Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Roots of Rice Seedlings under Nitrogen Deficiency

Dongfeng Qiu; Yan Wu; Kuaifei Xia; Mingyong Zhang; Zaijun Zhang; Zhihong Tian

doi:10.3390/plants12234047

Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Roots of Rice Seedlings under Nitrogen Deficiency

Plants (Basel). 2023 Nov 30;12(23):4047. doi: 10.3390/plants12234047.

Authors

Dongfeng Qiu^{1

2}, Yan Wu², Kuaifei Xia³, Mingyong Zhang³, Zaijun Zhang², Zhihong Tian¹

Affiliations

¹ Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Life Science, Yangtze University, Jingzhou 434025, China.
² Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
³ Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.

Abstract

Long non-coding RNAs (lncRNAs) regulate gene expression in eukaryotic organisms. Research suggests that lncRNAs may be involved in the regulation of nitrogen use efficiency in plants. In this study, we identified 1628 lncRNAs based on the transcriptomic sequencing of rice roots under low-nitrogen (LN) treatment through the implementation of an integrated bioinformatics pipeline. After 4 h of LN treatment, 50 lncRNAs and 373 mRNAs were significantly upregulated, and 17 lncRNAs and 578 mRNAs were significantly downregulated. After 48 h LN treatment, 43 lncRNAs and 536 mRNAs were significantly upregulated, and 42 lncRNAs and 947 mRNAs were significantly downregulated. Moreover, the interaction network among the identified lncRNAs and mRNAs was investigated and one of the LN-induced lncRNAs (lncRNA24320.6) was further characterized. lncRNA24320.6 was demonstrated to positively regulate the expression of a flavonoid 3'-hydroxylase 5 gene (OsF3'H5). The overexpression of lncRNA24320.6 was shown to improve nitrogen absorption and promote growth in rice seedlings under LN conditions. Our results provide valuable insights into the roles of lncRNAs in the rice response to nitrogen starvation.

Keywords: long non-coding RNA; nitrogen; rice; ssRNA-Seq; transcriptome.

Abstract

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