Genetic variation of cork oak a tool for improving regeneration of cork oak woodlands

The European Academies' Science Advisory Council (2017) reports that the Mediterranean forest is already being affected by climate change (IPCC, 2014) and cork oak woodlands are particularly vulnerable to high-end climate scenarios that go above the Paris Agreement 2° C increase in temperature. Since longer, more frequent, and more intense drought periods are expected, stress caused by the expansion of arid and semi-arid climate will affect the species distribution. Consequently, not only established stands may be prone to tree mortality, but also the current reforestation effort may be jeopardized by low survival rates attributed to the use of unsuitable genetic material. It is expected that, through genetic adaptation and/or phenotypic plasticity, cork oak populations may have developed significant differences in fitness and the traits related to it. In this context, provenance and progeny trials are the best resource of material to assess the variability between and within populations from seed sources sampled in a wide range of locations (stands) covering the geographical distribution of the species. Profiting from the multi-locality provenance and progeny trials belonging to a Network, established in 1998, in the initiative frame of FAIR I CT 0202 for the evaluation of genetic resources of cork oak for appropriate use in breeding and gene conservation strategies”, where 35 cork oak populations covering all the natural distribution area are represented. The provenance trials that where set up in different countries are entering now the age of first debarking and this should allow to have first data about the influence of genetics on production by different site qualities. INCREDIBLE project should document this knowledgeFAIR I CT 0202info:eu-repo/semantics/publishedVersio

High-density genetic map and QTL analysis of soluble solid content, maturity date, and mealiness in peach using genotyping by sequencing

Peach (Prunus persica) is one of the most important temperate fruit trees in the world, based on its production and cultivated area. Consumer acceptance is the principal objective of multiple breeding programs and it is dependent on many factors. Among these factors, an important role is played by the soluble solids content (SSC) and the postharvest performance represented by mealiness (M) susceptibility as a chilling injury disorder. Additionally, a major maturity date (MD) QTL has been reported to have a pleiotropic effect on both M and SSC. The aim of this work was QTL identification of SSC, MD, and M and to identify adequate candidate genes that are linked to regulation of these traits. The analysis was performed by evaluation of fruit quality traits during three consecutive seasons in an F1 progeny of 194 siblings, which were obtained from the intraspecific cross between the yellow-flesh peach “O’Henry” and the white-flesh nectarine NR-053. The main result was the construction of a genetic linkage map with 499 markers (486 SNPs, 11 SSRs, and two morphological markers) spanning 717.6 cM, with an average distance between markers of 1.5 cM/cluster. The analysis allowed the identification of consistent QTLs for SSC and M in the linkage group LG5 and for MD in LG1, LG2, LG5, and LG6. A large number of genes were annotated in QTL intervals, which was reduced by selecting the genes with at least one SNP, which caused an amino acid variation. For SSC, the data identified four transcription factors, one gene involved directly with the sugar accumulation process, and one cell wall remodeling-related gene. For MD, 23 cell wall-related genes, three jasmonic acid-linked genes, eight transcription factors, and one ripening-related gene were identified. Finally, only one cell wall gene was identified that was associated with M. In conclusion, these results improve our understanding of the genetic control of fruit quality traits with commercial relevance in P. persica and specifically in the O × N mapping population.info:eu-repo/semantics/publishedVersio

Provenance behavior in the cork-oak International network trials fair 202

The international network of provenance trials in cork-oak was established as a result of the EU Concerted Action FAIR 202, 1995-2000. 34 provenances were selected in the natural range of cork oak and trials were established in 1996/97 in France, Italy, Portugal, Tunisia and Spain. This study compares the behavior of provenances in the trials of Grighini (Sardinia), Monte Fava and Quinta da Nogueira (Portugal), Monfrague (Spain), Les Maures (France) and Tebabe (Tunisia). Observations on total height (Ht) and diameter at beast height (DBH) are used to compare and assess adaptation within sites and among sites. Climate at the provenance site seed collection and at trials sites is used to characterize the behavior of provenances. The results reveal that the provenances, ES 5 (1063 mm), IT16 (910 mm), IT12 (937 mm), 937, TU32 (948 mm), FR2 (958 mm, FR1 (963 mm, MA31 (970 mm), ES8 (993 mm) are able to adapt and show good growth under conditions of decrease of total annual rainfall and strong decrease in case of TU33 (1610mm), MA27 (1280 mm). On the other hand provenances coming from sites of low precipitation not always show relevant performance in sites of higher precipitation as IT14 (448 mm), ES10 (455 mm), MA29 (479 mm). These results are discussed in the impact climate change (CC) may have in adaptation and evolution of cork oak. Our results show that cork oak will not face serious threats if drought increases in the Mediterranean region, since some populations are showing capable to cope successfully with decrease of total precipitation. The ongoing results from the cork-oak international network trials FAIR 202 show the importance of this line of research and the need to establish harmonized criteria on data collection to enhance the comparability. As cork quality is a key issue on cork-oak economic sustainability it is critical to establish harmonized criteria in cork harvesting for further studies to compare cork quality with special reference for the assessment of the genetic control of cork production and heritability.info:eu-repo/semantics/publishedVersio

