Association of haplotypes of AAP family amino acid transporters with nitrogen response and nitrogen use efficiency in rice grown under hydroponics and field conditions

The low nitrogen use efficiency (NUE) of staple food crops like rice has both economic and environmental impact. Amino acids taken up from soil or synthesized in source tissues and transported to sink tissues influence plant development and NUE. Amino acid permeases (AAPs) mediate amino acid uptake and transport and influence plant development, yield and NUE. NUE is a complex trait critical for improving rice productivity under variable N supply. Amino acid permeases such as OsAAP3, OsAAP5, and OsAAP11 have been shown to function as negative regulators of NUE in Japonica rice, yet their roles in Indica rice remain to be fully elucidated. In this study, we evaluated selected Indica genotypes under contrasting N regimes—seedlings were tested under high nitrate (HN), high ammonium (HA), and low N (LN) conditions, and field performance was assessed under N120 (optimum N) and N0 (low N). Our aim was to relate performance differences to the SNP status in these three genes, thereby clarifying their influence on N uptake, assimilation, yield potential, and N stress adaptation. ARC 10799 had non-synonymous SNP in OsAAP3, OsAAP5 and OsAAP11. Rice accessions like “Local,” “NCS901,” and “Bhainsa Mundariya,” showed superior biomass accumulation relative to MTU1010. Interestingly, the trend observed in the NUE calculated in seedling stage was similar to those proven in field evaluation and this proves that in general, genotypes with non-synonymous mutation in AAP3, AAP5 and AAP11 in comparison to Japonica showed better growth and N content. Data suggests an N induced regulation of physiological parameters and the changes in NUE parameters was at least in part, related to variation in biomass, plant height, photosynthesis and pigment content related parameters. The comparatively dissimilar trends in shown by different AAP haplotypes indicates the possibility of high or low correlation trait-wise, offering an opportunity to identify significant contrasts in a divergent set of AAP haplotypes. The previous reports and current findings opens new avenues and insights for improving rice yield, quality and NUE by changes in AAP haplotypes that occur naturally or created by precise genome editing.