Complementing model species with model clades.

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade". These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis thaliana and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.

Elucidating the Genetic Relationships on the Original Old Sicilian Triticum Spp. Collection by SNP Genotyping.

Several Triticum species spread in cultivation in Sicily and neighboring regions over the centuries, which led to the establishment of a large genetic diversity. Many ancient varieties were widely cultivated until the beginning of the last century before being replaced by modern varieties. Recently, they have been reintroduced in cultivation in Sicily. Here, the genetic diversity of 115 and 11 accessions from Sicily and Calabria, respectively, belonging to Triticum species was evaluated using a high-density SNP array. Einkorn, emmer, and spelta wheat genotypes were used as outgroups for species and subspecies; five modern varieties of durum and bread wheat were used as references. A principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) showed four distinct groups among Triticum species and T. turgidum subspecies. The population structure analysis distinguished five gene pools, among which three appeared private to the T. aestivum, T. turgidum subsp. Turgidum, and 'Timilia' group. The principal component analysis (PCA) displayed a bio-morphological trait relationship of a subset (110) of ancient wheat varieties and their wide variability within the T. turgidum subsp. durum subgroups. A discriminant analysis of principal components (DAPC) and phylogenetic analyses applied to the four durum wheat subgroups revealed that the improved varieties harbored a different gene pool compared to the most ancient varieties. The 'Russello' and 'Russello Ibleo' groups were distinguished; both displayed higher genetic variability compared to the 'Timilia' group accessions. This research represents a comprehensive approach to fingerprinting the old wheat Sicilian germplasm, which is useful in avoiding commercial fraud and sustaining the cultivation of landraces and ancient varieties.

Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena.

Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.

Complete genome sequence of a new isolate of caper latent virus in caper.

The genome of a new carlavirus isolate from asymptomatic wild Capparis spinosa L. plants in Sicily was sequenced via high-throughput sequencing (HTS) and 5'/3' RACE experiments. The complete genomic sequence was found to be 8,280 nt in length, excluding the poly(A) tail, and contained five putative open reading frames (ORFs). Molecular characterization revealed a close relationship to caper latent virus (CapLV), with 87% and 90% nucleotide sequence identity to available partial sequences of the ORFs encoding the replicase and coat protein of that virus. According to the molecular criteria for species demarcation, which is based on the ORF-1- and ORF-5-encoded proteins, the virus characterized in this study could be considered a variant of CapLV, and we have thus designated it as CapLV-W.

Correction to: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination.

An amendment to this paper has been published and can be accessed via the original article.

Characterization of Sicilian rosemary (Rosmarinus officinalis L.) germplasm through a multidisciplinary approach.

In Sicily, small differences exist between wild and cultivated rosemary biotypes; VOCs and genetic profiles may be a useful tool to distinguish them. A germplasm collection of Rosmarinus officinalis L. was harvested from 15 locations in Sicily. Eleven wild and four cultivated populations were collected and, due to the surveyed area covered, they can be considered as a representative panel of Sicilian genetic background of the species. Ex situ plant collection was transferred to the field cultivation in homogeneous conditions for characterizing through a multidisciplinary approach. The study included morphological traits observations (growth habitus, flower color, number and size of leaves, length and number of internodes), VOC profiles using HS-SPME, genome size by flow cytometry analysis, and genetic characterization by means of DNA and nuclear microsatellite (nSSR) investigation. To detect any pattern within- and among-populations variability, all morphological and chemical data were submitted to ANOVA, while clustering and structure population analysis were carried out using genetic profiles. The present work allowed us to distinguish rather well between wild and cultivated genotypes and to underline the biodiversity richness among rosemary Sicilian germplasm, never highlighted, useful for future breeding programs addressed to exploit this important resource.

SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination.

BACKGROUND: Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined. RESULTS: A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18 K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved. CONCLUSIONS: This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars.

An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon.

KEY MESSAGE: Our results provide a comprehensive overview how the alloplasmic condition might lead to a significant improvement in citrus plant breeding, developing varieties more adaptable to a wide range of conditions. Citrus cybrids resulting from somatic hybridization hold great potential in plant improvement. They represent effective products resulting from the transfer of organelle-encoded traits into cultivated varieties. In these cases, the plant coordinated array of physiological, biochemical, and molecular functions remains the result of integration among different signals, which derive from the compartmentalized genomes of nucleus, plastids and mitochondria. To dissect the effects of genome rearrangement into cybrids, a multidisciplinary study was conducted on a diploid cybrid (C2N), resulting from a breeding program aimed to improve interesting agronomical traits for lemon, the parental cultivars 'Valencia' sweet orange (V) and 'femminello' lemon (F), and the corresponding somatic allotetraploid hybrid (V + F). In particular, a differential proteomic analysis, based on 2D-DIGE and MS procedures, was carried out on leaf proteomes of C2N, V, F and V + F, using the C2N proteome as pivotal condition. This investigation revealed differentially represented protein patterns that can be associated with genome rearrangement and cell compartment interplay. Interestingly, most of the up-regulated proteins in the cybrid are involved in crucial biological processes such as photosynthesis, energy production and stress tolerance response. The cybrid differential proteome pattern was concomitant with a general increase of leaf gas exchange and content of volatile organic compounds, highlighting a stimulation of specific pathways that can be related to observed plant performances. Our results contribute to a better understanding how the alloplasmic condition might lead to a substantial improvement in plant breeding, opening new opportunities to develop varieties more adaptable to a wide range of conditions.

