Abstract Background Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Results To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. Conclusions We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users. Keywords: Sugarcane-NGS-smallRNA-leaf absicission associated miRNA Background Abscission is the programmed developmental process that some of the organs such as leaves, flowers, or fruits are shed during the life of a plant [[49]1], which can be divided into four major steps: (i) development of the abscission zone (AZ) tissue, (ii) acquisition of competence to respond to abscission-promoting signaling, (iii) activation of abscission and (iv) post abscission trans-differentiation [[50]2]. Global gene expression studies have shown many genes in multiple pathways participate in the abscission process [[51]3, [52]4], including various transcription factors (TFs), cell wall hydrolysis enzymes, defense-related genes and genes involved in auxin/ethylene signal transduction [[53]5–[54]7]. However, the regulation mechanism of gene expression is not clear at present. MicroRNAs (miRNAs) are endogenous small (21–24 nt) and single stranded noncoding RNAs which are important regulators of gene expression through mRNA degradation, translational repression and chromatin modification [[55]8–[56]10]. They are incorporated in the RNA-induced silencing complex (RISC) with AGO protein and guide the cleavage or translational repression of the target mRNAs by complementary or uncomplimentary base pairing [[57]11]. In plants, miRNAs are involved in multiple crucial biological processes including organ development and plant responses to environmental stresses [[58]12–[59]16]. Notably, several miRNAs have been reported to be involved in the abscission process. miR159 targeting MYB transcription factors, miR160/miR167 targeting auxin response factors (ARFs), miR172 targeting AP2-like ethylene-responsive transcription factors, and miR396 targeting glutamate decarboxylase have been found with different expression in tomato during pedicel abscission [[60]17]. In fruit senescence of Fragaria ananassa, NAC TFs, ARFs and MYB TFs have been validated as targets of miR164, miR160, miR167 and miR159, respectively, by small RNA sequencing and degradome sequencing [[61]18]. Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel [[62]19]. Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Recently, we have reported leaf abscission associated genes in sugarcane using transcriptome sequencing [[63]20]. To study miRNA expression changes between leaf abscission sugarcane plants (LASP) and leaf packaging sugarcane plants (LPSP), we constructed six small RNA libraries and sequenced them using an Illumina HiSeq 2500 system. In total, we characterized 93 conserved miRNAs and 454 sugarcane novel miRNAs using the transcriptome sequences as reference and identified 38 differentially expressed miRNAs in LASP compared to LPSP. Target prediction showed several miRNA-mRNA modules might be involved in sugarcane leaf abscission, such as miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3. KEGG pathway analysis for the target genes showed similar results as our transcriptome study and indicated “plant-pathogen interaction” and “plant hormone signal transduction” might be related with sugarcane leaf abscission during the maturity time. We obtained highly conserved sugarcane pre-miRNAs and mature miRNAs, which are valuable resources for future sugarcane miRNA studies. Moreover, our findings will provide better understanding of the complex mechanism of leaf abscission, miRNAs and their targets involved in leaf abscission. Results Small RNA identification in sugarcane Previously, we reported leaf abscission associated genes in sugarcane using transcriptome sequencing [[64]20]. To study the post-transcriptional regulation of sugarcane leaf abscission, six small RNA (sRNA) libraries constructed for three leaf abscission sugarcane plants (Q1, T1, T2) and three leaf packaging sugarcane plants (Q2, B1, B2) were sequenced by using an Illumina HiSeq 2500 system. Initially, a total of 71,579,415 raw reads were generated (Table [65]1). After low quality reads and sequencing adapters were removed, we obtained 70,082,453 clean reads longer than 18 nt for all samples with an average of 11.68 M clean reads. Length distribution of clean reads (Fig. [66]1a) showed the most abundant classes of sRNA were 21 and 24 nt, which is consistent with many plant miRNA deep sequencing studies [[67]21–[68]23]. To annotate sRNAs in each library, we mapped the clean reads to Rfam database and found 5.10–10.93% of the clean reads were derived from rRNA, tRNA, snRNA and snoRNA (Table [69]1). Next, all clean reads were aligned to recently published sugarcane transcriptome [[70]20] for global miRNA characterization. Mapped reads were used to predict sugarcane miRNAs (pre-miRNAs and mature miRNAs) by MIREAP [[71]24] and a total of 93 conserved miRNAs (including mature and passenger miRNAs) from 25 families and 454 sugarcane novel miRNAs were identified (Additional file [72]1: Supplementary Dataset). These miRNAs were used as references for sRNA mapping, miRNA expression