Dataset Information

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

ABSTRACT: BACKGROUND:Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expression. RESULTS:In this study, we surveyed the intergenic/intronic lncRNAs in maize B73 leaves at the V7 stage under conditions of N-deficiency and N-sufficiency using ribosomal RNA depletion and ultra-deep total RNA sequencing approaches. By integration with mRNA expression profiles and physiological evaluations, 7245 lncRNAs and 637 nitrogen-responsive lncRNAs were identified that exhibited unique expression patterns. Co-expression network analysis showed that the nitrogen-responsive lncRNAs were enriched mainly in one of the three co-expressed modules. The genes in the enriched module are mainly involved in NADH dehydrogenase activity, oxidative phosphorylation and the nitrogen compounds metabolic process. CONCLUSIONS:We identified a large number of lncRNAs in maize and illustrated their potential regulatory roles in response to N stress. The results lay the foundation for further in-depth understanding of the molecular mechanisms of lncRNAs' role in response to nitrogen stresses.

SUBMITTER: Lv Y

PROVIDER: S-EPMC4865003 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

Lv Yuanda Y Liang Zhikai Z Ge Min M Qi Weicong W Zhang Tifu T Lin Feng F Peng Zhaohua Z Zhao Han H

BMC genomics 20160511

<h4>Background</h4>Nitrogen (N) is an essential and often limiting nutrient to plant growth and development. Previous studies have shown that the mRNA expressions of numerous genes are regulated by nitrogen supplies; however, little is known about the expressed non-coding elements, for example long non-coding RNAs (lncRNAs) that control the response of maize (Zea mays L.) to nitrogen. LncRNAs are a class of non-coding RNAs larger than 200 bp, which have emerged as key regulators in gene expressi ...[more]

PMID: 27169379

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Project description:Mulching and nitrogen are critical drivers of crop production for smallholders of the Loess Plateau in China. The purpose of this study was to investigate the effect of mulching and nitrogen fertilizer on the soil water content, soil nitrate-N content and vertical distribution in maize root-zone. The experiment was conducted over two consecutive years and used randomly assigned field plots with three replicates. The six treatments consisted of no fertilizer without plastic film (CK), plastic film mulching with no basal fertilizer and no top dressing (MN0), basal fertilizer with no top dressing and no mulching (BN1), plastic film mulching and basal fertilizer with no top dressing (MN1), basal fertilizer and top dressing with no mulching (BN2) and plastic film mulching with basal fertilizer and top dressing (MN2). In the top soil layers, the soil water content was a little high in the plastic film mulching than that without mulching. The mean soil water content from 0 to 40 cm without mulching were 3.35% lower than those measured in the corresponding mulching treatments in 31 days after sowing in 2012. The mulching treatment increased the soil nitrate-N content was observed in the 0-40-cm soil layers. The results indicate that high contents of soil nitrate-N were mainly distributed at 0-20-cm at 31 days after sowing in 2012, and the soil nitrate-N concentration in the MN2 treatment was 1.58 times higher than that did not receive fertilizer. The MN2 treatment greatly increased the soil nitrate-N content in the upper layer of soil (0-40-cm), and the mean soil nitrate-N content was increased nearly 50 mg kg-1 at 105 days after sowing compared with CK treatment in 2012. The soil nitrate-N leaching amount in MN1 treatment was 28.61% and 39.14% lower than BN1 treatment, and the mulch effect attained to 42.55% and 65.27% in MN2 lower than BN2 in both years. The yield increased with an increase in the basal fertilizer, top dressing and plastic film mulching, and the grain yield increase ranged from 31.41% to 83.61% in two consecutive years. The MN1 and MN2 treatment is recommended because it increased the grain yield and improved the fertilizer use efficiency, compared with the no-mulching treatment.

Dataset Information

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

Publications

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.).

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