31 research outputs found
Approfondimenti genetico-molecolari sulle risposte del pomodoro (Solanum lycopersicum L.) a stress ambientali
No full textTomato (Solanum lycopersicum L.) is one of the most important vegetable crops from the Solanaceae family extensively used across the globe for edible purposes. While with the rising population, agricultural demands have increased, recent climate changes have posed a huge threat to agricultural practices and food security. Major challenges include abiotic stress induced by rapid climate changes and biotic stress by a vast array of fast-evolving pathogens causing massive economic losses. Crop improvement using breeding and advancements in genomics and gene editing technologies is one of the most promising ways to overcome these challenges.
Toward this goal, this thesis is aimed to explore the genetic aspects of important agronomic traits in tomato. The focus of the three thesis chapters was mainly on understanding genomic and transcriptomic characteristics and changes happening between varieties with contrasting traits. Further emphasis was given to exploring the molecular pathways, use of vastly available public genomic data and developing resources and understanding in the context of plant breeding.
The first chapter was aimed at the genomic characterization of an important pre-breeding line A10 which carries many desirable traits like high anthocyanin content, tolerance to high pH, and resistance to blossom end rot. Genomic data from A10 was used to profile variants and their putative role in traits. Further, to understand the ancestry and introgressions from wild Solanum varieties, publicly available whole genome datasets of cultivars and wild lines were analysed and compared with A10. Results showing a close relationship of A10 with wild lines and characterization of introgressed genomic regions will further serve as a resource for the subsequent chapter exploring the genetic basis of blossom end rot.
The second chapter focused on Blossom end rot (BER); a physiological disorder characterized by necrotic lesions at the blossom end of tomato fruit. A10, a pre-breeding line with resistance against BER was studied to understand transcriptomic changes in BER-resistant and susceptible lines under water stress and well-watered conditions. The resistant A10 line to BER showed changes in important Ca2+-related genes and stomatal density-related genes which can play an important role in BER resistance.
Finally, the third chapter focused on the Late blight disease caused by the fungal agent Phytophthora infestans infecting tomato fruit and foliage. To understand disease dynamics, transcriptome sequencing was carried out to evaluate the gene expression dynamics of tomato varieties, resistant and susceptible to Phytophthora infection. Next, single nucleotide polymorphisms (SNPs) were studied by integrating the transcriptome dataset with large-scale public genomic data of varieties with known disease phenotypes. Subsequently, a panel of SNP markers correlated with disease resistance were identified and validated on multiple breeding lines with contrasting phenotypes for late blight resistance. The results generated by this study show a correlation with disease resistance across a broad set of plant materials that can be used as markers for molecular screening in tomato breeding
ASV vs OTUs clustering: Effects on alpha, beta, and gamma diversities in microbiome metabarcoding studies
No full textIn microbial community sequencing, involving bacterial ribosomal 16S rDNA or fungal ITS, the targeted genes are the basis for taxonomical assignment. The traditional bioinformatical procedure has for decades made use of a clustering protocol by which sequences are pooled into packages of shared percent identity, typically at 97%, to yield Operational Technical Units (OTUs). Progress in the data processing methods has however led to the possibility of minimizing technical sequencers errors, which were the main reason for the OTU choice, and to analyze instead the exact Amplicon Sequence Variants (ASV) which is a choice yielding much less agglomerated reads. We have tested the two procedures on the same 16S metabarcoded bacterial amplicons dataset encompassing a series of samples from 17 adjacent habitats, taken across a 700 meter-long transect of different ecological conditions unfolding in a gradient spanning from cropland, through meadows, forest and all successional transitions up to the seashore, within the same coastal area. This design allowed to scan a high biodiversity basin and to measure alpha, beta and gamma diversity of the area, to verify the effect of the bioinformatics on the same data as concerns the values of ten different ecological indexes and other parameters. Two levels of progressive OTUs clustering, (99% and 97%) were compared with the ASV data. The results showed that the OTUs clustering proportionally led to a marked underestimation of the ecological indicators values for species diversity and to a distorted behaviour of the dominance and evenness indexes with respect to the direct use of the ASV data. Multivariate ordination analyses resulted also sensitive in terms of tree topology and coherence. Overall, data support the view that reference-based OTU clustering carries several misleading disadvantageous biases, including the risk of missing novel taxa which are yet unreferenced in databases. Since its alternatives as de novo clustering have on the other hand drawbacks due to heavier computational demand and results comparability, especially for environmental studies which contain several yet uncharacterized species, the direct ASV based analysis, at least for prokaryotes, appears to warrant significand advantages in comparison to OTU clustering at every level of percent identity cutoff
Transcriptome-Assisted SNP Marker Discovery for Phytophthora infestans Resistance in Solanum lycopersicum L.