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis).

Sex chromosomes have evolved independently in phylogenetically diverse flowering plant lineages. The genes governing sex determination in dioecious species remain unknown, but theory predicts that the linkage of genes influencing male and female function will spur the origin and early evolution of sex chromosomes. For example, in an XY system, the origin of an active Y may be spurred by the linkage of female suppressing and male promoting genes. Garden asparagus (Asparagus officinalis) serves as a model for plant sex chromosome evolution, given that it has recently evolved an XX/XY sex chromosome system. In order to elucidate the molecular basis of gender differences and sex determination, we used RNA-sequencing (RNA-Seq) to identify differentially expressed genes between female (XX), male (XY) and supermale (YY) individuals. We identified 570 differentially expressed genes, and showed that significantly more genes exhibited male-biased than female-biased expression in garden asparagus. In the context of anther development, we identified genes involved in pollen microspore and tapetum development that were specifically expressed in males and supermales. Comparative analysis of genes in the Arabidopsis thaliana, Zea mays and Oryza sativa anther development pathways shows that anther sterility in females probably occurs through interruption of tapetum development before microspore meiosis.

Integrated omics approach reveals the molecular pathways activated in tomato by Kocuria rhizophila, a soil plant growth-promoting bacterium.

Plant microbial biostimulants application has become a promising and eco-friendly agricultural strategy to improve crop yields, reducing chemical inputs for more sustainable cropping systems. The soil dwelling bacterium Kocuria rhizophila was previously characterized as Plant Growth Promoting Bacteria (PGPB) for its multiple PGP traits, such as indole-3-acetic acid production, phosphate solubilization capability and salt and drought stress tolerance. Here, we evaluated by a multi-omics approach, the PGP activity of K. rhizophila on tomato, revealing the molecular pathways by which it promotes plant growth. Transcriptomic analysis showed several up-regulated genes mainly related to amino acid metabolism, cell wall organization, lipid and secondary metabolism, together with a modulation in the DNA methylation profile, after PGPB inoculation. In agreement, proteins involved in photosynthesis, cell division, and plant growth were highly accumulated by K. rhizophila. Furthermore, "amino acid and peptides", "monosaccharides", and "TCA" classes of metabolites resulted the most affected by PGPB treatment, as well as dopamine, a catecholamine neurotransmitter mediating plant growth through S-adenosylmethionine decarboxylase (SAMDC), a gene enhancing the vegetative growth, up-regulated in tomato by K. rhizophila treatment. Interestingly, eight gene modules well correlated with differentially accumulated proteins (DAPs) and metabolites (DAMs), among which two modules showed the highest correlation with nine proteins, including a nucleoside diphosphate kinase, and cytosolic ascorbate peroxidase, as well as with several amino acids and metabolites involved in TCA cycle. Overall, our findings highlighted that sugars and amino acids, energy regulators, involved in tomato plant growth, were strongly modulated by the K. rhizophila-plant interaction.

Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes.

Background: Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO3 -), acting as both an N source and a signal molecule, provokes very fast transcriptome reprogramming, allowing plants to adapt to its availability. These changes are genotype- and tissue-specific; thus, the comparison between contrasting genotypes is crucial to uncovering high NUE mechanisms. Methods: Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO3 - resupply. Results: Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2, and NPF8.3, were found differentially expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions in short-term LN regulation. In particular, an asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (UGT73C4), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. Discussion: Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.

Exploring the genetic landscape of nitrogen uptake in durum wheat: genome-wide characterization and expression profiling of NPF and NRT2 gene families.

