Quinoa (Chenopodium quinoa Willd.) is gaining global importance for its nutritional value and adaptability; however, breeding progress remains limited. Genomic selection (GS), combined with rapid generation cycles, offers a strategy to accelerate genetic improvement. We conducted whole-genome resequencing of 610 accessions and present the first evaluation of genomic prediction in quinoa evaluated across six field trials in Australia and Pakistan for seven phenological and yield-related traits. Using ∼1.8 million single-nucleotide polymorphisms, we compared four models-genomic best linear unbiased prediction, reproducing kernel Hilbert space, BayesC, and light gradient boosting machine-for genotype ranking under four cross-validation schemes: predicting new genotypes (CV1), sparse testing (CV2), leave-one-location-year-out (CV0), and across locations. Model performance was evaluated using Pearson's correlation for overall accuracy and normalized discounted cumulative gain (NDCG@10) for ranking top performers. The four models were similar, with no method dominating across traits. NDCG@10 scores revealed that predictions remained useful for selecting superior genotypes even for difficult traits. Prediction accuracy was strongly associated with heritability and trait correlations across and within- location environments. Accuracy was highest for developmental traits and lowest for seed yield, while seed traits showed location-specific responses with higher accuracy in Australia. These findings support GS as a promising tool for quinoa breeding and provide benchmarks for global implementation.

Quinoa (Chenopodium quinoa) is a nutrient-rich pseudocereal with diverse specialized metabolites, yet the genetic basis of this metabolic diversity is poorly understood. Here we integrate whole-genome sequencing and multi-tissue metabolic profiling of 603 quinoa accessions. We detected 4688 metabolic features and identified over 1000 metabolites in seeds, leaves, and roots. Using multi-tissue genome-wide association, we mapped the genetic architecture of quinoa metabolome by identifying 584 quantitative trait loci (QTL) and prioritized 219 candidate genes across 58 major QTL governing saponin, betalain, and flavonoid biosynthesis. Moreover, we constructed a drought-responsive multi-omics regulatory network and uncovered additional key genes involved in quinoa stress signaling and metabolic pathways. Finally, we cloned and functional validated the roles of cytochrome P450 76AD1 (CYP76AD1) in betalamate accumulation, UDP-glycosyltransferase (UGT91C1) in flavonoid glycosylation, and CYP72A154 and soyasapogenol B glucuronide galactosyltransferase in saponin biosynthesis. This multi-omic framework provides a high-resolution map of the quinoa metabolome and a foundation for breeding nutrient-rich and stress-resilient quinoa cultivars.

Salinity is a global threat to crop production, reducing yields and jeopardizing food and nutrition security. This study was performed to evaluate the salinity tolerance of high-yielding commercial tomato ‘Super Sweet F1’(SS), which was self-grafted, or cross-grafted with salt-tolerant rootstocks ‘Maxifort F1’ (MF), ‘Pimp-M021’(PM), and ‘Ramsi’ (RM). The plants were evaluated at low (18.2 mM NaCl) and high-water salinity (150 mM NaCl). The cross-grafted plants SS/MF and SS/PM showed similar responses under high salinity with increased leaf chlorophyll concentration, relative water content (RWC), membrane stability index (MSI), Na+ and K+ concentration, electrolyte leakage (EL), stomatal conductance, fruit number, and weight, when compared to non-grafted and self-grafted plants. Due to the salt stress, elevated activities of proline, total phenols (TPC), total flavonoids (TFC), polyphenol oxidase (PPO; EC 1.14.18.1), peroxidase (POD; EC 1.11.1.7), catalase (CAT; EC 1.11.1.6), and superoxide dismutase (SOD; EC 1.15.1.1) were also measured in the leaves of SS/MF, SS/PM, and SS/RM in comparison with SS and SS/SS. The principal component biplot analysis confirmed that the grafted tomatoes, SS/MF and SS/PM, showed improved performance under salt stress compared with non-grafted, self-grafted, and cross-grafted SS/RM plants. This study revealed that Pimp-M021’(PM) could be a promising candidate beside the commercial Maxifort F1 (MF) rootstock for tomato under salt stress conditions. Our findings demonstrated the positive effects of salt-tolerant rootstocks on tomato growth, yield, and fruit characteristics, and this could herald a sustainable tomato production practice in salinity-prone areas worldwide.

