High accuracy of genome-enabled prediction of belowground and physiological traits in barley seedlings

In plants, the study of belowground traits is gaining momentum due to their importance on yield formation and the uptake of water and nutrients. In several cereal crops, seminal root number and seminal root angle are proxy traits of the root system architecture at the mature stages, which in turn contributes to modulating the uptake of water and nutrients. Along with seminal root number and seminal root angle, experimental evidence indicates that the transpiration rate response to evaporative demand or vapor pressure deficit is a key physiological trait that might be targeted to cope with drought tolerance as the reduction of the water flux to leaves for limiting transpiration rate at high levels of vapor pressure deficit allows to better manage soil moisture. In the present study, we examined the phenotypic diversity of seminal root number, seminal root angle, and transpiration rate at the seedling stage in a panel of 8-way Multiparent Advanced Generation Inter-Crosses lines of winter barley and correlated these traits with grain yield measured in different site-by-season combinations. Second, phenotypic and genotypic data of the Multiparent Advanced Generation Inter-Crosses population were combined to fit and cross-validate different genomic prediction models for these belowground and physiological traits. Genomic prediction models for seminal root number were fitted using threshold and log-normal models, considering these data as ordinal discrete variable and as count data, respectively, while for seminal root angle and transpiration rate, genomic prediction was implemented using models based on extended genomic best linear unbiased predictors. The results presented in this study show that genome-enabled prediction models of seminal root number, seminal root angle, and transpiration rate data have high predictive ability and that the best models investigated in the present study include first-order additive × additive epistatic interaction effects. Our analyses indicate that beyond grain yield, genomic prediction models might be used to predict belowground and physiological traits and pave the way to practical applications for barley improvement

Malting Quality of ICARDA Elite Winter Barley (Hordeum vulgare L.) Germplasm Grown in Moroccan Middle Atlas

The use of barley (Hordeum vulgare L.) in Morocco is still limited to food and feed despite the amplified demand by local industries for imported malt. This study aims to evaluate 36 barley elite lines for major grain physicochemical parameters and malt quality traits. Analysis of variance, Pearson correlation, principal component analysis (PCA), and hierarchical cluster analysis (HCA) were performed. The results showed significant genotypic variation among genotypes for individual grain and malt traits. High broad sense heritability was obtained for all traits except for plump grain percentage, malt friability, and germination capacity. Starch, malt extract, Kolbach index, grain area, and test weight correlated significantly and negatively with barley protein. Malt extract correlated positively with Kolbach index and starch, but a negative correlation with soluble protein and malt protein was found. Based on 12 characters, 77% of the total genotypic variation was explained by the three first principal components following PCA and four clusters were depicted based on HCA. Genotypes of high interest with desirable levels of quality standards were identified to be used as a malt quality traits donor while designing crossing programs

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction

18 Pags.- 7 Figs.- 4 Tabls. © 2021 Puglisi, Delbono, Visioni, Ozkan, Kara, Casas, Igartua, Valè, Piero, Cattivelli, Tondelli and Fricano. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.This research was carried out in the framework of the iBarMed project, which has been funded through the ARIMNet2 initiative and the Italian “Ministry of Agricultural, Food and Forestry Policies” under grant agreement “DM n. 20120.” ARIMNet2 has received funding from the EU 7th Framework Programme for research, technological development and demonstration under grant agreement no. 618127. The work was also supported by YSTEMIC_1063 (An integrated approach to the challenge of sustainable food systems: adaptive and mitigatory strategies to address climate change and malnutrition: From cereal diversity to plant breeding), a research project funded by Italian “Ministry of Agricultural, Food and Forestry Policies” in the frame of the Knowledge Hub on Food and Nutrition Security.Peer reviewe

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Allelic Variations in Vernalization (<i>Vrn</i>) Genes in <i>Triticum</i> spp.

Rapid climate changes, with higher warming rates during winter and spring seasons, dramatically affect the vernalization requirements, one of the most critical processes for the induction of wheat reproductive growth, with severe consequences on flowering time, grain filling, and grain yield. Specifically, the Vrn genes play a major role in the transition from vegetative to reproductive growth in wheat. Recent advances in wheat genomics have significantly improved the understanding of the molecular mechanisms of Vrn genes (Vrn-1, Vrn-2, Vrn-3, and Vrn-4), unveiling a diverse array of natural allelic variations. In this review, we have examined the current knowledge of Vrn genes from a functional and structural point of view, considering the studies conducted on Vrn alleles at different ploidy levels (diploid, tetraploid, and hexaploid). The molecular characterization of Vrn-1 alleles has been a focal point, revealing a diverse array of allelic forms with implications for flowering time. We have highlighted the structural complexity of the different allelic forms and the problems linked to the different nomenclature of some Vrn alleles. Addressing these issues will be crucial for harmonizing research efforts and enhancing our understanding of Vrn gene function and evolution. The increasing availability of genome and transcriptome sequences, along with the improvements in bioinformatics and computational biology, offers a versatile range of possibilities for enriching genomic regions surrounding the target sites of Vrn genes, paving the way for innovative approaches to manipulate flowering time and improve wheat productivity

Cultivar Susceptibility to Olive Knot Disease and Association with Endophytic Microbiota Community

