A comprehensive atlas of long non-coding RNAs provides insight into grain development in wheat
Zhaoheng Zhang, Ruijie Zhang, Fengfan Meng, Yongming Chen, Wenxi Wang, Kai Yang, Yujiao Gao, Mingming Xin, Jinkun Du, Zhaorong Hu, Zhongfu Ni, Qixin Sun, Weilong Guo, Yingyin Yao
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of many biological processes, but our knowledge of lncRNAs associated with wheat (<italic>Triticum aestivum</italic>) grain development is limited. Here, to generate a comprehensive atlas of lncRNAs in wheat, we performed strand-specific RNA sequencing (ssRNA-seq) using wheat endosperm at 10 and 15 days after pollination and collected 545 publicly available transcriptome datasets. We identified 20,893 wheat lncRNAs and developed the comprehensive database wLNCdb (http://wheat.cau.edu.cn/wLNCdb) to provide their sequences, expression patterns, co-expressed genes, and single nucleotide polymorphisms among wheat accessions. To investigate the functions of lncRNAs, we focused on lncRNAs predicted to regulate genes related to grain size and weight and seed storage proteins via <italic>cis-</italic> or <italic>trans-</italic>regulation. We identified a lncRNA TraesLNC1D26001.1 negatively regulates seed germination, as its overexpression delayed wheat seed germination by upregulating <italic>Abscisic acid-insensitive 5</italic> (<italic>TaABI5</italic>). These results suggest wLNCdb as a useful resource for discovering the functions of lncRNAs in wheat during seed development and other processes.