Membrane transporter annotation has long relied on a homology-centric paradigm that treats evolutionary proximity as a proxy for substrate specificity. Yet transporter functional space is intrinsically long-tailed, partially multi-label, and often decoupled from phylogeny, creating systematic blind spots in substrate-level inference. We reformulate substrate annotation as a chemically coherent multi-label problem and construct benchmarks spanning 70 fine-grained substrate types and 1,352 TC families. We introduce ConTP, an evolution-informed contrastive framework that realigns pretrained protein language model embeddings around substrate semantics rather than sequence similarity, enabling taxon-agnostic, prototype-based inference. In this aligned manifold, cross-family convergence, exemplified by sodium transport across distinct TC superfamilies, and authentic multi-substrate specificity in NRAMP transporters are faithfully recovered. Furthermore, projection of generated sequences exposes substrate-fidelity violations in contemporary design models. Together, these findings support a geometry-aware view of transporter specificity beyond raw evolutionary similarity.

Salinity, projected to impact over 50% of arable land by 2050, threatens tomato-a crop of major agronomic and nutritional value. While salt stress effects on tomato shoot and fruit traits are well studied, the genetic basis of root development under salinity remains underexplored. Roots are the primary sensors of salt stress, making them central to plant adaptation. To uncover the genetic regulators of root system architecture (RSA) under salt, we analyzed a natural diversity panel consisting of 220 wild- and 25 cultivated-tomato varieties. We identified distinct RSA strategies, favouring either lateral root elongation or emergence. An F1 hybrid with superior root architecture under salt stress was used to generate an F2 population for Bulk Segregant Analysis (BSA), and a parallel GWAS was performed across the diversity panel. Integrating BSA and GWAS results yielded 22 candidate genes. RNA-seq analysis of contrasting accessions prioritised four candidates, including an l-ascorbate peroxidase involved in ROS homoeostasis. Further functional analysis revealed genotype-specific H₂O₂ dynamics, and exogenous ascorbate improved K⁺ retention under salt. Together, these results uncover a genetic link between lateral root development, ROS signalling, and ion homoeostasis under salinity, offering new targets for engineering salt-resilient tomato.

The occurrence of external L-glutamate at the Arabidopsis root tip triggers major changes in root architecture, but the mechanism of -L-Glu sensing is unknown. Members of the family of GLUTAMATE RECEPTOR-LIKE (GLR) proteins are known to act as amino acid-gated Ca2+-permeable channels and to have signalling roles in diverse plant processes. To investigate the possible role of GLRs in the root architectural response to L-Glu, we screened a collection of mutants with T-DNA insertions in each of the 20 AtGLR genes. Reduced sensitivity of root growth to L-Glu was found in mutants of one gene, GLR2.5. Interestingly, GLR2.5 was found to apparently produce four transcript variants encoding hypothetical proteins of 169-720 amino acids. One of these transcripts, GLR2.5c, encodes a truncated GLR protein lacking both the conserved amino-terminal domain and part of the ligand-binding domain. When a glr2.5 mutant was transformed with a construct constitutively expressing GLR2.5c, both L-Glu sensitivity of root growth and L-Glu-elicited Ca2+ currents in root tip protoplasts were restored. These results, along with homology modelling of the truncated ligand-binding domain of GLR2.5c, suggest that GLR2.5c has a regulatory or scaffolding role in heteromeric GLR complex(es) that may involve triggering the root architectural response to L-Glu.

