Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

Abstract

Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

“…These two types of miRNAs accounted for 75% of the total miRNAs of the ceRNA network, indicating that they might play important roles in regulating heat tolerance by interacting with lncRNAs and mRNAs in Chinese cabbage. This conclusion was consistent with those of previous reports on the function of these two miRNAs [48][49][50] . Therefore, lncRNAs interacting with these miRNAs might also play an important regulatory role in the heat tolerance of Chinese cabbage.…”

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

“…Immune response [98] miR397a, miR397b and miR6034 Various stresses [99] multiple miRNAs Drought and salt stress [100] Broccoli (Brassica oleracea) multiple miRNAs Heat stress [101] Cabbage (Brassica L.) multiple miRNAs Heat and drought stress [102] multiple miRNAs Turnip Mosaic Virus infection [103] Cassava (Manihot esculenta) miR160, miR393…”

“…The miRNA1514 and miRNA1509 were targeted using biolistic delivery of a CRISPR/Cas 9 vector for the transient expression [192]. Likewise, in rice, a specific mutation has been induced in miRNA156 recognition sites of the ipa1 gene using CRISPR/Cas 9 to improve the number of traits related to plant architecture [102]. In another report, mono-allelic and bi-allelic mutations in several miRNA genes of the T0 line of rice have successfully been incorporated using CRISPR/Cas 9, resulting in the loss of function of miRNA [193].…”

Small RNAs: The Essential Regulators in Plant Thermotolerance

“…miR319 targets TEOSINTE BRANCHED/CYCLOIDEA/PCF (TCP) genes and several MYB genes to control leaf growth (Palatnik et al, 2019). miR159 was upregulated by heat stress in flowering Chinese cabbage (Ahmed et al, 2019). In contrast, miR159 was downregulated after heat stress in Triticum aestivum, and the transgenic rice overexpressing tae-miR159 showed sensitivity to heat stress (Wang et al, 2012).…”