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Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes

1
ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India
2
School of Human and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2018, 9(4), 206; https://doi.org/10.3390/genes9040206
Received: 24 February 2018 / Revised: 3 April 2018 / Accepted: 6 April 2018 / Published: 11 April 2018
(This article belongs to the Section Plant Genetics and Genomics)
The nitrogen use efficiency (NUE) of crop plants is limited and enhancing it in rice, a major cereal crop, would be beneficial for farmers and the environment alike. Here we report the genome-wide transcriptome analysis of two rice genotypes, IR 64 (IR64) and Nagina 22 (N22) under optimal (+N) and chronic starvation (-N) of nitrogen (N) from 15-day-old root and shoot tissues. The two genotypes were found to be contrasting in their response to -N; IR64 root architecture and root dry weight remained almost equivalent to that under +N conditions, while N22 showed high foraging ability but a substantial reduction in biomass under -N. Similarly, the photosynthetic pigments showed a drastic reduction in N22 under low N, while IR64 was more resilient. Nitrate reductase showed significantly low specific activity under -N in both genotypes. Glutamate synthase (GOGAT) and citrate synthase CS activity were highly reduced in N22 but not in IR64. Transcriptome analysis of these genotypes revealed nearly double the number of genes to be differentially expressed (DEGs) in roots (1016) compared to shoots (571). The response of the two genotypes to N starvation was distinctly different reflecting their morphological/biochemical response with just two and eight common DEGs in the root and shoot tissues. There were a total of 385 nitrogen-responsive DEGs (106 in shoots and 279 in roots) between the two genotypes. Fifty-two of the 89 DEGs identified as specific to N22 root tissues were also found to be differentially expressed between the two genotypes under -N. Most of these DEGs belonged to starch and chloroplast metabolism, followed by membrane and signaling proteins. Physical mapping of DEGs revealed 95 DEGs in roots and 76 in shoots to be present in quantitative trait loci (QTL) known for NUE. View Full-Text
Keywords: nitrogen-responsive genes; rice; RNA-seq; nitrogen use efficiency; DEG-QTL integration nitrogen-responsive genes; rice; RNA-seq; nitrogen use efficiency; DEG-QTL integration
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Sinha, S.K.; Sevanthi V., A.M.; Chaudhary, S.; Tyagi, P.; Venkadesan, S.; Rani, M.; Mandal, P.K. Transcriptome Analysis of Two Rice Varieties Contrasting for Nitrogen Use Efficiency under Chronic N Starvation Reveals Differences in Chloroplast and Starch Metabolism-Related Genes. Genes 2018, 9, 206.

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