Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes

Summary Drought stress has adverse impacts on plant production and productivity. Micro RNA s (mi RNA s) are one class of noncoding RNA s regulating gene expression post‐transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue‐specific mi RNA s responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought‐responsive tomato genotypes ( Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved mi RNA s belonging to 578 families were determined and 688 mi RNA s were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 mi RNA families. Drought‐related mi RNA s and their targets were enriched functionally by Gene Ontology ( GO ) and Kyoto Encyclopedia of Genes and Genomes ( KEGG ) pathway analyses. Totally, 53 mi RNA s targeted 23 key drought stress‐ and tissue development‐related genes, including DRP (dehydration‐responsive protein), GT s (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II ) protein, HD ‐ ZIP (homeodomain‐leucine zipper), MYB and NAC ‐domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key mi RNA s functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of mi RNA s in drought response with plant hormone signal transduction and drought‐tolerant tomato breeding.