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RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage

Overview of attention for article published in BMC Genomics, November 2015
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Title
RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage
Published in
BMC Genomics, November 2015
DOI 10.1186/s12864-015-2141-9
Pubmed ID
Authors

Jun Yang, Xiaorong Chen, Changlan Zhu, Xiaosong Peng, Xiaopeng He, Junru Fu, Linjuan Ouyang, Jianmin Bian, Lifang Hu, Xiaotang Sun, Jie Xu, Haohua He

Abstract

Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world's population. However, grain yields are challenged by various abiotic stresses such as drought, fertilizer, heat, and their interaction. Rice at reproductive stage is much more sensitive to environmental temperatures, and little is known about molecular mechanisms of rice spikelet in response to high temperature interacting with nitrogen (N). Here we reported the transcriptional profiling analysis of rice spikelet at meiosis stage using RNA sequencing (RNA-seq) as an attempt to gain insights into molecular events associated with temperature and nitrogen. This study received four treatments: 1) NN: normal nitrogen level (165 kg ha(-1)) with natural temperature (30 °C); 2) HH: high nitrogen level (330 kg ha(-1)) with high temperature (37 °C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and natural temperature, respectively. The de novo assembly generated 52,553,536 clean reads aligned with 72,667 unigenes. About 10 M reads were identified from each treatment. In these differentially expressed genes (DEGs), we found 151 and 323 temperature-responsive DEGs in NN-vs-NH and HN-vs-HH, and 114 DEGs were co-expressed. Meanwhile, 203 and 144 nitrogen-responsive DEGs were focused in NN-vs-HN and NH-vs-HH, and 111 DEGs were co-expressed. The temperature-responsive genes were principally associated with calcium-dependent protein, cytochrome, flavonoid, heat shock protein, peroxidase, ubiquitin, and transcription factor while the nitrogen-responsive genes were mainly involved in glutamine synthetase, transcription factor, anthocyanin, amino acid transporter, leucine zipper protein, and hormone. It is noted that, rice spikelet fertility was significantly decreased under high temperature, but it was more reduced under higher nitrogen. Accordingly, numerous spikelet genes involved in pollen development, pollen tube growth, pollen germination, especially sporopollenin biosynthetic process, and pollen exine formation were mainly down-regulated under high temperature. Moreover, the expression levels of co-expressed DEGs including 5 sporopollenin biosynthetic process and 7 pollen exine formation genes of NN-vs-NH were lower than that of HN-vs-HH. Therefore, these spikelet genes may play important roles in response to high temperature with high nitrogen and may be good candidates for crop improvement. This RNA-seq study will help elucidate the molecular mechanisms of rice spikelet defense response to high temperature interacting with high nitrogen level.

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Mendeley readers

The data shown below were compiled from readership statistics for 53 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 1 2%
Unknown 52 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 14 26%
Researcher 11 21%
Student > Bachelor 5 9%
Student > Master 4 8%
Student > Doctoral Student 4 8%
Other 6 11%
Unknown 9 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 29 55%
Biochemistry, Genetics and Molecular Biology 6 11%
Environmental Science 2 4%
Computer Science 1 2%
Chemical Engineering 1 2%
Other 4 8%
Unknown 10 19%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 19 November 2015.
All research outputs
#9,880,995
of 12,378,687 outputs
Outputs from BMC Genomics
#5,640
of 7,251 outputs
Outputs of similar age
#215,938
of 320,913 outputs
Outputs of similar age from BMC Genomics
#400
of 474 outputs
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