Genome-Wide Small RNA Analysis of Soybean Reveals Auxin-Responsive microRNAs that are Differentially Expressed in Response to Salt Stress in Root Apex

Abstract

Root growth and the architecture of the root system in Arabidopsis are largely determined by root meristematic activity. Legume roots show strong developmental plasticity in response to both abiotic and biotic stimuli, including symbiotic rhizobia. However, a global analysis of gene regulation in the root meristem of soybean plants is lacking. In this study, we performed a global analysis of the small RNA transcriptome of root tips from soybean seedlings grown under normal and salt stress conditions. In total, 71 miRNA candidates, including known and novel variants of 59 miRNA families, were identified. We found 66 salt-responsive miRNAs in the soybean root meristem; among them, 22 are novel miRNAs. Interestingly, we found auxin-responsive cis-elements in the promoters of many salt-responsive miRNAs, implying that these miRNAs may be regulated by auxin and auxin signaling plays a key role in regulating the plasticity of the miRNAome and root development in soybean. A functional analysis of miR399, a salt-responsive miRNA in the root meristem, indicates the crucial role of this miRNA in modulating soybean root developmental plasticity. Our data provide novel insight into the miRNAome-mediated regulatory mechanism in soybean root growth under salt stress.

Legume genetic resources and transcriptome dynamics under abiotic stress conditions

“…Recently, genome‐wide miRNA analysis of soybean root tips under salt stress has identified 71 miRNA candidates (Sun et al, ), of which 66 candidates were salt‐responsive miRNA s and many of these salt‐responsive miRNAs contain auxin‐responsive cis ‐elements in their promoter regions. This implies that auxin signalling could play a crucial role in the regulation of root development in soybean plants under salt stress (Sun et al, ). Likewise, Khandal, Parween, Roy, Meena, and Chattopadhyay () investigated the miRNA expression profile in the chickpea root apex under drought and salinity.…”

Comparative Transcriptome Analysis Reveals Molecular Defensive Mechanism of Arachis hypogaea in Response to Salt Stress

“…Transcriptome data are valuable resources for exploring plants under stress conditions. To our knowledge, there have been an increasing number of studies on transcriptome analysis of legume species using high-throughput RNA sequencing approach, among those regarding the effects of salinity stress were reported on Medicago [40][41][42], glycine [43][44][45], and common bean [46][47][48]. Studies focusing on transcriptome research of the peanut under salt stress are rare, but there exists a substantial amount of reports regarding the physiological responses to salt stress in peanut based on a de novo transcriptomic sequence assembly method [49][50][51].…”

Mapping the Salt Stress-Induced Changes in the Root miRNome in Pokkali Rice

“…Individual members of miR393 and miR394 families were also up regulated in PKNR. These miRs are associated with various aspects of root development, like osa-miR160a, which regulates root tip growth, lateral root production, and gravity sensing by targeting ARF10 and ARF16 transcripts [28,41]. There are also reports on the role of auxins through ARFs in the salt stress-stimulated development of lateral root primordia [20,56,57].…”

“…There is also a role of the osa-miR399-regulated phosphate transporter in this pathway. Earlier reports on functional analyses of salt-responsive miR399 in the soybean root meristem indicated its crucial role in modulating root developmental plasticity [41]. DFR is an NADPH-dependent enzyme involved in the anthocyanin biosynthesis pathway.…”

“…The analysis showed that 43 miRs belonging to 27 families were specifically expressed in the root tissues. Many of these miRs have been reported to play an important role in root development [22][23][24]28,31] and salt stress [21,26,[39][40][41][42][43]. Within this set, 19 miRs were abundant in PK roots and among these, seven miRs viz.…”