Abstract
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.
Highlights
Nitrogen (N), being the constituent of most biomolecules, viz. amino acids, nucleotides, proteins, chlorophyll, and many plant hormones, it is considered the major essential nutrient required for plant growth and development [1,2]
A similar trend was observed for root dry weight, with IR 64 (IR64) showing less sensitivity (4.43%) to N stress compared to Nagina 22 (N22) (43.97%)
N starvation affected the overall growth of both rice genotypes; below ground, part of IR64 was either more tolerant or was non-responsive to N stress compared to N22, i.e., IR64 kept its biomass allocation almost constant in root tissue even in N stress conditions, while N22 increased its foraging ability of nitrogen
Summary
Nitrogen (N), being the constituent of most biomolecules, viz. amino acids, nucleotides, proteins, chlorophyll, and many plant hormones, it is considered the major essential nutrient required for plant growth and development [1,2]. Increased efficiency of N application in plants would result in higher crop yield under limited N supply, benefiting the farmers via higher net profit, and mitigate the environmental risks arising due to an excess of fertilizers used on agricultural land. In this context, improving the nitrogen use efficiency (NUE) of rice, a dominant dietary source in almost every part of the world, would be worthwhile
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