No full textLate blight, caused by oomycetes Phytophthora infestans is one of the most challenging fungal diseases to manage in tomato plants (Solanum lycopersicum L.). Toward managing the disease, conventional breeding has successfully introgressed genetic loci conferring disease resistance from various wild relatives of tomato into commercial varieties. The cataloging of disease-associated SNP markers and a deeper understanding of disease-resistance mechanisms are needed to keep up with the demand for commercial varieties resistant against emerging pathogen strains. To this end, we performed transcriptome sequencing to evaluate the gene expression dynamics of tomato varieties, resistant and susceptible to Phytophthora infection. Further integrating the transcriptome dataset with large-scale public genomic data of varieties with known disease phenotypes, a panel of single nucleotide polymorphism (SNP) markers correlated with disease resistance was identified. These SNPs were then validated on 31 lines with contrasting phenotypes for late blight. The identified SNPs are located on genes coding for a putative cysteine-rich transmembrane module (CYSTM), Solyc09g098310, and a nucleotide-binding site–leucine-rich repeat protein, Solyc09g098100, close to the well-studied Ph-3 resistance locus known to have a role in plant immunity against fungal infections. The panel of SNPs generated by this study using transcriptome sequencing showing correlation with disease resistance across a broad set of plant material can be used as markers for molecular screening in tomato breeding
Valutazione della diversità microbica del suolo di tre spiagge dell’altopiano di Devon (Devon Island, Nunavut, Canada)
No full textLa regione artica si contraddistingue per temperature rigide, un ecosistema unico e un microbiota
del suolo peculiare. Quest’ultimo svolge un ruolo cruciale nel ciclo dei nutrienti, nella
decomposizione della materia organica, nelle emissioni di gas serra e nel funzionamento generale
dell'ecosistema. È fondamentale comprendere in modo completo i processi ecologici in questo
ambiente in rapida evoluzione e minacciato dai cambiamenti climatici, aumentando le conoscenze
sulle caratteristiche e le dinamiche del microbiota dei suoli artici. In questo studio, abbiamo
confrontato i profili microbici di tre spiagge soggette ad incendi naturali, situate sull'isola di Devon
(Nunavut, CA), al fine di esplorarne le somiglianze e le differenze. I campioni sono stati prelevati
verticalmente dal solum al permafrost, da ciascuna spiaggia (AB1, AB2, AB3). Successivamente, il
DNA microbico del suolo è stato isolato e sottoposto a sequenziamento del gene 16S rRNA. La
quantificazione del DNA totale ha rivelato quantità comparabili di materiale genetico nelle tre
spiagge (AB1 μ=2.99±2.39 μg∙g-1, AB2 μ=3.25±3.21 μg∙g-1, AB3 μ=2.57±1.78 μg∙g-1),
indipendentemente dall'età dell'area investigata (AB1=6728 YBP, AB2=2362 YBP, AB3=8412 YBP). Il suolo superficiale ha mostrato un contenuto di DNA significativamente maggiore (p<0.01)
(μ=4.83±2.04 μg∙g-1) rispetto agli strati profondi (μ=0.03±0.01 μg∙g-1) e al permafrost (μ=0.03±0.01 μg∙g-1). Riguardo alla ricchezza tassonomica, è interessante notare che la spiaggia AB1, temporalmente più vicina alla spiaggia AB3, mostra un numero significativamente maggiore (p<0.01) di taxa rispetto ad AB3. Tuttavia, la spiaggia AB1 non mostra una differenza significativa nella ricchezza in taxa rispetto alla spiaggia AB2. Nonostante la mancanza di differenze sostanziali a livello di diversità alpha, le nostre osservazioni indicano che la profondità rappresenta uno dei fattori chiave responsabili del clustering delle comunità microbiche, come evidenziato dalla significatività di PERMANOVA (p<0.01) ed ANOSIM (R=0.5061, p<0.01). Infine, l'analisi del core microbiome rivela che gli Actinobacteriota, i Proteobacteria e i Firmicutes sono i tre phyla predominanti, con abbondanze relative rispettivamente del 38%, 21% e 17%. In conclusione, (i) il DNA totale del suolo è una molecola relativamente stabile che può essere rilevata ed analizzata anche dopo un lungo periodo di tempo, (ii) un evento sconosciuto, verificatosi tra la formazione delle spiagge AB3 e AB1, ha portato ad un significativo aumento della ricchezza in taxa in AB1, (iii) la profondità del suolo esercita un'importante influenza sulla composizione ed il clustering delle comunità microbiche e (iv) l'analisi del core microbiome conferma che gli incendi, anche in un ambiente crioturbato, sembrano favorire la predominanza di Actinobacteriota, Proteobacteria e Firmicutes
Microbial Diversity of Reconstituted, Degraded, and Agricultural Soils Assessed by 16S rDNA Multi-Amplicon Sequencing
No full textPlant species dominance over PFAAs in structuring bacterial communities and their functional profiles in treatment wetlands
