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.
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.
Synthetic nitrogen fertilizers have greatly increased crop yields, yet much of the applied nitrogen is lost from agroecosystems and contributes to environmental pollution and higher economic costs. Improving nitrogen uptake efficiency (NUpE) benefits from understanding how root system architecture (RSA) governs soil nitrogen capture. Although root traits have seldom been explicit breeding targets, selection for variation in above-ground nitrogen accumulation has also likely shaped differences in RSA. The Illinois Protein Strain Recombinant Inbred population, derived from more than a century of divergent selection for seed protein concentration, offers a powerful resource for dissecting RSA variation. Using multi-year field phenotyping of excavated root crowns and genome-wide association analysis, we identified a quantitative trait locus on chromosome 10 containing E1OGDH1, which encodes the E1 subunit of the 2-oxoglutarate dehydrogenase (OGDH) complex. OGDH performs a key step in the tricarboxylic acid cycle that also modulates 2-oxoglutarate, an important entry point into nitrogen metabolism and a co-factor for enzymes involved in hormone and secondary product synthesis. Long-read sequencing of inbreds derived from the divergent IHP and ILP parental populations revealed promoter polymorphisms defining E1OGDH1 alleles and differed in E1OGDH1 expression in root tissue. Field experiments in IPSRI lines carrying IHP- or ILP-associated E1OGDH1 alleles showed differences in root architectural traits over two years. CRISPR-Cas9 knockout mutants confirmed a functional role for E1OGDH1 in whole-plant performance and nitrogen-responsive root development. Mutants were shorter, had reduced biomass, and exhibited altered architectural responses to soil nitrogen levels. Transcriptome analysis further showed that loss of E1OGDH1 altered basal and nitrogen-responsive expression of genes associated with root development and nitrogen uptake and metabolism. Together, these findings identify E1OGDH1 as a strong candidate quantitative regulator of maize RSA and nitrogen plasticity, suggesting that central carbon–nitrogen metabolic genes can contribute to root developmental responses relevant to NUpE.
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The A allele (Hap1) was significantly associated with increased plant height, SPAD value, grain number, nitrogen accumulation, nitrogen accumulation, and biomass under LN stress, suggesting that SORBI_3001G116400 as a candidate gene requiring functional validation and testing in additional genetic backgrounds.
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The findings suggest that GmRD22 has undergone directional selection during soybean domestication and improvement, and offer new insights into the genetic control of SNF and establish promising targets for breeding soybean varieties with improved nitrogen fixation efficiency.
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Plants synthesize carbohydrates in mature leaves that act as primary carbon sources for biosynthesis, osmotic regulation, and signalling. Sugar transporter gene families regulate carbon partitioning, phloem loading and unloading, and sink uptake, thereby influencing growth, and yield. In pigeonpea, efficient sugar allocation to developing embryo/seed is critical for determining seed number per pod (SNPP). Photosynthate dynamics were studied in five pigeonpea genotypes contrasting for SNPP using integrated biochemical, in-silico, gene expression analyses and FT-IR spectroscopy. Quantification of soluble sugars and starch across ovule to seed developmental stages, coupled with bioinformatic analysis, identified 8 SUTs, 3 MSTs, and 24 SWEETs. Structural and phylogenetic analyses revealed conserved domains, chromosomal distribution, and gene duplications events, with most transporters predicted to localize to the plasma membrane. Anthrone assays and HPLC profiling showed peak soluble sugar accumulation at open flower stage, followed by redistribution to seeds and pod walls. Genotypes with low seeds accumulated higher sugars, reflecting lower sink demand while the reverse trend was observed in starch content. Spatio-temporal expression analysis revealed distinct regulatory roles of sugar transporters with CcSUT1, CcSUT3, and CcSUT7 were highly expressed during early reproductive stages, critical for ovule retention and seed set. CcSUT2 functioned as a negative regulator, potentially limiting sugar flux and contributing to low seed number. CcSWEET5, CcSWEET7, and CcSWEET20 showed higher expression in high-SNPP genotypes enhancing hexose transport into developing seeds and promoting seed number. This study identifies key sugar transporters regulating seed development and provides candidate genes for improving pigeonpea yield through molecular breeding.
Shubhi Sinha, Kumari Arpita, Lubhanshi Raje Shisodia et al.· International Journal of Bio...· 0 citations
The GmWIP gene family has expanded substantially in soybean relative to previously characterized species and shows genotype-dependent transcriptional responses to salt stress, suggesting that specific GmWIP members are candidate regulators of salt tolerance and warrant further functional investigation.
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Potato is a globally important food crop, but its production faces major challenges related to inefficient nitrogen fertilizer use. Excessive nitrogen application, particularly in intensive agricultural systems, compromises sustainability and increases environmental and health risks. Improving nitrogen use efficiency (NUE), defined as the capacity of plants for nitrogen uptake and assimilation, is therefore essential to optimize fertilization practices and enhance sustainable crop production. In this study, we analyzed candidate genes associated with NUE in a diploid potato diversity panel (Solanum tuberosum Group Phureja) by evaluating morphological, physiological, and biochemical variables under contrasting nitrogen levels. Association analyses were performed between these variables and genetic polymorphisms within NUE-related genes. Single nucleotide polymorphisms (SNPs) were identified in three candidate genes: AMT1.1 (ammonium transporter), 2OGDD (2-oxoglutarate-dependent dioxygenase), and PPR (pentatricopeptide repeat protein gene). These variants explained 8–20% of the phenotypic variation in traits such as relative chlorophyll content, aerial biomass, and NUE. Notably, a missense variant (Lys → Glu) in 2OGDD was associated with a 30.5% reduction in NUE under low nitrogen conditions, suggesting distinct adaptive strategies. Specific SNPs were associated with NUE-related traits, representing candidate variants for future functional validation and marker-assisted breeding.
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