ORIGINAL ARTICLE Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress Shikha Goel 1,2 & Kavita Goswami 2 & Vimal K. Pandey 2 & Maneesha Pandey 1 & Neeti Sanan-Mishra 2 Received: 22 June 2018 /Revised: 18 March 2019 /Accepted: 21 March 2019 # Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next- generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice. Keywords Rice . microRNA . High temperature stress . Salt stress . Time kinetics Abbreviations PB-1 Pusa Basmati-1 NGS Next Generation Sequencing miR microRNA miR* miR star sequence nt nucleotides HTS High Temperature Stress SS Salt Stress UTR Untranslated Region sRNA small RNA N-L-PB 15-day-old PB-1 seedling leaves grown under normal conditions N-R-PB 15-day-old PB-1 seedling roots grown under normal conditions N-FL-PB Flag Leaf from PB-1 plants grown under normal conditions HT-L-PB 15-day-old PB-1 seedling leaves grown under HTS conditions HT-R-PB 15-day-old PB-1 seedling roots grown under HTS conditions HT-FL-PB Flag Leaf from PB-1 plants grown under HTS conditions NL-Salt 15-day-old PB-1 seedling leaves grown under SS conditions NR-Salt 15-day-old PB-1 seedling roots grown under SS conditions GO Gene Ontology SPL2 Squamosa Promoter binding protein Like 2 TOE1 Target Of EAT1 GRF6 Growth-Regulating Factor 6 MFEI Minimal Folding free Energy Index DE Differentially Expressed TPM Transcript Per Million AGO Argonaute Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10142-019-00673-4) contains supplementary material, which is available to authorized users. * Neeti Sanan-Mishra neeti@icgeb.res.in 1 Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi 110068, India 2 Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India Functional & Integrative Genomics https://doi.org/10.1007/s10142-019-00673-4