. Acta Agronomica Sinica, 2021, 47(8): 1522-1530.
[10] SU Ya-Chun, LI Cong-Na, SU Wei-Hua, YOU Chui-Huai, CEN Guang-Li, ZHANG Chang, REN Yong-Juan, QUE You-Xiong. Identification of thaumatin-like protein family in Saccharum spontaneum and functional analysis of its homologous gene in sugarcane cultivar [J]. Acta Agronomica Sinica, 2021, 47(7): 1275-1296.
[11] LUO Lan, LEI Li-Xia, LIU Jin, ZHANG Rui-Hua, JIN Gui-Xiu, CUI Di, LI Mao-Mao, MA Xiao-Ding, ZHAO Zheng-Wu, HAN Long-Zhi. Mapping QTLs for yield-related traits using chromosome segment substitution lines of Dongxiang common wild rice (Oryza rufipogon Griff.) and Nipponbare (Oryza sativa L.) [J]. Acta Agronomica Sinica, 2021, 47(7): 1391-1401.
[12] CHENG Yan-Shuang, HU Mei-Yan, DU Zhi-Min, YAN Bing-Chun, LI Li, WANG Yi-Wei, JU Xiao-Tang, SUN Li-Li, XU Hai. Effects of nitrogen reduction on stem vascular bundles, panicle and yield characters of RIL populations in Liaojing 5/Akitakaomaqi and their correlation [J]. Acta Agronomica Sinica, 2021, 47(5): 964-973.
[13] WANG Heng-Bo, CHEN Shu-Qi, GUO Jin-Long, QUE You-Xiong. Molecular detection of G1 marker for orange rust resistance and analysis of candidate resistance WAK gene in sugarcane [J]. Acta Agronomica Sinica, 2021, 47(4): 577-586.
[14] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[15] XU Nai-Yin, ZHAO Su-Qin, ZHANG Fang, FU Xiao-Qiong, YANG Xiao-Ni, QIAO Yin-Tao, SUN Shi-Xian. Retrospective evaluation of cotton varieties nationally registered for the Northwest Inland cotton growing regions based on GYT biplot analysis [J]. Acta Agronomica Sinica, 2021, 47(4): 660-671.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No. 80 Xueyuan South Rd, Beijing 100081, P. R. China E-mail: zwxb301@caas.cn
Supported by Beijing Magtech Co.Ltd