De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.)

文献类型： 外文期刊

第一作者： Liang, Zhaoxu

作者： Liang, Zhaoxu;Jing, Yan;Wu, Kaichao;Liang, Jun;He, Shanshan;Mo, Zhanghong;Tan, Fang;Li, Song;Wang, Lunwang;Zeng, Yuan;Wang, Guanyu

作者机构：

关键词： Leaf abscission;Leaf shedding;Sugarcane;Plant-pathogen interaction;Abscisic acid;ABA;Saccharum officinarum;Transcriptome

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. The growing demands for sugar and biofuel is asking for breeding a sugarcane variety that can shed their leaves during the maturity time due to the increasing cost on sugarcane harvest. Results: To determine leaf abscission related genes in sugarcane, we generated 524,328,950 paired reads with RNA-Seq and profiled the transcriptome of new born leaves of leaf abscission sugarcane varieties (Q1 and T) and leaf packaging sugarcane varieties (Q2 and B). Initially, 275,018 transcripts were assembled with N50 of 1,177 bp. Next, the transcriptome was annotated by mapping them to NR, UniProtKB/Swiss-Prot, Gene Ontology and KEGG pathway databases. Further, we used TransDecoder and Trinotate to obtain the likely proteins and annotate them in terms of known proteins, protein domains, signal peptides, transmembrane regions and rRNA transcripts. Different expression analysis showed 1,202 transcripts were up regulated in leaf abscission sugarcane varieties, relatively to the leaf packaging sugarcane varieties. Functional analysis told us 62, 38 and 10 upregulated transcripts were involved in plant-pathogen interaction, response to stress and abscisic acid associated pathways, respectively. The upregulation of transcripts encoding 4 disease resistance proteins (RPM1, RPP13, RGA2, and RGA4), 6 ABC transporter G family members and 16 transcription factors including WRK33 and heat stress transcription factors indicate they may be used as candidate genes for sugarcane breeding. The expression levels of transcripts were validated by qRT-PCR. In addition, we characterized 3,722 SNPs between leaf abscission and leaf packaging sugarcane plants. Conclusion: Our results showed leaf abscission associated genes in sugarcane during the maturity period. The output of this study provides a valuable resource for future genetic and genomic studies in sugarcane.

分类号：

  • 相关文献

[1]RNA-seq analysis provides insight into reprogramming of culm development in Zizania latifolia induced by Ustilago esculenta. Wang, Zhi-Dan,Wang, Zheng-Hong,Zhang, Xiao-Huan,Xue, Hui-Min,Wang, Li-Xia,Zhan, Qi,Xu, Ying-Ping,Guo, De-Ping,Yan, Ning,Zhang, Jing-Ze. 2017

[2]Transcription Profiling Analysis of Mango-Fusarium Mangiferae Interaction. Liu, Feng,Wu, Jing-bo,Zhan, Ru-lin,Ou, Xiong-chang. 2016

[3]NPR1-dependent salicylic acid signaling is not involved in elevated CO2-induced heat stress tolerance in Arabidopsis thaliana. Li, Xin,Ahammed, Golam Jalal,Li, Xin,Yu, Jingquan,Shi, Kai. 2015

[4]Effects of Exogenous Abscisic Acid on Cell Membrane and Endogenous Hormone Contents in Leaves of Sugarcane Seedlings under Cold Stress. Yang, Li-Tao,Li, Yang-Rui,Wu, Jian-Ming,Huang, Xing,Chen, Ming-Hui,Yang, Li-Tao. 2015

[5]Complex molecular mechanisms underlying seedling salt tolerance in rice revealed by comparative transcriptome and metabolomic profiling. Wang, Wen-Sheng,Zhao, Xiu-Qin,Li, Min,Huang, Li-Yu,Xu, Jian-Long,Zhang, Fan,Cui, Yan-Ru,Fu, Bin-Ying,Li, Zhi-Kang,Li, Min,Xu, Jian-Long,Fu, Bin-Ying,Li, Zhi-Kang.

