Small RNA Sequencing in Sugar Beet Under Alkaline Stress
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RESEARCH ARTICLE
Small RNA Sequencing in Sugar Beet Under Alkaline Stress Chunlei Zou1 • Yubo Wang1 • Bin Wang1 • Dan Liu1 • Lei Liu1 • Caifeng Li1
•
Feng Chen2
Received: 1 May 2020 / Accepted: 25 July 2020 Ó Society for Sugar Research & Promotion 2020
Abstract MiRNAs have been proved to participate in the abiotic stress responses in plants. Sugar beet can adapt itself to different abiotic stresses, in particular the alkaline and salinity stresses. Nonetheless, the number, features, sequences and possible effects of miRNAs on the plant responses to alkaline stress remain largely unclear. Small RNA sequencing was carried out in sugar beet cultivar KWS0143 seedling leaves under alkaline solution treatments for 0 (control, C), 3 (short term, ST) as well as 7 (long term, LT) days, respectively. As a result, the RNAs 24 nt in length showed the highest abundance among three sugar beet libraries, followed by those 21 nt and 22 nt in length. Besides, among these three libraries, a total of 2134 miRNAs were identified, which belonged to 47 families. Each of identified known miRNA showed high conservation level among different plant species. 24 novel miRNAs were also identified that possessed standard miRNA* sequences and hairpin precursors, with the length of 20–24 nt. Expression of 222 miRNAs was detected under each treatment, including 169 known and 53 novel miRNAs. Sixteen miRNAs showed specific expression in ST treatment, while twenty-nine showed expression in LT
Chunlei Zou and Yubo Wang have contributed equally to this work.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12355-020-00869-0) contains supplementary material, which is available to authorized users. & Caifeng Li [email protected] 1
College of Agronomy, Northeast Agricultural University, Harbin, China
2
College of Public Administration and Law, Northeast Agricultural University, Harbin, China
treatment. Besides, we estimated 45 characteristic coding genes as the targets for 67 alkali-responsive miRNAs. According to GO analysis, numerous target genes of differentially expressed miRNAs (DEmiRNAs) showed enrichment into the ‘‘redox process,’’ such as polyphenol oxidase gene LOC04900758. Our results provided a valuable resource on alkali-responsive miRNAs and should benefit the improvement in alkaline stress tolerance in sugar beet. Keywords Sugar beet Alkali stress miRNAs RNA sequencing
Introduction Micro-RNAs (miRNAs) have been identified as the endogenous short non-coding RNAs, which show high conservation within eukaryotes. miRNAs bind to mRNA to modulate the expression of related genes at post-transcriptional level, and then lead to direct target mRNA degradation or translation suppression (Bartel 2004; Vazquez 2006). Many studies have been conducted to examine the miRNAs’ effects on higher plants. Transcription factors (TF) are the targets of miRNAs, which participate in the diverse developmental periods, such as cell differentiation, organ morphogenesis, seed germination, floral transi
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