Understanding how leaf morphology mediates plant responses to environmental variability is critical for predicting species adaptability under climate change. This study examines whether intraspecific variation in leaf shape among Chenopodium hircinum populations is linked to physiological and functional trait differences and whether such variation reflects adaptive responses to source climate. We cultivated 11 populations of C. hircinum from diverse climatic origins in a common garden experiment. Leaf shape was quantified using descriptors (aspect ratio, circularity, solidity), landmarks, and Elliptical Fourier Descriptors. Physiological traits (stomatal conductance, leaf temperature, chlorophyll content) and functional traits (leaf area, leaf dry weight and leaf mass per area) were measured and analysed in relation to shape and environmental data. Leaf morphology varied significantly among populations and was associated with climatic conditions at origin, especially mean summer temperature. Functional and physiological traits were not directly correlated with environmental variables but showed strong associations with leaf shape. Landmark-based PC2 (lobed vs. rounded forms) and aspect ratio emerged as key predictors of trait variation. Most trait variation occurred at the individual level rather than among populations. Our findings highlight leaf shape as a central mediator linking environmental heterogeneity to physiological function. This suggests that morphology-driven trait integration may enhance adaptability in C. hircinum. Intraspecific diversity in shape and associated traits could serve as a reservoir of resilience under climate change, reinforcing the evolutionary and applied significance of wild relatives in crop improvement.

Climate change induces many abiotic stresses, including soil salinity, significantly challenging global agriculture. Salinity stress tolerance (SST) is a complex trait, both physiologically and genetically, and is conferred at various levels of plant functional organization. As both the sustainability and profitability of agricultural production systems are critically dependent on SST, plant breeders are trying to design and develop salinity-smart crop plants capable of thriving under high salinity conditions. The accessibility of extreme-quality reference genomes for cultivated crops, naturally salinity-smart plants, and crop wild relatives has fast-tracked the discovery of key genes and quantitative trait loci (QTLs), marker development, genotyping assays and molecular breeding products with improved SST. Employing fast-forward breeding tools, namely genomic selection (GS), haplotype-based breeding (HBB), artificial intelligence (AI) and high-throughput phenotyping (HTP), has shown influence not only for fast-tracking genetic gains but also for reducing the time and cost of developing commercial cultivars with enhanced SST and yield stability. This review discusses the advancement and prospects of various genomics-assisted breeding (GAB) tools, including genome sequencing, QTL mapping, GWAS, GS, HBB, pan-genomics, single-cell/tissue genomics and phenotyping, epigenomics and transgenomics, to exploit the genetic landscape for improving SST. Additionally, we explore the integration of HTP and AI, which demonstrates how these innovative approaches can optimize breeding efficiency and guide large-scale breeding efforts for designing salinity-smart crops to ensure sustainable agriculture and global food security. The collective adoption of these tools suggests bridging the gap between research and field application to deliver stress-smart varieties designed for saline-affected regions worldwide.

The occurrence of external L-glutamate at the Arabidopsis root tip triggers major changes in root architecture, but the mechanism of -L-Glu sensing is unknown. Members of the family of GLUTAMATE RECEPTOR-LIKE (GLR) proteins are known to act as amino acid-gated Ca 2+ -permeable channels and to have signalling roles in diverse plant processes. To investigate the possible role of GLRs in the root architectural response to L-Glu, we screened a collection of mutants with T-DNA insertions in each of the 20 AtGLR genes. Reduced sensitivity of root growth to L-Glu was found in mutants of one gene, GLR2.5 . Interestingly, GLR2.5 was found to apparently produce four transcript variants encoding hypothetical proteins of 169–720 amino acids. One of these transcripts, GLR2.5c , encodes a truncated GLR protein lacking both the conserved amino-terminal domain and part of the ligand-binding domain. When a glr2.5 mutant was transformed with a construct constitutively expressing GLR2.5c , both L-Glu sensitivity of root growth and L-Glu-elicited Ca 2+ currents in root tip protoplasts were restored. These results, along with homology modelling of the truncated ligand-binding domain of GLR2.5c, suggest that GLR2.5c has a regulatory or scaffolding role in heteromeric GLR complex(es) that may involve triggering the root architectural response to L-Glu.