[6]Transcriptome of High-Sucrose Sugarcane Variety GT35. Gao, Yi-Jing,Gui, Yi-Yun,Chen, Zhong-Liang,Qin, Cui-Xian,Wang, Miao,Li, Yang-Rui,Liao, Qing,Li, Yang-Rui,Yang, Li-Tao. 2016

[7]Verification of the introgression of Erianthus arundinaceus germplasm into sugarcane using molecular markers. Cai, Q,Aitken, K,Deng, HH,Chen, XW,Fu, C,Jackson, PA,McIntyre, CL. 2005

[8]Evaluation of sugarcane introgression lines for resistance to brown rust disease caused by Puccinia melanocephala. Wang, Xiao-Yan,Li, Wen-Feng,Huang, Ying-Kun,Lu, Xin,Luo, Zhi-Ming,Yin, Jiong,Shan, Hong-Li,Zhang, Rong-Yue. 2013

[9]Expression of the Grifola frondosa Trehalose Synthase Gene and Improvement of Drought-Tolerance in Sugarcane (Saccharum officinarum L.). Zhang, SZ,Yang, BP,Feng, CL,Chen, RK,Luo, JP,Cai, WW,Liu, FH.

[10]Immunohistochemical analysis of cell wall hydroxyproline-rich glycoproteins in the roots of resistant and susceptible wax gourd cultivars in response to Fusarium oxysporum f. sp Benincasae infection and fusaric acid treatment. Ma, Li,Xu, Chunxiang,Xie, Dasen,Samaj, Jozef. 2011

[11]Origin of hydrogen peroxide during the cowpea- Xanthomonas interaction. Zhu, Yan,Li, Yanhong,Hu, Ronghui,Zheng, Yani,Feng, Na,Li, Hongyu,Chen, Fu,Wang, Jing. 2012

[12]Invasive properties of Ralstonia solanacearum virulent and avirulent strains in tomato roots. Zheng, Xuefang,Zhu, Yujing,Liu, Bo,Lin, Naiquan,Zheng, Desen. 2017

[13]Gene expression changes in leaves of Citrus sinensis (L.) Osbeck infected by Citrus tristeza virus. Cheng, Chunzhen,Cheng, Chunzhen,Zhang, Yongyan,Zhong, Yun,Yang, Jiawei,Yan, Shutang.

[14]Complex genetic networks underlying the defensive system of rice (Oryza sativa L.) to Xanthomonas oryzae pv. oryzae. Li, ZK,Arif, M,Zhong, DB,Fu, BY,Xu, JL,Domingo-Rey, J,Ali, J,Vijayakumar, CHM,Yu, SB,Khush, GS.

[15]A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies. Liu, Xiaohui,Lu, Tingting,Yu, Shuliang,Li, Ying,Huang, Yuchen,Huang, Tao,Zhang, Lei,Zhu, Jingjie,Zhao, Qiang,Fan, Danlin,Mu, Jie,Shangguan, Yingying,Feng, Qi,Guan, Jianping,Ying, Kai,Zhang, Yu,Lin, Zhixin,Sun, Zongxiu,Qian, Qian,Lu, Yuping,Han, Bin.

[16]ZmFKBP20-1 improves the drought and salt tolerance of transformed Arabidopsis. Yu, Yanli,Li, Yanjiao,Zhao, Meng,Li, Wencai,Sun, Qi,Li, Wenlan,Meng, Zhaodong,Jia, Fengjuan,Jia, Fengjuan,Li, Nana. 2017

[17]Exogenous nitric oxide delays salt-induced leaf senescence in cotton (Gossypium hirsutum L.). Kong, Xiangqiang,Wang, Tao,Li, Weijiang,Tang, Wei,Zhang, Dongmei,Dong, Hezhong,Wang, Tao,Dong, Hezhong.

[18]H2O2 and ABA signaling are responsible for the increased Na+ efflux and water uptake in Gossypium hirsutum L. roots in the non-saline side under non-uniform root zone salinity. Kong, Xiangqiang,Luo, Zhen,Dong, Hezhong,Eneji, A. Egrinya,Li, Weijiang.

[19]Transcriptional Regulation of Genes Encoding Key Enzymes of Abscisic Acid Metabolism During Melon (Cucumis melo L.) Fruit Development and Ripening. Sun, Yufei,Chen, Pei,Duan, Chaorui,Wang, Yanping,Ji, Kai,Hu, Yin,Li, Qian,Dai, Shengjie,Wu, Yan,Luo, Hao,Sun, Liang,Leng, Ping,Tao, Pang. 2013

[20]Effects of exogenous ABA and cytokinin on leaf photosynthesis and grain protein accumulation in wheat ears cultured in vitro. Xie, ZJ,Jiang, D,Dai, TB,Jing, Q,Cao, WX. 2004

作者其他论文 更多>>

微信小程序