Identification and Analysis of Small Interfering RNAs Associated With Heat Stress in Flowering Chinese Cabbage Using High-Throughput Sequencing.

Waqas Ahmed,Hua Zhang,Yanshi Xia,Peiguo Guo,Kadambot H.M Siddique,Ronghua Li

doi:10.3389/fgene.2021.746816

Abstract

Endogenous small interfering RNAs (siRNAs) are substantial gene regulators in eukaryotes and play key functions in plant development and stress tolerance. Among environmental factors, heat is serious abiotic stress that severely influences the productivity and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, how siRNAs are involved in regulating gene expression during heat stress is not fully understood in flowering Chinese cabbage. Combining bioinformatical and next-generation sequencing approaches, we identified heat-responsive siRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0, 1, 6, and 12 h after a 38°C heat-stress treatment; 536, 816, and 829 siRNAs exhibited substantial differential expression at 1, 6, and 12 h, respectively. Seventy-five upregulated and 69 downregulated differentially expressed siRNAs (DE-siRNAs) were common for the three time points of heat stress. We identified 795 target genes of DE-siRNAs, including serine/threonine-protein kinase SRK2I, CTR1-like, disease resistance protein RML1A-like, and RPP1, which may play a role in regulating heat tolerance. Gene ontology showed that predictive targets of DE-siRNAs may have key roles in the positive regulation of biological processes, organismal processes, responses to temperature stimulus, signaling, and growth and development. These novel results contribute to further understanding how siRNAs modulate the expression of their target genes to control heat tolerance in flowering Chinese cabbage.

Highlights

Environmental stresses such as salinity, drought, and heat can impede crop productivity and even cause plant death (Bita and Gerats, 2013)
Heat stress tolerance is a quantitative trait, and its expression can involve the fine regulation of stress-related genes in plants (Golldack et al, 2014; Suzuki et al, 2014)
Recent advances in nextgeneration sequencing have identified and functionally characterized many genes involved in responses to environmental stresses, signifying their functions in the maintenance of stress tolerance (Ahmed et al, 2020b). small interfering RNAs (siRNAs) are involved in regulating abiotic stress responses in plants, but limited information is available on their function in response to heat stress

Summary

Introduction

Environmental stresses such as salinity, drought, and heat can impede crop productivity and even cause plant death (Bita and Gerats, 2013). Identification of Heat-Responsive siRNAs in Cabbage significant functions in modulating plant responses to environmental factors (biotic and abiotic stresses) by regulating gene expression during transcriptional and posttranscriptional processes (Srivastava et al, 2017; Wang et al, 2017; Ahmed et al, 2020b). These molecules are classified into different types depending on their function and synthesis: small interfering RNAs (siRNAs), microRNAs (miRNAs), and long noncoding RNAs (Shukla et al, 2008; Khraiwesh et al, 2012; Zhu et al, 2015). Transcript levels of HEAT-INDUCED TAS1 TARGET1 (HTT1) and HTT2 were significantly upregulated under heat stress and targeted by TAS1-derived siRNAs in Arabidopsis (Li et al, 2014)

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