Intraspecific variation in plant traits, such as leaf morphology, offers insights into local adaptation and the ecological niche breadth of species. Chenopodium hircinum, the wild ancestor of quinoa, is widely distributed across various ecoregions in Argentina. A detailed comparative analysis of leaf morphology across 23 populations covering its entire known distribution was conducted to understand patterns of intraspecific variation along geographic gradients. A total of 104 leaves from these populations were analysed using shape, landmarks, and Fourier descriptors. Significant variability in leaf shapes was observed across all ecoregions, with notable admixture among populations. Although landmark-based and Fourier analyses differentiated populations, shape descriptors added intricacy to identification. Leaf morphology ranged from rounded and toothed to sharply lobed, with lobes primarily located at the base or middle of the leaf. Key environmental factors influencing leaf shape were mean annual temperature (MAT) and altitude. The study suggests that leaf shape variability in C. hircinum extends beyond a simple lobed vs. entire dichotomy. Leaf morphology and margin traits are primarily governed by the relative position of the lobes, which correlate strongly with MAT at the population’s origin. This convergence across ecoregions highlights the need to explore the functional significance of this variation further.

Understanding how leaf morphology mediates plant responses to environmental variation is essential for predicting species adaptability under climate change. In this study, we investigated natural variation in leaf shape and associated functional– physiological traits (FPTs) across populations of Chenopodium hircinum grown in a common garden. We found that leaf shape strongly correlates with the climatic conditions of population provenance, while functional and physiological traits are independently associated with morphology rather than directly with climate. Landmark-based morphometric analysis revealed that the second principal component, distinguishing deeply lobed from rounded leaves, is significantly linked to key traits such as leaf mass per unit area (LMA) and stomatal conductance. These relationships suggest that morphology mediates a functional continuum between resource-use strategies. Notably, within-population phenotypic variation accounted for much of the observed trait diversity, underscoring the role of individual-level phenotypic plasticity in shaping ecological function. Our results challenge traditional views on the thermoregulatory role of leaf lobation and highlight morphology as a central axis of adaptation. This work advances understanding of trait integration in response to environmental heterogeneity and suggests that plasticity in leaf shape and function may enhance resilience of C . hircinum across its native range. ### Competing Interest Statement The authors have declared no competing interest.

Quinoa (Chenopodium quinoa) is well-known for high nutritional value and wide adaptability, but it is considered to be heat sensitive. To address this issue, accessions from two tetraploid wild relatives, C. berlandieri and C. hircinum, both native to hot environments, were evaluated alongside lowland and highland ecotypes of cultivated quinoa under field conditions with differing planting dates. Chenopodium berlandieri showed the best yield under the extreme heat experienced during the last planting, followed by lowland quinoa, C. hircinum, and highland quinoa. The yield advantage of C. berlandieri was achieved by maintaining higher grain number/seed set. Pollen viability was positively correlated with seed set under heat stress in cultivated quinoa, indicating its limiting effects. Considerable variation was observed for pollen viability among representative accessions of each species/ecotypes after a 38/33 °C day/night treatment for 5 d, ranging from an 80% reduction observed in highland quinoa to a 30% reduction in C. berlandieri. The most heat-sensitive period for pollen viability was 8-10 d before flowering, corresponding to the early pollen mother cell stage and it was conserved among the different species. In vitro pollen germination tests also demonstrated the heat tolerance of C. berlandieri. Taken together, our results suggest that wild relatives, particularly C. berlandieri, could be crossed with cultivated quinoa to introduce reproductive heat tolerance.

