Abstract
Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein–protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.
Highlights
The Phenomenal growth in the use of fertilizers for crop production, coupled with poor nitrogen-use efficiency (NUE) is increasingly polluting the soil, water and air, which adversely affects health, biodiversity, and climate change (Sutton et al, 2019)
The net photosynthetic rate was measured in terms of assimilated CO2, as μ mol CO2/m2s1, transpiration was measured in terms of mol (H2O)/m2s1, stomatal conductance was measured in terms of mol [(H2O) m−2 sec−1], internal water-use efficiency was measured in terms of μ mol CO2/mol(H2O), and transpiration efficiency was measured in terms of μ mol CO2/m mol H2O/m2/s
We identified 1,064 common genes between 14,791 Nresponsive genes and 1,842 yield-related genes known in rice and analyzed them as outlined in Figures 1, 2A
Summary
The Phenomenal growth in the use of fertilizers for crop production, coupled with poor nitrogen-use efficiency (NUE) is increasingly polluting the soil, water and air, which adversely affects health, biodiversity, and climate change (Sutton et al, 2019). An inability to biologically distinguish between the N-response and NUE and the poor characterization of the phenotype and genotype for NUE have hampered crop improvement (Mandal et al, 2018), till they were discovered recently (Sharma et al, 2018, 2021). Rice has the lowest NUE among cereals (Norton et al, 2015) and consumes most N-fertilizer among them. It is the third most produced and consumed crop in the world. Rice has the most N-responsive transcriptomic data sets reported in any crop (Pathak et al, 2020 and the references cited therein)
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