Global warming is negatively impacting on crop yield and Earth's climate changes can bring possible negative effects on the growth and reproductive success of crops ....
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.
Several thrips species (Insecta, Thysanoptera) are globally known as important crop pests and vectors of viral diseases, but their identification is difficult because of their small body size and ...inconspicuous morphological differences. Sequencing variation in the mitochondrial cytochrome c oxidase I (COI) region has been proven to be useful for the identification of species of many groups of insect pests. Here, DNA barcoding has been used to identify thrips species collected with the use of sticky traps placed in an open onion field. A total of 238 thrips specimens were analyzed, 151 of which could be identified to species and 27 to genera belonging to the family Thripidae. Fifty-one specimens could not be assigned to any genus, with the closest BLAST match in the GenBank queries being below 98%, whilst six specimens were not recognized as Thysanoptera. The results indicate that, although there are a few pest thrips species not yet barcoded, most of the species that may cause damage to crops in Europe are represented in GenBank and other databases, enabling correct identification. Additionally, DNA barcoding can be considered a valuable alternative to the classic morphology method for identification of major thrips species.
Fig fruits are usually highly sensitive to some physiopathological disorders during post-harvest life, such as softening and skin cracking. Indeed, the use of edible coating (EC) has been evaluated ...in several fruit crops to reduce fruit post-harvest transpiration and to maintain fruit visual quality. The aim of this study was to determine the post-harvest metabolic response of breba figs treated with mucilage extract from
cladodes, using an untargeted metabolomic approach. Coated and non-coated (control) fruit were sealed in plastic bags, and stored at 4°C for 7 days. The effect of the ECs on their quality fruit during cold storage and qualitative attributes were evaluated by analyzing the fruit primary metabolism and other qualitative parameters such as total soluble solids (TSS) content, titratable acidity (TA), fresh weight loss and firmness. Results underlined that EC was effective in maintaining fruit fresh weight, and fruit firmness. Stepwise discriminant analysis was able to discriminate fruit conditions. Alanine, xylulose, aspartic acid, glutamic, acid and 2,5-dihydroxypyrazine showed a significant role on discriminating edible coated fruit from untreated ones. Principal component analysis (PCA) was able to highlight clear differences in the overall metabolism changes between untreated and treated fruit. The application of EC significantly mitigated the decrease of most of the aminoacid content during cold storage. EC treatment caused the changes of several organic acids in comparison to untreated control, increasing the amount of carbohydrates and other key metabolites, such as beta-sitosterol, glycerol, and uracil. These results clearly showed the drastic effects of EC on fig metabolism during post-harvest and shed light on the beneficial mechanisms of this treatment.
Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal ...endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi-belonging to Aspergillus, Quambalaria and Bjerkandera genera-and bacteria-belonging to Staphylococcus genus-were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.
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.
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.
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.
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.
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.
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.
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 (NO
), 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.
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) NO
resupply.
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
and
, 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 (
), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (
), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (
) and two TFs
and
were identified in the root.
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.
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