Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Peanut (Arachis hypogaea L.) Cold Response

Xin Zhang; Chao Ren; Yunyun Xue; Yuexia Tian; Huiqi Zhang; Na Li; Cong Sheng; Huifang Jiang; Dongmei Bai

doi:10.3389/fpls.2022.920195

Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Peanut (Arachis hypogaea L.) Cold Response

Front Plant Sci. 2022 Jun 2:13:920195. doi: 10.3389/fpls.2022.920195. eCollection 2022.

Authors

Xin Zhang^{1

2}, Chao Ren¹, Yunyun Xue¹, Yuexia Tian¹, Huiqi Zhang¹, Na Li¹, Cong Sheng^{3

4}, Huifang Jiang⁵, Dongmei Bai¹

Affiliations

¹ Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China.
² State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China.
³ Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
⁴ Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, China.
⁵ Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

Abstract

Cold stress is a major environmental factor that affects plant growth and development, as well as fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play crucial roles in various abiotic stresses. Peanuts (Arachis hypogaea L.), one of the most important grain legumes and source of edible oils and proteins, are cultivated in the semi-arid tropical and subtropical regions of the world. To date, there has been no report on the role of miRNAs in the response to cold stress in cultivated peanuts. In this study, we profiled cold-responsive miRNAs in peanuts using deep sequencing in cold-sensitive (WQL20) alongside a tolerant variety (WQL30). A total of 407 known miRNAs and 143 novel peanut-specific miRNAs were identified. The expression of selected known and novel miRNAs was validated by northern blotting and six known cold-responsive miRNAs were revealed. Degradome sequencing identified six cold-responsive miRNAs that regulate 12 target genes. The correlative expression patterns of several miRNAs and their target genes were further validated using qRT-PCR. Our data showed that miR160-ARF, miR482-WDRL, miR2118-DR, miR396-GRF, miR162-DCL, miR1511-SRF, and miR1511-SPIRAL1 modules may mediate cold stress responses. Transient expression analysis in Nicotiana benthamiana found that miR160, miR482, and miR2118 may play positive roles, and miR396, miR162, and miR1511 play negative roles in the regulation of peanut cold tolerance. Our results provide a foundation for understanding miRNA-dependent cold stress response in peanuts. The characterized correlations between miRNAs and their response to cold stress could serve as markers in breeding programs or tools for improving cold tolerance of peanuts.

Keywords: cold response; cold stress; cold tolerance; microRNA; peanut.