No full textThis study investigates the impact of different plant species (Iris pseudacorus L., Phragmites australis (Cav.) Trin. Ex Steud., Typha latifolia L.) and solutions containing increasing perfluoroalkyl acids (PFAAs) concentrations (11 perfluorocarboxylic acids and three perfluorosulfonic acids, 500, 2500, and 5000 ng L−1, each) on bacterial communities in treatment wetland (TW) mesocosm systems. The aim was to rank the respective importance of plant species and pollutant concentration in shaping the structure of the selected bacterial communities. While microbial community structure was mainly a function of plant species, PFAAs had some effect on the predictable bacterial functional profiles. Among the tested species, Typha demonstrated exceptional versatility in supporting bacterial communities with enhanced nitrogen, sulfur, and organic compound metabolism, outperforming Iris and Phragmites. Different PFAA concentrations did not modify the overall taxonomical community structure, although they significantly altered the relative abundances of single functional groups. The observed variations in taxonomy-predictable functional groups highlighted the impact of PFAAs on specific plant bacteria, with potential implications also for the metabolism of other specific compounds. The study also identified distinct bacterial functional profiles associated with specific plant species, revealing that bacteria linked to Typha exhibited more specialized functions, while those associated with Phragmites qualified more within the generalist category. This suggests that Typha may be particularly suitable for TWs under PFAA-rich wastewaters, due to its ability to support the metabolism of organic compounds. Additionally, results indicated that phylum diversity may be used as a reliable proxy of functional diversity patterns. Overall, this study contributes to cast light on the intricate relationships between plant species, PFAA concentrations, and bacterial communities and their catabolic functions, which provides an exploitable advancement of knowledge for the optimization of treatment wetlands
Transcriptional and Physiological Analyses to Assess the Effects of a Novel Biostimulant in Tomato
No full text: This work aimed to study the effects in tomato (Solanum lycopersicum L.) of foliar applications of a novel calcium-based biostimulant (SOB01) using an omics approach involving transcriptomics and physiological profiling. A calcium-chloride fertilizer (SOB02) was used as a product reference standard. Plants were grown under well-watered (WW) and water stress (WS) conditions in a growth chamber. We firstly compared the transcriptome profile of treated and untreated tomato plants using the software RStudio. Totally, 968 and 1,657 differentially expressed genes (DEGs) (adj-p-value < 0.1 and |log2(fold change)| ≥ 1) were identified after SOB01 and SOB02 leaf treatments, respectively. Expression patterns of 9 DEGs involved in nutrient metabolism and osmotic stress tolerance were validated by real-time quantitative reverse transcription PCR (RT-qPCR) analysis. Principal component analysis (PCA) on RT-qPCR results highlighted that the gene expression profiles after SOB01 treatment in different water regimes were clustering together, suggesting that the expression pattern of the analyzed genes in well water and water stress plants was similar in the presence of SOB01 treatment. Physiological analyses demonstrated that the biostimulant application increased the photosynthetic rate and the chlorophyll content under water deficiency compared to the standard fertilizer and led to a higher yield in terms of fruit dry matter and a reduction in the number of cracked fruits. In conclusion, transcriptome and physiological profiling provided comprehensive information on the biostimulant effects highlighting that SOB01 applications improved the ability of the tomato plants to mitigate the negative effects of water stress
Difference in composition and functional analysis of bacterial communities between Mytilus galloprovincialis gills and surrounding water in a brackish inshore bay, analyzed by 16S rDNA multi-amplicon sequencing
No full textBackground. Lagoons are important natural systems, with attractive favorable conditions for aquaculture production, such as shellfish cultivation. Despite their socio-economic relevance for human activity, information on the microbial diversity, community composition, and putative functions of gill-associated microbiota and seawater is still limited, particularly as regards the extent of specific taxa enrichment within the gills and the relative effects of the temporal and spatial variables. In this study, we used a 16S rDNA multi-amplicon sequencing approach using an Ion GeneStudio S5 System and a function prediction method (Functional Annotation of Prokaryotic Taxa (FAPROTAX), to inspect
the springtime dynamics of microbial communities and their inferred metabolic features in an Adriatic lagoon (Po Delta, Italy).
