Segmental duplications are hot spots of copy number variants affecting barley gene content

Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shaping genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and identifying sequence features associated with CNV formation. Using exome sequencing and read count data, we detected 16,605 deletions and duplications that affect barley gene content by surveying a diverse panel of 172 cultivars, 171 landraces, 22 wild relatives and other 32 uncategorized domesticated accessions. The quest for segmental duplications (SDs) in the reference sequence revealed many low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, indicating that these sequence elements act as hot spots for the formation of CNVs. This study delivers a comprehensive genome-wide study of CNVs affecting barley gene content and implicates SDs in the molecular mechanisms that lead to the formation of this class of CNVs

Responses to Drought Stress in Poplar: What Do We Know and What Can We Learn?

Poplar (Populus spp.) is a high-value crop for wood and biomass production and a model organism for tree physiology and genomics. The early release, in 2006, of the complete genome sequence of P. trichocarpa was followed by a wealth of studies that significantly enriched our knowledge of complex pathways inherent to woody plants, such as lignin biosynthesis and secondary cell wall deposition. Recently, in the attempt to cope with the challenges posed by ongoing climate change, fundamental studies and breeding programs with poplar have gradually shifted their focus to address the responses to abiotic stresses, particularly drought. Taking advantage from a set of modern genomic and phenotyping tools, these studies are now shedding light on important processes, including embolism formation (the entry and expansion of air bubbles in the xylem) and repair, the impact of drought stress on biomass yield and quality, and the long-term effects of drought events. In this review, we summarize the status of the research on the molecular bases of the responses to drought in poplar. We highlight how this knowledge can be exploited to select more tolerant genotypes and how it can be translated to other tree species to improve our understanding of forest dynamics under rapidly changing environmental conditions

Parametri chimici e vegetazione spontanea in parcelle di suoli naturali e ricostituiti: primo anno di osservazioni

Il progetto Life+ “Recupero ambientale di un suolo degradato e desertificato mediante una nuova tecnologia di trattamento di ricostituzione del terreno” (Life 10 ENV/IT/000400 “New Life”), co-finanziato dall'Unione Europea, ha come obiettivo quello di testare l’efficacia del processo di ricostituzione applicato a suoli degradati e/o desertificati. La ricostituzione è una tecnologia innovativa (brevettata dalla società m.c.m. Ecosistemi) di trattamento chimico-meccanico applicato a suoli degradati per la produzione di suoli detti ricostituiti che hanno caratteri agronomici migliori e quindi maggiore fertilità. La fase sperimentale del progetto “New Life” si basa sullo studio di parcelle sperimentali in cui sono confrontati suoli naturali e ricostituiti. In questo lavoro si presentano i risultati ottenuti dal confronto delle parcelle sperimentali dopo il primo anno di sperimentazione. Di tali parcelle è stata analizzata la vegetazione spontanea e sono stati determinati sul suolo parametri fisici e chimici tra cui: granulometria, densità reale e apparente, pH, salinità, carbonio organico e azoto totale al fine di valutare attraverso test statistici quali parametri abbiano influenzato la colonizzazione durante il primo dei tre anni di indagine

Genome-Wide Analysis of japonica Rice Performance under Limited Water and Permanent Flooding Conditions

A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering. Significant MTAs were detected across all the 12 rice chromosomes, while clusters of effects influencing different traits under LW or in both watering conditions were, respectively, observed on chromosomes 4, 8, and 12 and on chromosomes 1, 3, 4, 5, and 8. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to traits related to plant morphology, grain yield, and physiological parameters allowed the identification of genes that were demonstrated to affect the respective traits. Among these, three (OsOFP2, Dlf1, OsMADS56) and seven (SUI1, Sd1, OsCOL4, Nal1, OsphyB, GW5, Ehd1) candidate genes were, respectively, identified to co-localize with LW-specific associations and associations in common between the two water treatments. For several LW-specific MTAs, or in common among the two treatments, positional co-localizations with previously identified QTLs for rice adaptation to water shortages were observed, a result that further supports the role of the loci identified in this work in conferring adaptation to LW. The most robust associations identified here could represent suitable targets for genomic selection approaches to improve yield-related traits under LW