Heat stress poses a serious threat to plant survival and productivity, and has a direct influence on crop yield stability. Plants response to high temperature is tightly controlled by complex genetic networks. Plants can be acclimated through gradual pre-exposure to increasing temperatures and that in turn causes higher survival in subsequent and otherwise lethal heat stress conditions. To investigate the physiological and molecular processes underlying heat acclimation and recovery, we examined changes in Arabidopsis thaliana transcriptome throughout the acclimation and the subsequent heat shock treatment. Groups of differentially expressed genes and enriched biological pathways that constitute the heat transcriptional memory were identified. The function of flavonoids in plant heat stress were further explored experimentally. In addition, we observed altered stomata density and aperture responses in heat acclimated plants, and this might be partially controlled by AGAMOUS-LIKE16 ( AGL16 ) transcription factor and its negative regulator microRNA824 ( miR824 ).

Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as Salt Root:shoot Ratio Regulator Gene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that SR3G expression is modulated by WRKY75 transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of wrky75 mutant is completely diminished when it is combined with sr3g mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.

Plant responses to salt stress involve complex processes integrating short- and long-term adaptations, including changes in ion transport, systemic signaling, root architecture, and biomass distribution. A key adaptive mechanism involves the regulation of sodium (Na+) and potassium (K+) ion transport via Class 1 HKT1 transporters, which reduce Na+ accumulation in shoots, thereby enhancing salinity tolerance but at the expense of lateral root development. In this study, we identified differential roles of TMAC2 in modulating ABA accumulation and lateral root development under salt stress in two distinct Arabidopsis genotypes, Col-0 and C24. Overexpression of TMAC2 in the Col-0 background increased ABA accumulation, resulting in reduced lateral root development, suggesting a positive feedback loop involving HKT1, TMAC2, and ABA signaling. In contrast, TMAC2 overexpression in C24 reduced ABA accumulation in lines overexpressing HKT1, indicating genotype-specific differences in the TMAC2-HKT1 interaction. Additionally, we observed that the co-expression of TMAC2 and HKT1 in Col-0 induced ABI4 and ABI5 transcription factors, which are known to mediate salt sensitivity. These findings reveal a regulatory network where TMAC2 and HKT1 modulate salt stress responses through genotype-dependent feedback mechanisms. Our results highlight the complexity of root remodeling under salt stress and the crucial role of genetic background in shaping these adaptive responses. ### Competing Interest Statement The authors have declared no competing interest.

The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.

Grafting can be a useful technology to improve productivity of vegetable crops, including tomato, particularly under the serious challenges of climate change for agricultural systems. This study aimed to evaluate the impact of some local tomato interspecific hybrid rootstocks along with Maxifort on the vegetative growth, productivity, and fruit quality of tomato under field production conditions. Heat-tolerant tomato hybrid 023 F1 was used as a scion over the two late summer seasons of 2021 and 2022. Grafting 023 F1 onto Maxifort or KFS-16 rootstocks resulted in the maximum plant growth. Similarly, Maxifort and KFS-16 rootstocks significantly increased the fruit setting percentage from 22.2% to 23.5% and 17.8% to 24.6%, total fruit yield from 33.5% to 53.7% and 29.6% to 51.6%, and marketable yields from 34.1% to 56.0% and 27.3% to 56.7%, respectively, during both seasons compared with nongrafted plants. These two rootstocks enhanced nutrient (nitrogen, phosphorus, potassium) uptake compared with nongrafted planted. However, grafting with the interspecific hybrid rootstocks (KFS-8 and KWS-9) significantly decreased the content of catalase, peroxidase, and proline, which might be associated with lower plant vigor and yield in these rootstocks. All rootstocks had an impact on fruit chemical composition; however, generally, Maxifort and KFS-16 had greater contents of vitamin C, β-carotene, and total antioxidants than nongrafted plants. KFS-16 had also greater lycopene content than nongrafted plants. These results demonstrate the potential use of Maxifort and local rootstock KFS-16 to boost the growth and yield of tomato plants under high-temperature stress in the late summer season.

