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

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

doi:10.1186/s12864-016-2552-2

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2552-2) contains supplementary material, which is available to authorized users.

Highlights

Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production
It is important to study the mechanism of leaf abscission in sugarcane and breed sugarcane varieties which can shed their leaves during the maturity time
Differential expression analysis revealed 1,202 transcripts upregulated in leaf abscission sugarcane plants (LASP) which can shed their leaves during the maturity time, compared to the leaf packaging sugarcane plants (LPSP) which are packed by the leaves during the maturity time

Summary

Introduction

Sugarcane (Saccharum officinarum L.) is an important sugar crop which belongs to the grass family and can be used for fuel ethanol production. Sugarcane (Saccharum officinarum L.) is an important sugar crop, which is widely grown in the tropical and subtropical areas [1]. Abscission is the programmed developmental process by which some of the organs such as leaves, flowers, or fruits are shed during the life of a plant [4]. It occurs within a specific tissue, called abscission zone (AZ), which is formed at the base of the petiole [5]. It is interesting that different plant species and different organs share a majority of genes involved in steps 2 and 3, including genes involved in ethylene and auxin biosynthesis and signal transduction, cell wall modification and various stress responses [12]

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Results

Conclusion