Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.)

Abstract

Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. In the present study, systematic identification and functional analysis of miRNAs under chilling stress were carried out to clarify the molecular mechanism of chilling resistance. Two independent small RNA libraries from leaves of soybean were constructed and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and 3 novel miRNAs were identified. Thirty-five miRNAs were verified by qRT-PCR analysis. Furthermore, their gene targets were identified via high-throughput degradome sequencing. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 51 miRNAs differentially expressed between chilling stress and control conditions. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. Our qRT-PCR analysis confirmed a negative relationship among the miRNAs and their targets under chilling stress. Our work thus provides comprehensive molecular evidence supporting the involvement of miRNAs in chilling-stress responses in vegetable soybean.

High throughput deep sequencing reveals the important roles of microRNAs during sweetpotato storage at chilling temperature

“…Similar to previous studies in sweetpotato 14 , 15 and other plant species 9 – 11 , miRNAs were predicted to cleave more than two targets. In this study, miR156a-5p was predicted to splice 16 targets belonging to SPB-like (SPL) transcription factors, probable magnesium transporter NIPA2 and transmembrane 9 superfamily member 4.…”

“…2500 in the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol for small RNAs. Data processing occurred as described previously 9 by LC Sciences Service. An average of 11,374,096 and 11,885,609 raw sequences were generated from LTS and ATS libraries, respectively.…”

“…Since the expression levels of miRNAs differ among different tissues, developmental stages and even genotype- and environmental stress-dependent, this result is not surprising 6 . For example, in a recent study, nearly half of the identified soybean miRNAs were not found in public miRNA database miRBase, likely due to different ecotypes 9 . In this study, 183 different loci were identified which code 191 novel miRNAs.…”

“…Numerous reports show that miRNAs are involved in plant growth and development as well as response to different abiotic stresses, including extreme temperatures, drought, salinity and even nutrient deprivation as well as heavy metals 6 . Several miRNAs, including miR156, miR172 and miR398, have been identified to be responsive to chilling stress in Prunus persica 7 , Camellia sinensis 8 Glycine max 9 , Solanum habrochaites 10 , Solanum lycopersicum 11 , and Manihot esculenta 12 . However, no any reports on miRNA response to chilling stress in sweet potato.…”

Small RNA-mediated responses to low- and high-temperature stresses in cotton

“…miRNAs predominantly play important gene-regulatory roles through base-pairing with target mRNAs for cleavage or translational repression 6 . They play regulatory roles in almost all aspects of plant development and response to stress 7 8 , and have been shown to be either up- or down-regulated in plant responses to abiotic stresses such as cold, salt, heat, drought, and oxidative stress 9 10 .…”