Nitrate uptake by plants primarily relies on two gene families: Nitrate transporter 1/peptide transporter (NPF) and Nitrate transporter 2 (NRT2). Here, we extensively characterized the NPF and NRT2 families in the durum wheat genome, revealing 211 NPF and 20 NRT2 genes. The two families share many Cis Regulatory Elements (CREs) and Transcription Factor binding sites, highlighting a partially overlapping regulatory system and suggesting a coordinated response for nitrate transport and utilization. Analyzing RNA-seq data from 9 tissues and 20 cultivars, we explored expression profiles and co-expression relationships of both gene families. We observed a strong correlation between nucleotide variation and gene expression within the NRT2 gene family, implicating a shared selection mechanism operating on both coding and regulatory regions. Furthermore, NPF genes showed highly tissue-specific expression profiles, while NRT2s were mainly divided in two co-expression modules, one expressed in roots (NAR2/NRT3 dependent) and the other induced in anthers and/ovaries during maturation. Our evidences confirmed that the majority of these genes were retained after small-scale duplication events, suggesting a neo- or sub-functionalization of many NPFs and NRT2s. Altogether, these findings indicate that the expansion of these gene families in durum wheat could provide valuable genetic variability useful to identify NUE-related and candidate genes for future breeding programs in the context of low-impact and sustainable agriculture.

Transcriptome changes induced by Arbuscular mycorrhizal symbiosis in leaves of durum wheat (Triticum durum Desf.) promote higher salt tolerance.

The salinity of soil is a relevant environmental problem around the world, with climate change raising its relevance, particularly in arid and semiarid areas. Arbuscular Mycorrhizal Fungi (AMF) positively affect plant growth and health by mitigating biotic and abiotic stresses, including salt stress. The mechanisms through which these benefits manifest are, however, still unclear. This work aimed to identify key genes involved in the response to salt stress induced by AMF using RNA-Seq analysis on durum wheat (Triticum turgidum L. subsp. durum Desf. Husn.). Five hundred sixty-three differentially expressed genes (DEGs), many of which involved in pathways related to plant stress responses, were identified. The expression of genes involved in trehalose metabolism, RNA processing, vesicle trafficking, cell wall organization, and signal transduction was significantly enhanced by the AMF symbiosis. A downregulation of genes involved in both enzymatic and non-enzymatic oxidative stress responses as well as amino acids, lipids, and carbohydrates metabolisms was also detected, suggesting a lower oxidative stress condition in the AMF inoculated plants. Interestingly, many transcription factor families, including WRKY, NAC, and MYB, already known for their key role in plant abiotic stress response, were found differentially expressed between treatments. This study provides valuable insights on AMF-induced gene expression modulation and the beneficial effects of plant-AMF interaction in durum wheat under salt stress.

Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy.

Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.

Bioactive Metabolite Survey of Actinobacteria Showing Plant Growth Promoting Traits to Develop Novel Biofertilizers.

The use of chemical fertilizers and pesticides has caused harmful impacts on the environment with the increase in economic burden. Biofertilizers are biological products containing living microorganisms capable of improving plant growth through eco-friendly mechanisms. In this work, three actinobacterial strains Streptomyces violaceoruber, Streptomyces coelicolor, and Kocuria rhizophila were characterized for multiple plant growth promoting (PGP) traits such as indole acetic acid production, phosphate solubilization, N2-fixation, and drought and salt tolerance. Then, these strains were investigated for their secreted and cellular metabolome, revealing a rich arsenal of bioactive molecules, including antibiotics and siderophores, with S. violaceoruber being the most prolific strain. Furthermore, the in vivo assays, performed on tomato (Solanum lycopersicum L.), resulted in an improved germination index and the growth of seedlings from seeds treated with PGP actinobacteria, with a particular focus on S. violaceoruber cultures. In particular, this last strain, producing volatile organic compounds having antimicrobial activity, was able to modulate volatilome and exert control on the global DNA methylation of tomato seedlings. Thus, these results, confirming the efficacy of the selected actinobacteria strains in promoting plant growth and development by producing volatile and non-volatile bioactive molecules, can promote eco-friendly alternatives in sustainable agriculture.

Rootstocks with Different Tolerance Grade to Citrus Tristeza Virus Induce Dissimilar Volatile Profile in Citrus sinensis and Avoidance Response in the Vector Aphis gossypii Glover.

The citrus tristeza virus (CTV) is an agent of devastating epidemics of the citrus plant grafted on Citrus aurantium, one of the main rootstocks still used in the Mediterranean area. Consequently, CTV-tolerant alternative citrus rootstocks are considered necessary to manage this disease and/or its vector; that in Mediterranean countries is the aphid Aphis gossypii. In this study, we analyzed the VOCs emitted from Citrus sinensis plants grafted on the CTV-susceptible C. aurantium and on the CTV-tolerant Volkamer lemon, Forner-Alcaide no. 5, and Carrizo citrange. Furthermore, the aphid preference/avoidance response toward these combinations was evaluated in a semi-field experiment. The VOC profiles recorded on the leaves of C. sinensis grafted on the four rootstocks listed above showed significant differences in the abundances and ratios of the compounds emitted. The behavioral experiments indicated that A. gossypii prefers to orient and establish on the C. sinensis plants grafted on C. aurantium rather than on that grafted on the three CTV-tolerant varieties. The possibility that this avoidance mechanism is triggered by the different profile of the VOC emitted by the different combinations and the consequent susceptibility/tolerance shown toward CTV is discussed.

