Abstract
The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali’s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture.
Highlights
The foundation of modern agriculture is based on the use of high-yielding cultivars that are responsive to heavy doses of nitrogenous-fertilizers because nitrogen (N) is the single most critical macronutrient used for commercial crop production
In contrast to the earlier green revolution strategy that focuses on developing genotypes responding to higher doses of N, current research is directed at genotypes that perform well under N limited environments without compromising crop productivity
We found several differentially expressed genes (DEGs) co-localized with the selected quantitative trait loci (QTL) for low N responses (Table S5), and only 81 of these were Pokkali-specific (Figure 9)
Summary
The foundation of modern agriculture is based on the use of high-yielding cultivars that are responsive to heavy doses of nitrogenous-fertilizers because nitrogen (N) is the single most critical macronutrient used for commercial crop production. In rice growing areas of the USA, an alternate wetting and drying technique is slowly gaining popularity to reduce the cost of cultivation by reducing water usage This strategy will require the development of rice cultivars with improved water and nitrogen use efficiency to reduce N loss during the process. The superior ability of indica rice for N uptake and mobilization [9,10] offers a unique opportunity to design nitrogen use-efficient cultivars by providing insights into the molecular genetic basis of NUE. Many QTLs from NUE mapping studies in rice and other crops overlapped with genes that were involved in nitrogen uptake and assimilation [23,24,25].
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