Association of nitrogen utilisation efficiency with sustenance of reproductive stage nitrogen assimilation, transcript abundance and sequence variation of nitrogen metabolism genes in rice (Oryza sativa L.) sub-species

To maintain yield stability and environmental sustainability of rice cultivation, improvement in nitrogen use efficiency (NUE) is essential. We identified rice genotypes showing high NUE in control (N120) and N deficient (N0) field conditions by analyzing different NUE parameters. Reproductive stage N assimilatory and signalling gene expression correlated to the variation in N utilization efficiency (NutE) variation. The sequence variation in N metabolism and signaling (NLP) genes was analyzed in selected genotypes (Apo (Indica) and Nerica-L-42 (Oryza glaberrima*Indica)). Significant non-synonymous SNPs were found in NPF2.2, PTR2, NGR9 (DEP1), Fd-GOGAT, NLP3, NLP4 and NLP5 genes of Apo, Nerica-L-42 and w.r.to japonica genotype Nipponbare. The significant variation in reproductive stage gene expression and changes in the amino acid sequence of NLP3, NLP4, and NLP5 among rice genotypes differing in NUtE is a new and potent genome editing target improving rice NUE. The non-synonymous SNPs identified in the study will be important genomic resources for improving rice NUE.