Genomic Evolution and Nitrogen Response Analysis of Glutamate Synthase Gene Family in Rice Source–Sink Tissues During Grain Filling

Abstract

Background/Objectives: Rice (Oryza sativa) is the staple food for over half the global population, and nitrogen availability is the primary limiting factor determining rice yield. As the rate-limiting enzyme in nitrogen assimilation and allocation, glutamate synthase (GOGAT) plays an irreplaceable role throughout the plant life cycle. The evolutionary history, natural genetic variation, and regulatory networks of the GOGAT family in rice source–sink tissues during grain filling remain largely elusive. Methods: Here, we combined comparative genomics, population genetics, transcriptomic and biochemical approaches to systematically characterize the GOGAT gene family. Genome-wide identification was performed across 12 angiosperm species, followed by haplotype analysis using resequencing data from ~2000 rice accessions. Transcriptomic, enzymatic activity and metabolite content determination were integrated to investigate their responses to three nitrogen gradient treatments in source (roots, flag leaves) and sink (developing embryos) tissues. Results: A total of 48 GOGAT genes were identified, clustered into two ancient subfamilies (GLU/GLT), with a Poaceae-specific duplication event generating GLT1 and GLT2 subgroups. Specifically, three rice GOGAT genes exhibited distinct domestication signatures: Fd-GOGAT showed strong indica-japonica subspecific differentiation, while NADH-GOGAT2 harbored tropical japonica-specific haplotypes. Furthermore, tissue-specific and developmental stage-dependent nitrogen response patterns were revealed, identifying 5 days after pollination as the critical metabolic switch point. OsGOGAT promoters are enriched with light-, ABA- and stress-responsive cis-elements, suggesting coordinated hormonal and environmental regulation. Conclusions: This study provides comprehensive insights into the functional divergence of the plant GOGAT gene family and coordinated strategies that rice employs under exogenous nitrogen stress, and identifies elite haplotypes for nitrogen-efficient rice breeding.