Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [ Setar
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RESEARCH ARTICLE
Open Access
Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.] Zilong Zhao1,2†, Dan Liu3†, Yanjiao Cui2†, Suying Li2, Dan Liang3, Daizhen Sun1*, Jianhe Wang3* and Zhengli Liu2*
Abstract Background: Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results: In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion: Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding. Keywords: Foxtail millet, Long non-coding RNA, Yield regulation
Background Long noncoding RNAs (lncRNAs) are generally defined as RNA transcripts that contain more than 200 nucleotides (nts) but lack a coding sequence (CDS) or open reading frame (ORF) [1]. Based on their genomic locations in relation to the neighboring protein-coding genes, lncRNAs can be divided into three classes: (1) * Correspondence: [email protected]; [email protected]; [email protected] † Zilong Zhao, Dan Liu and Yanjiao Cui contributed equally to this work. 1 College of Agronomy, Shanxi Agricultural University, Taigu, China 3 Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China 2 Department of Life Sciences, Tangshan Normal University, Tangshan, China
long intergenic non-coding RNAs (lincRNAs), which are located within the genomic interval between two protein-coding genes; (2) intronic lncRNAs, which are derived from an intron; (3) long non-coding natural antisense transcripts (lncNATs), which are produced from the opposite strand and overlap with the exons [2]. According to their effects exerted on DNA sequences, lncRNAs can be classified to cis-acting lncRNAs and trans-acting lncRNAs, which regulate the expression of neighbouring genes and distant genes, respectively [3]. For example, the lncRNA Morrbid are reported to control the lifespan of eosinophils, neutrophils and monocytes in mouse, through recruiting the Polycomb
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