Olive knot disease (OKD) induced by the bacterium Pseudomonas&nbsp;savastanoi pv. savastanoi seriously affects olive production in the Mediterranean basin. Nowadays, the only strategies to control the disease are pruning and the application of cupric products. An essential strategy to enhance protection is represented by the identification of resistant cultivars, which represents a crucial opportunity for future investments and breeding. We undertook a three-year-long survey at the International Olive Germplasm Collection of &ldquo;Villa Zagaria&rdquo; (Sicily, Italy) on thirty-six Sicilian cultivars that were monitored for symptom development. Cultivars with different levels of susceptibility were divided into five clusters. Moreover, in order to investigate possible interactions with endophytic microbial communities, two cultivars with contrasting susceptibilities, Zaituna (highly resistant) and Giarraffa (highly susceptible), were selected for an amplicon-based metagenomic analysis. Distinct endophytic communities colonized the two cultivars, suggesting an interaction between the resident bacterial community and the pathogen. Significantly higher bacterial richness was detected in the shoots of the susceptible cv. Giarraffa, although it had lower diversity. The opposite trend was observed for fungal communities. Among the microbes resulted to be enriched in cv. Giarraffa, it is important to underline the presence of Pseudomonas among the bacterial genera, and Alternaria, Neofusicoccum, Epicoccum, Ascochyta, and Elsinoe among the fungal genera, which include many species often described as plant pathogens and biocontrol agents. Starting from this basic information, new strategies of control, which include breeding for resistance and integrated disease management, can be envisaged

Cultivar Susceptibility to Olive Knot Disease and Association with Endophytic Microbiota Community

Olive knot disease (OKD) induced by the bacterium Pseudomonas savastanoi pv. savastanoi seriously affects olive production in the Mediterranean basin. Nowadays, the only strategies to control the disease are pruning and the application of cupric products. An essential strategy to enhance protection is represented by the identification of resistant cultivars, which represents a crucial opportunity for future investments and breeding. We undertook a three-year-long survey at the International Olive Germplasm Collection of “Villa Zagaria” (Sicily, Italy) on thirty-six Sicilian cultivars that were monitored for symptom development. Cultivars with different levels of susceptibility were divided into five clusters. Moreover, in order to investigate possible interactions with endophytic microbial communities, two cultivars with contrasting susceptibilities, Zaituna (highly resistant) and Giarraffa (highly susceptible), were selected for an amplicon-based metagenomic analysis. Distinct endophytic communities colonized the two cultivars, suggesting an interaction between the resident bacterial community and the pathogen. Significantly higher bacterial richness was detected in the shoots of the susceptible cv. Giarraffa, although it had lower diversity. The opposite trend was observed for fungal communities. Among the microbes resulted to be enriched in cv. Giarraffa, it is important to underline the presence of Pseudomonas among the bacterial genera, and Alternaria, Neofusicoccum, Epicoccum, Ascochyta, and Elsinoe among the fungal genera, which include many species often described as plant pathogens and biocontrol agents. Starting from this basic information, new strategies of control, which include breeding for resistance and integrated disease management, can be envisaged

Nitrato reduttasi e beta-galattosidasi come indicatori d'adattamento microbico in un suolo contaminato da zinco

Le attività enzimatiche ed in generale le proprietà biologiche sono ampiamente studiate per valutare la risposta ecotossicologica dei microorganismi del suolo alla presenza di contaminanti. Prove condotte in passato hanno dimostrato come i microorganismi nitrificanti siano in grado di adattarsi alla presenza di elementi in tracce. Il presente studio è stato condotto per valutare se altri di microrganismi del suolo siano in grado di adattarsi alla presenza di zinco in concentrazione tossiche. Microcosmi contaminati con zinco (350 mg kg-1 s.s.) sono stati incubati insieme a dei controlli non contaminati con zinco per un periodo di 4 mesi, ed ad intervalli regolari sono state determinate nitrificazione potenziale, nitrato redattasi e β-galattosidasi. Le 3 attività hanno mostrato immediatamente dopo la contaminazione una significativa riduzione nei microcosmi contaminati rispetto ai controlli, ed un incremento nei campionamenti successivi, sino a raggiungere valori statisticamente non differenti dai controlli a 99 giorni di incubazione per la nitrificazione potenziale, a 71 giorni per la nitrato reduttasi e già a 41 giorni per la β-galattosidasi. Per confermare che il recupero delle funzionalità fosse dovuto a reale adattamento e non a fenomeni di aging, sia i campioni contaminati da zinco, sia i campioni controllo alla fine del periodo di incubazione (113 giorni) sono stati reinoculati in suoli sterilizzati e contaminati da poche ore con concentrazioni crescenti di zinco (0-5000 mg kg-1 s.s.). Il confronto delle curve-dose risposta ha mostrato significativi incrementi nell’EC50 nei suoli inoculati con i microcosmi pre-esposti per tutte e 3 le attività. Si è così potuto dimostrare come non solo la nitrificazione, ma anche la nitrato redattasi e la β-galattosidasi siano indicatori di adattamento microbico alla contaminazione da zinco

Potential nitrification, nitrate reductase, and β-galactosidase activities as indicators of restoration of ecological functions in a Zn contaminated soil.

he present study was conducted to assess the possible restoration of different ecological functions in a Zn- contaminated soil. Experiments were conducted in a soil microcosm contaminated with 350 mg kg−1 of Zn and in an uncontaminated control microcosm, both incubated for 4 months. At regular intervals, potential nitrification, nitrate reductase, and β-galactosidase activity were determined. All these activities were significantly reduced just after Zn contamination in contaminated microcosms compared to the activities of the control, but then increased. In order to confirm that the restoration of ecological functions was not due to an aging phenomenon, a reinoculation protocol was also applied. A significant restoration was found for β-galactosidase activity, while for nitrate re- ductase activity and potential nitrification, there was a clear shift of dose–response curves but with partial over- lap of the EC50 ranges estimation, thus indicating that different ecological functions are restored over time in Zn-contaminated soils