title: De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.).
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. mingli9606@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. 33350797@qq.com.
authors.forename: Zhaoxu
authors.initials: Z
authors.lastname: Liang
authors.affiliation: Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. 50506252@qq.com.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. gxjingyan@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Jing
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. kaichaowu@126.com.
authors.forename: Kaichao
authors.initials: K
authors.lastname: Wu
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. jliang@biotgr.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Liang
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. Shanbh613@126.com.
authors.forename: Shanshan
authors.initials: S
authors.lastname: He
authors.affiliation: Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. 2593998841@qq.com.
authors.forename: Guanyu
authors.initials: G
authors.lastname: Wang
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. mozhanghong@126.com.
authors.forename: Zhanghong
authors.initials: Z
authors.lastname: Mo
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. tanfang64@163.com.
authors.forename: Fang
authors.initials: F
authors.lastname: Tan
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. ls19009@163.com.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, P.R. China. wlunwang@163.com.
authors.forename: Lunwang
authors.initials: L
authors.lastname: Wang
mesh_terms: D000040:Abscisic Acid / Q000502:physiology; D030562:Databases, Protein; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D018515:Plant Leaves / Q000502:physiology*; D020641:Polymorphism, Single Nucleotide; D018749:RNA, Plant / Q000235:genetics; D031786:Saccharum / Q000235:genetics* / Q000502:physiology; D059467:Transcriptome
chemical_list: D018749:RNA, Plant; D000040:Abscisic Acid