Development of a new tool (4TREE) for adapted genome selection in European tree species

Resumé : The 4TREE Axiom 50K SNP array is one of the main deliverables of the H2020 project B4EST which aims at transferring know-how and tools to improve breeding for production, resilience and diversity of forest trees. This array is developed for: Populus sp, Fraxinus sp, Pinus pinaster and Pinus pinea. It is based on de novo sequencing resources and existing genomic resources of loci of interest for breeders. 4TREE is primarily aimed at breeders by providing low genotyping costs for economically important species in Europe, fostering collaboration between breeding programs across Europe. One of its first uses will be genome wide association studies and genomic predictions, being also extremely useful for monitoring and characterizing novel sources of variation. Material/ Methods : The 4Tree array will be designed after the screening of 420K SNP. Except for the orphan species P. pinea, SNP were identified from existing genomic resources: whole genome and RNA sequencing, exome capture, SNP arrays. SNP gathered by these resources were filtered for inclusion in a screening array of 420K (105K/species) and checked over a panel of 480 samples (120/species). SNP without other polymorphisms within 30bp flanking sequences were preferentially selected and those in unique region were prioritized, limiting A/T and C/G which require more space on the array. The selection included several SNP in candidate genes or regions found via transcriptomic, QTL and GWAS analysis. Results : For P. pinea, 128K SNPs were submitted to ThermoFisher, resulting in 37K recommended SNPs for the screening array. P. pinaster submitted 197K SNPs (5K SNPs from Plomion et al. 2016), leading to 140K inclusions in the screening array, including several from candidate genes for abiotic and biotic stress. For Fraxinus sp, 126K SNP were selected from the 327K scored. SNPs were selected in order to prioritize candidate SNPs associated to dieback disease tolerance and incompatibility (Stocks & Metheringham et al. 2019). SNPs were additionally selected according to the genomic coverage (maximum possible representation of genes and scaffolds with respect to the reference genome). For Populus, a subset of SNPs was identified for two species: P. nigra and P. deltoides. These SNPs were either species specific or shared between the two species. For P. nigra, SNPs from a previous array (Faivre-Rampant et al. 2016) and from candidate regions from GWAS were also selected. The final coverage of the genome was 100 SNP/Mb with a ratio of genic and intergenic SNPs of 60/40%. In total, 3 000K SNP were submitted to ThermoFisher for Populus to select 120,500 for the screening array. Conclusion: From this screening genotyping, 12.5K high value SNPs per species will be retained for the final array 4TREE dedicated to gene discovery, pre-breeding monitoring of diversity and genomic selection studies in B4EST. This final array will be a highly valuable genome-assisted breeding tool, made commercially available for cost effective HT genotyping for four important tree species in Europe

