Comparative Analysis on Transcriptome Among Different Sugarcane Cultivars Under Low Temperature Stress

doi:10.13560/j.cnki.biotech.bull.1985.2018-0522

Abstract

Abstract: In order to comparatively analyze the variations of molecular mechanism among different cultivars in cold resistance,RNA-seqs of GT08-1180 and ROC22 were conducted under cold stress and normal temperature. The results showed that a total of 57.41 G clean reads were produced and 183515 unigenes were obtained after de novo assembly. All unigenes were annotated in NR,NT,Swiss-Prot,PFAM,KOG/COG,KEGG,and GO,and 110 021 unigenes were functionally annotated. There were 16 145 and 20 317 differentially expressed genes（DEGs）in GT08-1180 and ROC22 respectively in the cold stress. In addition,there were more up-regulated DEGs than down-regulated DEGs in both GT08-1180 and ROC22. Total 13 113 DEGs were found to be the same in both GT08-1180 and ROC22,while 7 204 specific DEGs in ROC22,and 3 032 specific DEGs in GT08-1180. The result of GO enrichment analysis of the common DEGs in 2 varieties showed that common DEGs were enriched in sub-groups of cold stress response,membrane system,and photosynthesis. GT08-1180 enriched more in DEGs related to DNA integration,RNA polymerase,ADP binding,and metabolic enzymes. ROC22 presented more enrichment in DEGs related to synthesis and transfer of organic substances,and transporter proteases.

Key words: sugarcane, cold stress, transcriptome

TANG Shi-yun, YANG Li-tao, LI Yang-rui. Comparative Analysis on Transcriptome Among Different Sugarcane Cultivars Under Low Temperature Stress[J]. Biotechnology Bulletin, 2018, 34(12): 116-124.

References

[1] 位明明, 李维国, 高新生, 等. 中国热带作物抗寒育种研究进展与展望[J]. 热带作物学报, 2015, 36(4):821-828.
[2] 杨荣仲, 周会, 王伦旺, 等. 甘蔗家系农艺性状遗传力分析[J]. 南方农业学报, 2016, 47(3):337-342.
[3] 徐超华, 李纯佳, 苏火生, 等. 甘蔗非生物胁迫抗性研究进展[J]. 植物遗传资源学报, 2017, 18(3):483-493.
[4] Coasta V, Angelini C, Defeis I, et al.Uncovering the complexity of transcriptomes with RNA-Seq[J]. J Biomed Biotechnol, 2010:853916.
[5] 祁云霞, 刘永斌, 荣威恒. 转录组研究新技术及其应用[J]. 遗传, 2011, 33(11):1191-1202.
[6] Wang Z, Gerstein M, Snyder M.RNA-Seq:a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1):57-63.
[7] 王跃, 毛开云, 王恒哲, 等. 转录组学测序技术应用与市场分析[J]. 生物产业技术, 2017, 5(9):11-17.
[8] 刘红亮, 郑丽明, 刘青青, 等. 非模式生物转录组研究[J]. 遗传, 2013, 35(8):955-970.
[9] 唐仕云, 杨丽涛, 李杨瑞. 低温胁迫下不同甘蔗品种(系)光合特性的变化及其与耐寒性的关系[J]. 广西植物, 2012, 32(5):679-685.
[10] 李洋, 曲彦婷, 周爱民, 等. 针叶福禄考(Phlox subulata)抗寒基因的克隆及分析[J]. 基因组学与应用生物学, 2015, 34(9):1917-1927.
[11] 刘洪博, 刘新龙, 等. 干旱胁迫下割手密根系转录组差异表达分析[J]. 中国农业科学, 2017, 50(6):1167-1178.
[12] 李穆, 程志远, 何丽莲, 等. 甘蔗印度种响应干旱胁迫的数字基因表达谱[J]. 分子植物育种, 2018, 16(7):2099-2106.
[13] 苏亚春. 甘蔗应答黑穗病菌侵染的转录组与蛋白组研究及抗性相关基因挖掘[D]. 福州:福建农林大学, 2014.
[14] 丘立航, 罗含敏, 陈荣发, 等. 基于RNA-Seq的甘蔗主茎和分蘖茎转录组建立及初步分析[J]. 基因组学与应用生物学, 2018, 37(3):1271-1279.
[15] 姚晓华. 植物抗寒相关功能与调控基因研究进展. 中国农学通报[J]. 2013, 29(27):141-147.
[16] Palta JP, Whitaker BD, Weiss IS.Plasma membrane lipids associated with genetic variability in freezing tolerance and cold acclimation of Solanum species[J]. Plant Physiology, 1993, 103(3):793-803.
[17] Orvar BL, Sangwan V, Omann F, et al.Early stepsin cold sensing by plant cells:the role of actin cytoskeleton and membrane fluidity[J]. Plant J, 2000, 23(6):785-794.
[18] Sudesh KY.Cold stress tolerance mechanisms in plants. A review[J]. Agronomy for Sustainable Development, 2010, 30(3):515-527
[19] Yukio K, Matsuo U.Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associa-ted with cold acclimation[J]. Plant J, 2003, 36:141-154.
[20] 王庆杰, 王立. 植物抗寒性基因研究综述[J]. 农村经济与科技, 2018, 29(8):23-25.
[21] Li SL, Li ZG, Yang LT, et al.Differential effects of cold stress on chloroplasts structures and photosynthetic characteristics in cold-sensitive and cold tolerant cultivars of sugarcane[J]. Sugar Tech, 2018, 20(1):11-20.
[22] 刘贝贝, 陈利娜, 等. 果树响应低温胁迫的分子机制及抗寒性鉴定方法研究进展[J]. 北方园艺, 2017(15):174-179.
[23] Fu JJ, Geng JC, Miao YJ, et al.Transcriptomic analyses reveal genotype- and organ-specific molecular responses to cold stress in Elymus nutans[J]. Biologia Plantarum, 2018, (6):1-14.
[24] Eremina M, Rozhon W, Poppenberger B.Hormonal control of cold stress responses in plants[J]. Cellular and Molecular Life Sciences, 2016, 73:797-810.