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

BMC Genomics

Research Article

Guanyu Wang¹  Yuan Zeng¹  Ming Li²  Shanshan He²  Lunwang Wang²  Zhaoxu Liang²  Fang Tan²  Song Li²  Kaichao Wu²  Zhanghong Mo²  Jun Liang²  Yan Jing² 

[1] Guangxi Academy of Agricultural Sciences, 530007, Nanning, P.R. China;Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, 530007, Nanning, P.R. China;

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

DOI  :  10.1186/s12864-016-2552-2

 received in 2015-10-26, accepted in 2016-02-28,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSugarcane (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.ResultsTo 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.ConclusionOur 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.

【 授权许可】

CC BY   
© Li et al. 2016