Control of sucrose accumulation in sugarcane (Saccharum spp. hybrids) involves miRNA-mediated regulation of genes and transcription factors associated with sugar metabolism

Sugarcane is an established industrial crop providing sugar, ethanol and biomass-derived electricity worldwide. Cane sugar content is an important breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at the crop level, mainly due to the limited understanding of its regulation. miRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remain unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two early-maturing sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. The stem sucrose content in both genotypes increased steadily with time during sucrose accumulation stage. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed. A combined transcriptome and miRNA data analysis revealed differentially expressed miRNA-target mRNA pairs related to sugar metabolism, of which 46 targets were transcription factors (TFs). miR172, miR164, miR396 and miR169 appear to regulate AP2/ERF, NAC, GRF and bZIP TF members associated with sugar metabolism. This is the first report of sugarcane miRNAs associated with sugar accumulation.