Tomatoes are crucial for global food security and agricultural economies. With over 50% of arable land projected to become saline by 2050, understanding tomato responses to saline environments is essential. Soil salinization, prevalent in arid regions, leads to salt stress. Roots are primary salinity sensors and integrate stress responses like nutrient deficiency. Understanding the molecular processes maintaining root growth is vital for crop resilience. While salt stress impacts on tomato seed germination, shoot growth, and fruit yield are documented, root development remains underexplored. Most studies have focused on a limited number of cultivars and their physiological responses, not the genetic basis of salt resilience. Wild tomato relatives, such as Solanum pimpinellifolium , offer traits that are beneficial for breeding resilient crops. However, few studies have examined the genetics of salinity tolerance in S. pimpinellifolium . This study characterizes salt stress-induced changes in root system architecture (RSA) using a natural diversity panel of 220 wild tomato accessions. We identified natural variation in lateral root development and several candidate loci through Genome-Wide Association Study (GWAS). Bulk segregant analysis (BSA) revealed 22 candidate genes overlapping with GWAS findings. Exploring root transcriptome reprogramming in two accessions with differing lateral root responses highlighted genotype-specific changes. Integrating GWAS, BSA, and RNA sequencing data identified four key genes underlying differential lateral root development under salt stress. These findings offer novel genetic targets for improving salt resilience in tomatoes, providing opportunities for future research and breeding programs to enhance crop sustainability and productivity. ### Competing Interest Statement The authors have declared no competing interest.

Quinoa (Chenopodium quinoa) is an important crop for the future challenges of food and nutrient security. Deep characterization of quinoa diversity is needed to support the agronomic improvement and adaptation of quinoa as its worldwide cultivation expands. In this study, we report the construction of chromosome-scale genome assemblies of eight quinoa accessions covering the range of phenotypic and genetic diversity of both lowland and highland quinoas. The assemblies were produced from a combination of PacBio HiFi reads and Bionano Saphyr optical maps, with total assembly sizes averaging 1.28 Gb with a mean N50 of 71.1 Mb. Between 43,733 and 48,564 gene models were predicted for the eight new quinoa genomes, and on average, 66% of each quinoa genome was classified as repetitive sequences. Alignment between the eight genome assemblies allowed the identification of structural rearrangements including inversions, translocations, and duplications. These eight novel quinoa genome assemblies provide a resource for association genetics, comparative genomics, and pan-genome analyses for the discovery of genetic components and variations underlying agriculturally important traits.

Greenhouse agriculture is expected to play a critical role in sustainable crop production in the coming decades, opening new markets in climate zones that have been traditionally unproductive for agriculture. Extreme hot and humid conditions, prevalent in rapidly growing economies including the Arabian Peninsula, present unique design and operational challenges to effective greenhouse climate control. These challenges are often poorly understood by local operators and inadequately researched in the literature. This study addresses this knowledge gap by presenting, for the first time, a comprehensive set of benchmarks for water and energy usage, CO2 2 emissions (CO2e) 2 e) contribution, and economic performance for low-, mid-, and high-tech greenhouse designs in such climates. Utilising a practical and adaptable model-based framework, the analysis reveals the high-tech design generated the best results for economic return, achieving a 4.9-year payback period with superior water efficiency compared to 5.8 years for low-tech and 7.0 years for mid-tech; however, the high-tech design used significantly more energy to operate its mechanical cooling system, corresponding with higher CO2e 2 e per unit area (8.3 and 4.0 times higher than the low- and mid-tech, respectively). These benchmarks provide new insights for greenhouse operators, researchers, and other stakeholders, facilitating the development of effective greenhouse design and operational strategies tailored to meet the challenges of hot and humid climates.