title: RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage.
abstract: BACKGROUND
  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).
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  This RNA-seq study will help elucidate the molecular mechanisms of rice spikelet defense response to high temperature interacting with high nitrogen level.
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. yangjun1024love@163.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. ccxxrr80@163.com.
authors.forename: Xiaorong
authors.initials: X
authors.lastname: Chen
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. zhuchanglan@163.com.
authors.forename: Changlan
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. pxs63@163.com.
authors.forename: Xiaosong
authors.initials: X
authors.lastname: Peng
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. hxpeng@163.com.
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: He
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. fujunru2002@163.com.
authors.forename: Junru
authors.initials: J
authors.lastname: Fu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. oylj4562@163.com.
authors.forename: Linjuan
authors.initials: L
authors.lastname: Ouyang
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. jmbian81@126.com.
authors.forename: Jianmin
authors.initials: J
authors.lastname: Bian
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. lfhu_hn337@163.com.
authors.forename: Lifang
authors.initials: L
authors.lastname: Hu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. xtsun80@163.com.
authors.forename: Xiaotang
authors.initials: X
authors.lastname: Sun
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. xujie198615@foxmail.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China. hhhua64@163.com.
authors.forename: Haohua
authors.initials: H
authors.lastname: He
mesh_terms: D004305:Dose-Response Relationship, Drug; D005298:Fertility / Q000187:drug effects / Q000235:genetics; D020869:Gene Expression Profiling; D006358:Hot Temperature; D008540:Meiosis / Q000187:drug effects / Q000235:genetics*; D009584:Nitrogen / Q000494:pharmacology*; D012275:Oryza / Q000166:cytology* / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D017423:Sequence Analysis, RNA
chemical_list: D009584:Nitrogen