Prospects for evolution in European tree breeding

International audienceGenetically improved forest reproductive materials are now widely accessible in many European countries due to decades of continuous breeding efforts. Tree breeding does not only contribute to higher-value end products but allows an increase in the rate of carbon capture and sequestration, helping to mitigate the effects of climate change. The usefulness of breeding programmes depends on (i) the relevance of the set of selected traits and their relative weights (growth, drought tolerance, phenology, etc.); (ii) the explicit management of targeted and “neutral” diversity; (iii) the genetic gain achieved; and (iv) the efficiency of transferring diversity and gain to the plantation. Several biological factors limit both operational breeding and mass reproduction. To fully realise the potential of tree breeding, the introduction of new technologies and concepts is pivotal for overcoming these constraints. We reviewed several European breeding programmes, examining their current status and factors that are likely to influence tree breeding in the coming decades. The synthesis was based on case studies developed for the European Union-funded B4EST project, which focused on eight economically important tree species with breeding histories and intensities ranging from low-input breeding (stone pine, Douglas-fir and ash) to more complex programmes (eucalyptus, maritime pine, Norway spruce, poplar, and Scots pine). Tree breeding for these species is managed in a variety of ways due to differences in species’ biology, breeding objectives, and economic value. Most programmes are managed by governmental institutes with full or partial public support because of the relatively late return on investment. Eucalyptus is the only tree species whose breeding is entirely sponsored and managed by a private company. Several new technologies have emerged for both phenotyping and genotyping. They have the potential to speed up breeding processes and make genetic evaluations more accurate, thereby reducing costs and increasing genetic gains per unit of time. In addition, genotyping has allowed the explicit control of genetic diversity in selected populations with great precision. The continuing advances in tree genomics are expected to revolutionise tree breeding by moving it towards genomic-based selection, a perspective that requires new types of skills that are not always available in the institutions hosting the programmes. We therefore recognise the importance of promoting coordination and collaboration between the many groups involved in breeding. Climate change is expected to bring in new pests and diseases and increase the frequency of extreme weather events such as late frosts and prolonged droughts. Such stresses will cause slow growth and mortality, reducing forest productivity and resilience. Most of these threats are difficult to predict, and the time-consuming nature of conventional breeding does not allow for an adequate and timely reaction. We anticipate that most breeding programmes will need to revise their selection criteria and objectives to place greater emphasis on adaptive performance, tolerance to multiple environmental stresses, stability in different environments, and conservation of genetic diversity. Testing breeding materials in a variety of environments, including potentially contrasting climates, will become increasingly important. Climate change may also force the incorporation of new genetic resources that provide new useful adaptations, which may involve the use of new, previously unexplored gene pools or hybridisation, with the enormous challenge of incorporating useful alleles without adding along an unfavourable genetic background. Decision-support tools to help landowners and foresters select the best-performing forest reproductive material in each specific environment could also help reduce the impact of climate change

Development of a new tool (4TREE) for adapted genome selection in European tree species

Resumé : The 4TREE Axiom 50K SNP array is one of the main deliverables of the H2020 project B4EST which aims at transferring know-how and tools to improve breeding for production, resilience and diversity of forest trees. This array is developed for: Populus sp, Fraxinus sp, Pinus pinaster and Pinus pinea. It is based on de novo sequencing resources and existing genomic resources of loci of interest for breeders. 4TREE is primarily aimed at breeders by providing low genotyping costs for economically important species in Europe, fostering collaboration between breeding programs across Europe. One of its first uses will be genome wide association studies and genomic predictions, being also extremely useful for monitoring and characterizing novel sources of variation. Material/ Methods : The 4Tree array will be designed after the screening of 420K SNP. Except for the orphan species P. pinea, SNP were identified from existing genomic resources: whole genome and RNA sequencing, exome capture, SNP arrays. SNP gathered by these resources were filtered for inclusion in a screening array of 420K (105K/species) and checked over a panel of 480 samples (120/species). SNP without other polymorphisms within 30bp flanking sequences were preferentially selected and those in unique region were prioritized, limiting A/T and C/G which require more space on the array. The selection included several SNP in candidate genes or regions found via transcriptomic, QTL and GWAS analysis. Results : For P. pinea, 128K SNPs were submitted to ThermoFisher, resulting in 37K recommended SNPs for the screening array. P. pinaster submitted 197K SNPs (5K SNPs from Plomion et al. 2016), leading to 140K inclusions in the screening array, including several from candidate genes for abiotic and biotic stress. For Fraxinus sp, 126K SNP were selected from the 327K scored. SNPs were selected in order to prioritize candidate SNPs associated to dieback disease tolerance and incompatibility (Stocks & Metheringham et al. 2019). SNPs were additionally selected according to the genomic coverage (maximum possible representation of genes and scaffolds with respect to the reference genome). For Populus, a subset of SNPs was identified for two species: P. nigra and P. deltoides. These SNPs were either species specific or shared between the two species. For P. nigra, SNPs from a previous array (Faivre-Rampant et al. 2016) and from candidate regions from GWAS were also selected. The final coverage of the genome was 100 SNP/Mb with a ratio of genic and intergenic SNPs of 60/40%. In total, 3 000K SNP were submitted to ThermoFisher for Populus to select 120,500 for the screening array. Conclusion: From this screening genotyping, 12.5K high value SNPs per species will be retained for the final array 4TREE dedicated to gene discovery, pre-breeding monitoring of diversity and genomic selection studies in B4EST. This final array will be a highly valuable genome-assisted breeding tool, made commercially available for cost effective HT genotyping for four important tree species in Europe

