Abstract
BackgroundLong noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.ResultsHere, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521.ConclusionsThese lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.
Highlights
Long noncoding RNAs play important roles in essential biological processes
High-throughput sequencing of Long noncoding RNAs (lncRNAs) and small RNA libraries In total, 1,241,588,130 and 168,839,937 raw reads were generated from the libraries of lncRNAs and small
For lncRNAs, we based our analysis on the results of transcript splicing and following the structural characteristics and noncoding proteins, setting up a series of strict screening conditions (Fig. 1a)
Summary
Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. Our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. Nitrogen (N) is an important plant macronutrient and improving N uptake is a key option for increasing crop yield [1]. Nitrate (NO3) and ammonium (NH4) are the main inorganic nitrogen sources that plant roots take up and assimilate in aerobic soil and flooded soil conditions, respectively [2]. Researchers found that growth-regulating factor 4 (GRF4) and growth-repressing DELLA proteins act in equilibrium in the regulation of growth and nitrogen metabolism in plants [3], which should help us understand the nitrogen metabolism of plants and contribute to sustainable development of global safe food supply
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