Aug 2026· ACS Agricultural Science & Technology· 0 citations· 51 references
TL;DR
Analysis of candidate genes associated with NUE in a diploid potato diversity panel by evaluating morphological, physiological, and biochemical variables under contrasting nitrogen levels suggested distinct adaptive strategies.
Abstract
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.
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.
Michelle S. Cho, Zhengbin Liu, Collin Luebbert et al.· bioRxiv· 0 citations
The first integrated phenotypic, genetic and molecular characterization of WUEL in octoploid strawberry is provided and candidate loci and pathways are identified, thereby establishing a foundation for improving WUEL-related traits.
Mario Ruiz-Velázquez, Cristina Castillejo, J. F. Sánchez-Sevilla et al.· Horticulture Research· 0 citations
Chlorophyll is the primary pigment responsible for capturing light energy and driving photosynthetic conversion. As the key photosynthetic organ during grain filling, the flag leaf plays a critical role in carbon assimilation, consequently, its chlorophyll content (FLC) represents a promising target for enhancing wheat yield and ensuring food security. Dissecting the genetic basis underlying FLC and elucidating its relationships with other agronomic traits are essential for accelerating molecular breeding aiming at improving photosynthetic efficiency and yield in wheat varieties. In this study, a major and environmentally stable quantitative trait locus (QTL) for FLC was detected using a population of 197 recombinant inbred lines (RILs). This QTL, designated
QFLC.scwl-4B
, was consistently mapped to chromosome arm 4BS across multiple environments, explaining 9.36%–31.82% of the phenotypic variance (PVE). The effect of
QFLC.scwl-4B
was further validated in an additional RIL population under diverse environmental conditions. Correlation and effect analyses revealed that
QFLC.scwl-4B
exhibits pleiotropic, leading to increased FLC, spikelet number per spike (SNS), and flag leaf thickness (FLT), alongside reduced productive tiller number (PTN). Furthermore, a putative candidate gene for
QFLC.scwl-4B
,
TraesCS4B03G0098300
, was identified as an ortholog of gene in BBX family, which is known to repress chlorophyll degradation and senescence, and likely involved in chlorophyll synthesis. Further, the promoter region of
TraesCS4B03G0098300
harbors a single nucleotide polymorphism (G/C) between the two parents. Collectively, these findings provide valuable QTL resources and candidate gene targets for marker-assisted selection in breeding programs aiming at developing wheat varieties with high photosynthetic efficiency and yield.
Jia-Jun Liu, Na-Na Qin, De-Fu Wang et al.· Frontiers in Plant Science· 0 citations
: Excessive nitrogen fertilizer application increases production costs and environmental burdens in rice cultivation, highlighting the need to identify low-nitrogen-tolerant germplasm. In this study, 266 rice accessions were evaluated in hydroponic culture for 35 d under normal-nitrogen conditions (NN: 1.6 mM NO 3 − and 1.6 mM NH 4+ ) and low-nitrogen conditions (LN: 0.4 mM NO 3 − and 0.4 mM NH 4+ ). Fifteen seedling traits related to growth, chlorophyll status, nitrogen accumulation, and nitrogen utilization were measured, and the corresponding low-nitrogen tolerance indices were evaluated using correlation analysis, principal component analysis (PCA), membership-function analysis, and cluster analysis. All measured traits had coefficients of variation greater than 10%, indicating substantial variation among accessions. PCA extracted six principal components that explained 82.533% of the total variation. Relative shoot dry weight, relative total dry weight, and relative aboveground nitrogen accumulation were major indicators of seedling performance under LN. The LNTI-based D-values classified the 266 accessions into four tolerance groups. Comparison of this classification with the treatment-specific comprehensive evaluation identified six overlapping accessions—Q3-2, Q3-3, Q5-1, TD201, Jijing 88, and Jiadao 37—with both high relative low-nitrogen tolerance and high nitrogen-efficiency-related performance under NN and LN. These accessions represent preliminary candidates for further evaluation across nitrogen gradients, reproductive stages, field environments, and years before their breeding value and underlying physiological and molecular mechanisms can be confirmed.
Shuting Zhao, Yu-Zhuo Yan, Feisal Mohamed Osman et al.· Phyton· 0 citations
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.
Hanyu Zhao, Jiaying Zhong, Chao Ma et al.· Plants· 0 citations
Limited genetic variability remains a major constraint to genetic improvement in guar (Cyamopsis tetragonoloba L.) restricting both its productivity and cultivation in Pakistan. As a drought adapted legume with significant value as fodder, green manure, and a soil-enhancing nitrogen fixer, guar holds considerable untapped potential for sustainable agriculture. Enhancing its genetic base is therefore essential for developing high-yielding, nutritionally superior varieties suited to arid and semi-arid environments. To address this need, a field experiment was conducted in October 2022 at the University of Agriculture, Faisalabad, using a Randomized Complete Block Design (RCBD) with three replications to assess genetic variability and trait associations among 24 guar genotypes. Five plants per genotype were evaluated for agronomic traits (plant height, branches, tillers, leaves, leaf area, clusters plant⁻¹, pods cluster⁻¹, pods plant⁻¹, fresh and dry biomass) and forage quality attributes (crude protein, crude fiber, ash, moisture, NDF, and ADF), with quality traits quantified via Near Infrared Spectroscopy (NIRS). Significant phenotypic variability was recorded among genotypes. Plant height ranged from 78–141.2 cm, branches 2.16–10.06, leaves 44.87–330.33, fresh biomass 200–700 g, dry biomass 70–244 g, and crude protein 15.16–23.37%. Plant height showed strong positive correlations with fresh biomass, leaf area, and crude protein, whereas branches and clusters exhibited negative associations. Tillers were positively correlated with several yield components but not with leaf area or protein. Crude protein was positively associated with NDF, ash, and crude fiber. Superior genotypes identified included Guar-401 (plant height), Guar-303 and Guar-701 (number of branches), Guar-102 and Guar-701 (number of leaves), and Guar-103 and Guar-803 (protein). These high performing genotypes provide valuable genetic resources for developing improved guar cultivars with enhanced fodder yield and nutritional quality.
Muaeen Khan, Muhammad Usman, M. T. Mahmood et al.· Journal of Pharma and Biomed...· 0 citations
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