Results. Mussels and surrounding seawater were sampled in two rearing areas three times between April and June 2021. Sequencing results showed significant (p ≤ 0.05) differences in bacterial community composition and diversity between gills and seawater. Gills were dominated by the Methylobacterium-Methylorubrum and Burkholderia-Caballeronia-Paraburkholderia genera, while in seawater samples Izamaplasma, Planktomarina, and Candidatus Aquiluna were detected as being dominant. The microbiota composition did not differ significantly between the two rearing areas. The sampling time, although limited to a 3-month timeframe, instead revealed a structural variation of the bacterial profile both in gills and seawater for alpha and beta diversities respectively. The functional prediction analysis highlighted an overexpression of human gut-associated bacteria in relation to the season-related increase in seawater temperature.
Conclusions. These findings enhance our understanding of the differences between gill-associated and seawater microbiota composition and provide novel insights into the functions carried out by bacteria inhabiting these niches, as well as on the key host-symbiont relationships of bivalves in lagoon environments
Classification of Grain Amaranths Using Chromosome-Level Genome Assembly of Ramdana, A. hypochondriacus
No full textIn the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Toward this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman (A.hyp.V.2.1). The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly Amaranthus cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few
Multi-omics analysis reveals molecular and biochemical mechanisms underlying alkaline stress adaptation in Solanum lycopersicum L
No full textAlkaline stress poses a major constraint that limits tomato (Solanum lycopersicum L.) productivity worldwide by disrupting ion homeostasis and causing oxidative damage, yet the underlying genotype-dependent mechanisms remain incompletely understood. This study employed an integrative multi-omics approach combining transcriptomics, targeted RT-qPCR validation, biochemical assays, and ionomic profiling to investigate contrasting responses in two tomato genotypes, A10 (tolerant) and M56 (sensitive). Plants were hydroponically grown under control (pH 5.9) and alkaline stress conditions (pH 8.2 and 9.2, adjusted with NaOH) in a controlled environment. Principal component analysis of the RNA-Seq data confirmed distinct genotype-dependent clustering under stress. Comprehensive transcriptomic analyses revealed that A10 exhibited extensive transcriptional reprogramming, with over 500 differentially expressed genes and significant enrichment of MAPK-ethylene signalling and glutamate decarboxylase (SlGAD1, SlGAD2) pathways, with RT-qPCR validation supporting differential expression of key ion transporters (HKT1;1, HKT1;2, SOS1). In contrast, M56 displayed minimal transcriptional adjustments (<50 DEGs). Biochemical analyses confirmed genotype-specific osmoprotectant accumulation: A10 showed significant increases in proline (+37 %) and polyphenols (+96 %) at high pH, while M56 levels declined. Free amino acid profiling further revealed that A10 maintained elevated GABA and glutamate content under stress, supporting metabolic adjustments that sustain osmotic balance. Ionomic analysis demonstrated that A10 effectively restricted Na+ accumulation (4 and 5-fold increase) compared to M56's higher influx (6.5 and 9-fold), while maintaining K+ levels and a more favourable K+/Na+ ratio. These integrated results indicate that A10's superior tolerance involves coordinated transcriptional, metabolic, and ionic responses that mitigate osmotic and oxidative stress. This work identifies robust candidate pathways and genes for breeding alkaline-tolerant tomato cultivars to support sustainable production in high-pH soils