Different Cell Types Affect the Transition from Juvenile to Mature Phase in Citrus Plants Regenerated through Somatic Embryogenesis.

Robust protocols for the regeneration of somatic embryos in vitro are essential for the efficient use of the most modern biotechnologies. Unfortunately, in perennial trees such as Citrus, plants regenerated from juvenile tissues usually exhibit strong, undesirable juvenile characters such as thorny habit and delayed flowering and fruit production. In this work, we tested whether the cell types (nucellar and stigma/style) used to regenerate Citrus plants through somatic embryogenesis affected the transition from the juvenile to mature phase. The results show that regenerants from nucellar cells presented persistent juvenile characters, whereas plants originating from stigma/style explants transited to the mature phase more rapidly. Our observations support the hypothesis that the totipotent cells originated from different cell types are not equivalent, possibly by maintaining memory of their previously differentiated state.

WRKY Gene Family Drives Dormancy Release in Onion Bulbs.

Onion (Allium cepa L.) is an important bulb crop grown worldwide. Dormancy in bulbous plants is an important physiological state mainly regulated by a complex gene network that determines a stop of vegetative growth during unfavorable seasons. Limited knowledge on the molecular mechanisms that regulate dormancy in onion were available until now. Here, a comparison between uninfected and onion yellow dwarf virus (OYDV)-infected onion bulbs highlighted an altered dormancy in the virus-infected plants, causing several symptoms, such as leaf striping, growth reduction, early bulb sprouting and rooting, as well as a lower abscisic acid (ABA) level at the start of dormancy. Furthermore, by comparing three dormancy stages, almost five thousand four hundred (5390) differentially expressed genes (DEGs) were found in uninfected bulbs, while the number of DEGs was significantly reduced (1322) in OYDV-infected bulbs. Genes involved in cell wall modification, proteolysis, and hormone signaling, such as ABA, gibberellins (GAs), indole-3-acetic acid (IAA), and brassinosteroids (BRs), that have already been reported as key dormancy-related pathways, were the most enriched ones in the healthy plants. Interestingly, several transcription factors (TFs) were up-regulated in the uninfected bulbs, among them three genes belonging to the WRKY family, for the first time characterized in onion, were identified during dormancy release. The involvement of specific WRKY genes in breaking dormancy in onion was confirmed by GO enrichment and network analysis, highlighting a correlation between AcWRKY32 and genes driving plant development, cell wall modification, and division via gibberellin and auxin homeostasis, two key processes in dormancy release. Overall, we present, for the first time, a detailed molecular analysis of the dormancy process, a description of the WRKY-TF family in onion, providing a better understanding of the role played by AcWRKY32 in the bulb dormancy release. The TF co-expressed genes may represent targets for controlling the early sprouting in onion, laying the foundations for novel breeding programs to improve shelf life and reduce postharvest.

Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant.

Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30-40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant.

Nitrate uptake along the maize primary root: an integrated physiological and molecular approach.

The spatial variability of the nitrate (NO3-) uptake along the maize primary root axis was investigated at physiological and molecular levels. Net NO3- uptake rate (NNUR) and its kinetic parameters, together with the gene expression of a high-affinity NO3- transporter (NRT2.1), were evaluated. The activity and the expression of plasma membrane H⁺ -ATPase (PM H⁺ -ATPase), key enzyme in plant nutrition, were also analysed. The NNUR showed a heterogeneous spatial pattern along the root, where the regions closer to the root tip early exhibited higher capacity to absorb NO3- than the basal regions, because of a higher maximum NNUR and faster induction of the inducible high-affinity transport system (iHATS), the presence of the high-affinity transport system (HATS) also at external NO3- concentrations >100 µm and an improved NO3- transport because of lower K(m) values. ZmNRT2.1 transcript abundances were not spatially correlated with NNUR, suggesting that post-translational effects or NAR2 protein co-expression could be involved. By contrast, PM H⁺ -ATPase displayed a similar spatial-temporal pattern as that of nitrate uptake, resulting in higher activity in the root tip than in the basal regions. Increased activities of the enzyme after nitrate supply resulted in enhanced expression of MAH3 and MAH4, PM H⁺ -ATPase subfamily II genes, while MAH1 was not expressed.