A low-cost parallel implementation of direct numerical simulation of wall turbulence

A numerical method for the direct numerical simulation of incompressible wall turbulence in rectangular and cylindrical geometries is presented. The distinctive feature resides in its design being targeted towards an efficient distributed-memory parallel computing on commodity hardware. The adopted discretization is spectral in the two homogeneous directions; fourth-order accurate, compact finite-difference schemes over a variable-spacing mesh in the wall-normal direction are key to our parallel implementation. The parallel algorithm is designed in such a way as to minimize data exchange among the computing machines, and in particular to avoid taking a global transpose of the data during the pseudo-spectral evaluation of the non-linear terms. The computing machines can then be connected to each other through low-cost network devices. The code is optimized for memory requirements, which can moreover be subdivided among the computing nodes. The layout of a simple, dedicated and optimized computing system based on commodity hardware is described. The performance of the numerical method on this computing system is evaluated and compared with that of other codes described in the literature, as well as with that of the same code implementing a commonly employed strategy for the pseudo-spectral calculation.Comment: To be published in J. Comp. Physic

Inheritance analysis and identification of SNP markers associated with ZYMV resistance in Cucurbita pepo

[EN] Cucurbit crops are economically important worldwide. One of the most serious threats to cucurbit production is Zucchini yellow mosaic virus (ZYMV). Several resistant accessions were identified in Cucurbita moschata and their resistance was introgressed into Cucurbita pepo. However, the mode of inheritance of ZYMV resistance in C. pepo presents a great challenge to attempts at introgressing resistance into elite germplasm. The main goal of this work was to analyze the inheritance of ZYMV resistance and to identify markers associated with genes conferring resistance. An Illumina GoldenGate assay allowed us to assess polymorphism among nine squash genotypes and to discover six polymorphic single-nucleotide polymorphisms (SNPs) between two near-isogenic lines, "True French" (susceptible to ZYMV) and Accession 381e (resistant to ZYMV). Two F-2 and three BC1 populations obtained from crossing the ZYMV-resistant Accession 381e with two susceptible ones, the zucchini True French and the cocozelle "San Pasquale," were assayed for ZYMV resistance. Molecular analysis revealed an approximately 90% association between SNP1 and resistance, which was confirmed using High Resolution Melt (HRM) and a CAPS marker. Co-segregation up to 72% in populations segregating for resistance was observed for two other SNP markers that could be potentially linked to genes involved in resistance expression. A functional prediction of proteins involved in the resistance response was performed on genome scaffolds containing the three SNPs of interest. Indeed, 16 full-length pathogen recognition genes (PRGs) were identified around the three SNP markers. In particular, we discovered that two nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-encoding genes were located near the SNP1 marker. The investigation of ZYMV resistance in squash populations and the genomic analysis performed in this work could be useful for better directing the introgression of disease resistance into elite C. pepo germplasm.This work was supported by the Ministry of University and Research (GenHORT project).Capuozzo, C.; Formisano, G.; Iovieno, P.; Andolfo, G.; Tomassoli, L.; Barbella, M.; Picó Sirvent, MB.... (2017). Inheritance analysis and identification of SNP markers associated with ZYMV resistance in Cucurbita pepo. Molecular Breeding. 37(8). https://doi.org/10.1007/s11032-017-0698-5S378Addinsoft (2007) XLSTAT, Analyse de données et statistique avec MS Excel. Addinsoft, NYAndolfo G, Ercolano MR (2015) Plant innate immunity multicomponent model. Front Plant Sci 6:987Andolfo G, Sanseverino W, Rombauts S et al (2013) Overview of tomato (Solanum lycopersicum) candidate pathogen recognition genes reveals important Solanum R locus dynamics. 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APPROCCI INTEGRATI PER LO STUDIO DEI MECCANISMI FISIOLOGICI E MOLECOLARI DI RISPOSTA AGLI STRESS IDRICI E TERMICI IN POMODORO

Il pomodoro (Solanum lycopersicum) è una delle più importanti specie vegetali coltivate al mondo. La crescita, lo sviluppo e la produttività del pomodoro sono fortemente influenzati dagli stress abiotici come ad esempio ridotta disponibilità d’acqua ed elevate temperature. Lo sviluppo di varietà di pomodoro in grado di garantire buone rese produttive e ottime caratteristiche qualitative dei frutti anche in condizioni ambientali non ottimali, è uno degli obiettivi del miglioramento genetico di questa specie per lo sviluppo di sistemi produttivi realmente sostenibili per l’ambiente in termini di risparmio di risorse naturali e in grado di soddisfare le richieste dei mercati globali. In tale ambito, gli scopi del presente lavoro di tesi sono stati: 1) La caratterizzazione della risposta fisiologica, biochimica e molecolare di diversi genotipi di pomodoro tolleranti/suscettibili a condizioni di ridotto apporto idrico; 2) L’analisi funzionale di alcuni geni di pomodoro noti per essere coinvolti nella risposta/tolleranza alle alte temperature. Le attività di ricerca svolte e risultati ottenuti hanno consentito: uno studio dettagliato ed integrato della complessa risposta della pianta di pomodoro a condizioni di stress idrico. In particolare sono stati identificati parametri fisiologici (assimilazione fotosintetica, conduttanza stomatica e potenziale idrico) e biochimici (accumulo di ABA e prolina), le cui variazioni in condizioni di stress, sono correlate a modificazioni dell’espressione genotipo-specifica di un set di geni selezionati la cui attivazione è strettamente dipendente dall’intensità e dalla durata dello stress imposto e coinvolge anche geni espressi nelle radici, sito primario di percezione del segnale di stress; è stata effettuata una preliminare analisi funzionale fisiologica e molecolare del ruolo dei geni hsfA2 e hsp17.6, nella risposta a stress cronico da alte temperature, condizioni che inducono un forte calo della vitalità e germinabilità del polline, confermando che le antere sono un sito di danno particolarmente sensibile allo stress imposto