Understanding the use and outcomes of high-flow nasal cannula among infants admitted to Canadian hospitals with bronchiolitis (CanFLO): a protocol for a multicentre, retrospective cohort study

Introduction Bronchiolitis is the most common viral lower respiratory tract infection in children under 2 years of age. Respiratory support with high-flow nasal cannula (HFNC) is increasingly used in this patient population with limited understanding of the patients most likely to benefit and considerable practice variability of use. This study aims to understand the factors associated with failure of HFNC support among patients with bronchiolitis and to describe the current practice variations of HFNC use in patients with bronchiolitis in Canadian hospitals including fluid management and parameters to initiate, escalate and discontinue HFNC support.Methods and analysis This is a multicentre retrospective cohort study including hospitalised patients aged 0–24 months with bronchiolitis requiring support with HFNC between January 2017 and December 2021. Clinical data will be collected from patient medical records from Canadian hospitals (n=12), including academic and community centres. HFNC failure will be defined as the need for escalation to non-invasive or invasive mechanical ventilation. Factors associated with HFNC failure will be analysed using logistic regression. Descriptive statistics will be used to describe practice variations of HFNC utilisation and management.Ethics and dissemination Approval from the Research Ethics Boards (REBs) has been obtained for each participating study site prior to onset of data collection including Clinical Trials Ontario for all Ontario hospital sites and REBs from British Columbia Children’s Hospital, Stollery Children’s Hospital, Montreal Children’s Hospital and CHU Sainte-Justine. Study results will be disseminated through presentation at national/international conferences and publication in high-impact, peer-reviewed journals

Emotional status and fear in patients scheduled for elective surgery during COVID-19 pandemic: a nationwide cross-sectional survey (COVID-SURGERY)

Background Fragmented data exist on the emotional and psychological distress generated by hospital admission during the pandemic in specific populations of patients, and no data exists on patients scheduled for surgery. The aim of this multicentre nationwide prospective cross-sectional survey was to evaluate the impact of pandemic on emotional status and fear of SARS-CoV-2 contagion in a cohort of elective surgical patients in Italy, scheduled for surgery during the COVID-19 pandemic. Results Twenty-nine Italian centres were involved in the study, for a total of 2376 patients surveyed (mean age of 58 years ± 16.61; 49.6% males). The survey consisted of 28 total closed questions, including four study outcome questions. More than half of patients had at least one chronic disease (54%), among which cardiovascular diseases were the commonest (58%). The most frequent type of surgery was abdominal (20%), under general anaesthesia (64%). Almost half of the patients (46%) declared to be frightened of going to the hospital for routine checkups; 55% to be afraid of getting SARS-CoV-2 infection during hospitalization and 62% were feared of being hospitalised without seeing family members. Having an oncological disease and other patient-related, centre-related or perioperative factors were independently associated with an increased risk of fear of SARS-CoV-2 infection during hospitalization and of being hospitalised without seeing family members. A previous infection due to SARS-COV-2 was associated with a reduced risk of worse emotional outcomes and fear of SARS-CoV-2 infection during hospitalization. Patients who showed the most emotionally vulnerable profile (e.g. use of sleep-inducing drugs, higher fear of surgery or anaesthesia) were at higher risk of worse emotional status towards the hospitalization during COVID-19 pandemic. Being operated in hospitals with lower surgical volume and with COVID-19 wards was associated with worse emotional status and fear of contagion. Conclusions Additional fear and worse emotional status may be frequent in patients scheduled for elective surgery during COVID-19 pandemic. More than half of the participants to the survey were worried about not being able to receive family visits. Psychological support may be considered for patients at higher risk of psychological distress to improve perioperative wellbeing during the pandemic