Understanding the role of miRNAs in governing the drought sensitive response of a rice mega variety, Swarna at reproductive stage

To combat drought stress, the major abiotic stress in rice, major genomic regions governing stress tolerance under field conditions have been identified and exploited, though their molecular basis remains elusive till date. We have recently reported the miRNAs/mRNA modules important for drought stress response in these genomic regions. To further understand this secondary regulation by miRNA/mRNA modules in a mega variety, Swarna, which is sensitive to drought stress at reproductive stage, we generated sRNA-seq data. Our analysis identified 9 putative novel miRNAs and 27 differentially expressed known miRNAs at booting stage under drought stress. The major miRNA/transcript modules, identified through degradome analysis and transcript abundance studies, that had an impact on drought stress response of plant and yield included osa-miR169a/LOC_Os07g41720, Osa-miR171b/f, Osa-miR172d-3p/5p, Osa-miR1876/ LOC_Os11g38330, Osa-miR397a and Osa-miR530–3p. The results indicated a basis for the low spikelet fertility and high grain chalkiness of the mega variety Swarna under drought stress through the modulation of expression of Osa-miR397a/ LOC_Os03g03510 and LOC_Os03g51220 and Osa-miR530–3p/ LOC_Os10g40510 modules. This study provides the potential target genes for improving Swarna, a globally important variety, so as to ensure food security under climate change scenario.