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

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Not AvailableDeeper Rooting 1 (DRO1) gene identified from a major QTL on chromosome 9 increases the root growth angle (RGA) and thus facilitates survival under drought and hence is an excellent candidate for rice improvement. Twenty-four major Indian upland and lowland genotypes including the ‘yield under drought’ (DTY) QTL donors were subjected to allele mining of DRO1 (3058 bp) using four pairs of overlapping primers. A total of 216 and 52 SNPs were identified across all genotypes in the gene and coding region (756 bp) respectively with transversions 3.6 fold more common than transitions in the gene and 2.5 times in the CDS. In 251 amino acid long protein, substitutions were found in 19 positions, wherein change in position 92 was the most frequent. Based on allele mining, the 24 genotypes can be classified into 16 primary structure variants ranging from complete functional allele (Satti, IR36 and DTY 3.1 donor, IR81896-B-B-195) to truncated non-functional alleles in PMK2, IR64, IR20 and Swarna. All the DTY donors, other than IR81896-B-B-195, and most of the upland drought tolerant cultivars (Nagina 22, Vandana and Dhagaddeshi) had accumulated 6–19 SNPs and 4–8 amino acid substitutions resulting in substantial differences in their protein structure. The expression analysis revealed that all the genotypes showed upregulation under drought stress though the degree of upregulation varied among genotypes. The information on structural variations in DRO1 gene will be very useful for the breeders, especially in the light of recent breeding programmes on improving drought tolerance using several DTY donors and upland accessions