Deep sequencing identified potential mi RNA s involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of mi RNA s in plant biotic stress responses. In the current study, mi RNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential mi RNA s representing 42 families, including monocot/tissue‐specific and 14 novel mi RNA s in both genotypes. Significant differences in mi RNA family abundance between the libraries were observed in read frequencies. A total of 19 mi RNA s (from known mi RNA s) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known mi RNA families in wild and 1025 potential targets for 42 known mi RNA families in cultivar genotypes. The differential expression analysis revealed that most mi RNA s identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified mi RNA s from the mi RNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT ‐ PCR confirmed mi RNA s were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm mi RNA – mRNA target pairing using RNA ligase‐mediated 5′ Rapid Amplification of cDNA Ends (5′ RLM ‐ RACE ) PCR.