Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

Abstract

Background: Phosphorus (P) plays important roles in plant growth and development. MicroRNAs involved in P signaling have been identified in Arabidopsis and rice, but P-responsive microRNAs and their targets in soybean leaves and roots are poorly understood. Results: Using high-throughput sequencing-by-synthesis (SBS) technology, we sequenced four small RNA libraries from leaves and roots grown under phosphate (Pi)-sufficient (+Pi) and Pi-depleted (-Pi) conditions, respectively, and one RNA degradome library from Pi-depleted roots at the genome-wide level. Each library generated ∼ 21.45 − 28.63 million short sequences, resulting in ∼ 20.56 − 27.08 million clean reads. From those sequences, a total of 126 miRNAs, with 154 gene targets were computationally predicted. This included 92 new miRNA candidates with 20-23 nucleotides that were perfectly matched to the Glycine max genome 1.0, 70 of which belong to 21 miRNA families and the remaining 22 miRNA unassigned into any existing miRNA family in miRBase 18.0. Under both +Pi and -Pi conditions, 112 of 126 total miRNAs (89%) were expressed in both leaves and roots. Under +Pi conditions, 12 leaf-and 2 root-specific miRNAs were detected; while under -Pi conditions, 10 leaf-and 4 root-specific miRNAs were identified. Collectively, 25 miRNAs were induced and 11 miRNAs were repressed by Pi starvation in soybean. Then, stem-loop real-time PCR confirmed expression of four selected P-responsive miRNAs, and RLM-5' RACE confirmed that a PHO2 and GmPT5, a kelch-domain containing protein, and a Myb transcription factor, respectively are targets of miR399, miR2111, and miR159e-3p. Finally, P-responsive cis-elements in the promoter regions of soybean miRNA genes were analyzed at the genome-wide scale. Conclusions: Leaf-and root-specific miRNAs, and P-responsive miRNAs in soybean were identified genome-wide. A total of 154 target genes of miRNAs were predicted via degradome sequencing and computational analyses. The targets of miR399, miR2111, and miR159e-3p were confirmed. Taken together, our study implies the important roles of miRNAs in P signaling and provides clues for deciphering the functions for microRNA/target modules in soybean.

A Wheat CCAAT Box-Binding Transcription Factor Increases the Grain Yield of Wheat with Less Fertilizer Input

“…In plants, a subset of miR169 members are repressed by N and P starvation (Pant et al, 2009;Liang et al, 2012;Xu et al, 2013), and several miR169 NFYA targets are induced in such conditions (Pant et al, 2009;Zhao et al, 2011). We observed similar results in this study in wheat: low-N and low-P treatments decreased tae-miR169 abundance ( Fig.…”

“…Different members of this microRNA family show distinct response patterns to N or P starvation (Pant et al, 2009;Liang et al, 2012;Xu et al, 2013). As such, miR169 and its targets may be valuable resources for engineering plants with altered N and/or P use efficiencies.…”

“…The microRNA169 (miR169) family is known to be regulated by both N and P starvation (Pant et al, 2009;Lundmark et al, 2010;Xu et al, 2011Xu et al, , 2013Zhao et al, 2011;Liang et al, 2012). Different members of this microRNA family show distinct response patterns to N or P starvation (Pant et al, 2009;Liang et al, 2012;Xu et al, 2013).…”

Dynamic roles of microRNAs in nutrient acquisition and plant adaptation under nutrient stress: A review

“…In Arabidopsis, members of miR399 genes contain PHR1-binding sites PIBS (GNATATNC); a motif that is required for binding to most of P-responsive genes and is critical for their transcriptional regulatory functions (Bari et al, 2006). Interestingly, other P-related cis elements such as PHR1, PHO-like, W-box, TATA-box and P-responsive elements were also found in the upstream promoter sites of P-responsive miRNAs including miR399 Xu et al, 2013). Under P deficiency, Arabidopsis phr1 mutants showed significantly reduced expressions of miR399 as well as group of other P related genes, while set of P deficiency-responsive genes were found upregulated in pho2 mutants under sufficient P availability, hence, concluded that PHR1 functions upstream of miR399 and PHO2, however, it is not the only element required for miR399 induction in P signaling network (Bari et al, 2006).…”

Insights into the Small RNA-Mediated Networks in Response to Abiotic Stress in Plants

“…All miR399 genes present in Arabidopsis harbor PHR1-binding site P1BS in their promoters (Bari et al 2006 ). Also several other P-responsive cis -regulatory elements were identifi ed in the promoters of these phosphate-responsive miRNAs including PHO, PHO-like, W-box, NIT2, and MYB-binding sites (Zeng et al 2010 ;Xu et al 2013 ;Baek et al 2013 ). Further fi ndings also indicated that miR399-mediated regulation of PHO2 is under the control of target mimicry.…”