Genome-Editing Technologies for Enhancing Plant Disease Resistance

One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture

Organic Fertilizer Sources Distinctively Modulate Productivity, Quality, Mineral Composition, and Soil Enzyme Activity of Greenhouse Lettuce Grown in Degraded Soil

Intensive greenhouse vegetable production is often associated with a decline of crop productivity due to the increase of soil salinity and/or a reduction of biological fertility. The aim of the current work was to assess the effects of three organic fertilizers on morpho-physiological and agronomic traits of greenhouse lettuce as well as soil enzyme activity under poor soil quality conditions. The tested organic fertilizers (poultry manure, vinasse-based fertilizer, and insect’s frass fertilizer) were applied pre-planting at the same equivalent nitrogen (N) rate (90 kg N ha−1). Laboratory incubation assay results showed that vinasse-based fertilizer was the most suitable fertilizer in supplying the mineral N in the short term. All fertilizers increased shoot fresh and dry weight compared to unfertilized control with a more pronounced effect (+75%) with vinasse-based fertilizer and insect’s frass. Insect frass reduced by 27% the leaf nitrate concentration in comparison with the other treatments. The toxic heavy metal Pb was 46% lower in all organically fertilized lettuce leaves. Soil enzymatic activities of acid phosphatase, alkaline phosphatase, arylsulfatase (ArS), N-acetyl-β-D-glucosaminidase (NAGase), dehydrogenase, and total hydrolase (THA) were enhanced by poultry manure and insect’s frass in comparison with unfertilized control while vinasse-based fertilizer increased ArS, NAGase, and THA. Taken together, our data demonstrate that the application of organic fertilizers especially vinasse-based fertilizer and insect’s frass during intensive crop production is a suitable approach for mitigating the negative impact of soil salinity, enhancing soil biological fertility, and improving agronomic performance of greenhouse lettuce

Evolutionary conservation of MLO gene promoter signatures

Powdery mildew (PM) is a widespread fungal disease of plants in temperate climates, causing significant economic losses in agricultural settings. Specific homologs of the MLO gene family are PM susceptibility factors, as their loss-of function results in PM durable resistance (mlo resistance) in several plant species. The role of MLO susceptibility genes in plant-pathogen interactions is still elusive, however it is known that they are strongly upregulated following PM infection. In this study, we investigated the structure of 414 Putative Promoter Regions (PPRs) of MLO genes and highlighted motif and regulatory element patterns related to genomic relationships among species and phylogenetic distance among homologs. A TC box-like motif and a thymine-rich motif were found to be overrepresented in MLO genes transcriptionally upregulated upon infection with PM fungi. As proof of concept, we show that the expression of a melon (Cucumis melo L.) gene enriched for the motifs above mentioned was strongly upregulated upon infection with the PM fungus Podosphaera xanthii. While identifying a candidate MLO susceptibility gene in melon, this study provides insight on the transcriptional control of MLO genes and indicates diagnostic features useful to identify MLO susceptibility genes across species affected by the PM disease

Structure, evolution and functional inference on the Mildew Locus O (MLO) gene family in three cultivated Cucurbitaceae spp

Background: The powdery mildew disease affects thousands of plant species and arguably represents the major fungal threat for many Cucurbitaceae crops, including melon (Cucumis melo L.), watermelon (Citrullus lanatus L.) and zucchini (Cucurbita pepo L.). Several studies revealed that specific members of the Mildew Locus O (MLO) gene family act as powdery mildew susceptibility factors. Indeed, their inactivation, as the result of gene knock-out or knock-down, is associated with a peculiar form of resistance, referred to as mlo resistance. Results: We exploited recently available genomic information to provide a comprehensive overview of the MLO gene family in Cucurbitaceae. We report the identification of 16 MLO homologs in C. melo, 14 in C. lanatus and 18 in C. pepo genomes. Bioinformatic treatment of data allowed phylogenetic inference and the prediction of several ortholog pairs and groups. Comparison with functionally characterized MLO genes and, in C. lanatus, gene expression analysis, resulted in the detection of candidate powdery mildew susceptibility factors. We identified a series of conserved amino acid residues and motifs that are likely to play a major role for the function of MLO proteins. Finally, we performed a codonbased evolutionary analysis indicating a general high level of purifying selection in the three Cucurbitaceae MLO gene families, and the occurrence of regions under diversifying selection in candidate susceptibility factors. Conclusions: Results of this study may help to address further biological questions concerning the evolution and function of MLO genes. Moreover, data reported here could be conveniently used by breeding research, aiming to select powdery mildew resistant cultivars in Cucurbitaceae

Assessment of Genetic Diversity of the "Acquaviva Red Onion" (Allium cepa L.) Apulian Landrace

Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the "Acquaviva red onion" (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders