The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea ). Arachis hypogaea cultivar:C76-16

MicroRNAs (miRNAs) are 21-24 nt small RNAs (sRNAs) that negatively regulate protein coding genes and/or trigger phased small-interfering RNA (phasiRNA) production. 2,900 miRNA families, of which ~40 are deeply conserved, have been identified in ~80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant-like MIRNA loci were predicted in the diploid peanut progenitor A. duranensis genome. We explored by computational analysis of a leaf, peanut pod sRNA library and publicly available sRNA, degradome-, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several non-canonical targets and novel phasiRNA-producing non-coding and mRNA loci with validated siRNA novel targets such as penta-tricopeptide repeats (PPRs). We characterized the inverse correlations of significantly differentially expressed drought- and heat-regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta-analysis of an expression atlas and over representation of miRNA target genes in co-expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome-wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value-added traits