The Peach v2.0 release: High-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

Background: The availability of the peach genome sequence has fostered relevant research in peach and related Prunus species enabling the identification of genes underlying important horticultural traits as well as the development of advanced tools for genetic and genomic analyses. The first release of the peach genome (Peach v1.0) represented a high-quality WGS (Whole Genome Shotgun) chromosome-scale assembly with high contiguity (contig L50 214.2 kb), large portions of mapped sequences (96%) and high base accuracy (99.96%). The aim of this work was to improve the quality of the first assembly by increasing the portion of mapped and oriented sequences, correcting misassemblies and improving the contiguity and base accuracy using high-throughput linkage mapping and deep resequencing approaches. Results: Four linkage maps with 3,576 molecular markers were used to improve the portion of mapped and oriented sequences (from 96.0% and 85.6% of Peach v1.0 to 99.2% and 98.2% of v2.0, respectively) and enabled a more detailed identification of discernible misassemblies (10.4 Mb in total). The deep resequencing approach fixed 859 homozygous SNPs (Single Nucleotide Polymorphisms) and 1347 homozygous indels. Moreover, the assembled NGS contigs enabled the closing of 212 gaps with an improvement in the contig L50 of 19.2%. Conclusions: The improved high quality peach genome assembly (Peach v2.0) represents a valuable tool for the analysis of the genetic diversity, domestication, and as a vehicle for genetic improvement of peach and related Prunus species. Moreover, the important phylogenetic position of peach and the absence of recent whole genome duplication (WGD) events make peach a pivotal species for comparative genomics studies aiming at elucidating plant speciation and diversification processes

Évaluation préliminaire des essais de provenances de chêne-liège et perspectives de recherche

Le réseau international des essais de provenance et de descendance de chêne-liège (établie dans le cadre du projet Action Concertée FAIR CT 95-202 “European network for the evaluation of genetic resources of cork oak for appropriate use in breeding and gene conservation strategies” financé par l’Union Européenne) constitue un matériel vivant unique pour la recherche, qu’elle soit appliquée, ou fondamental, sur l’espèce. Les essais génétiques ont été réalisés sur une base méthodologique harmonisée au niveau des plants utilisés (tous les plants ont été élevées dans une même pépinière au Portugal) et sur terrain un même dispositif expérimental a été suivi. En 1997/98, 13 essais de provenances ont été établis. Ceux ayant réussi sont situés en Espagne (2), France (1), Italie (3), Portugal (3) et Tunisie (1). Concernent les essais de descendances il existe 4 des 5 initiales - Espagne (1), Portugal (2) et Tunisie (1). Dans ce travail nous présentons quelques résultats du comportement des provenances à travers des caractéristiques adaptatifs tels que la survie, l’efficacité d’utilisation de l’eau et des études de génomique. Nous avons procédé à la comparaison de chaque provenance dans les essais - niveau horizontal- et à la comparaison de chaque provenance entre les essais - niveau vertical afin de discuter la plasticité phénotypique et l’interaction génotype X environnement. Les données disponibles pour hauteur en 2006 montre des différences de comportement entre provenances et entre les essais. Par exemple, les provenances du Maroc montre une croissance supérieure dans l’essai plus au Sud au Portugal et aussi dans un essai en Espagne. Pour l’essai de Sardaigne les meilleures provenances sont de Tunisie et d’Espagne. A la fin on discute sur les avantages des essais comme matériel vivant dénominateur commun pour une recherche avancée, multidisciplinaire, synergétique, transnational et concertée. Les perspectives pour la recherche sur les grands thèmes tels que la gestion durable du chêne-liège, notamment la sélection, amélioration génétique, adaptation aux changements globaux, fluxes génétiques, problèmes phytosanitaires, qualité du liège en liaison avec la respective génomique sont adressées.PTDC/AGR-AAM/104364/200

Pro-Environmental Behaviors: Determinants and Obstacles among Italian University Students

The awareness of citizens concerning the health risks caused by environmental pollution is growing, but studies on determinants of pro-environmental behaviors have rarely examined health-related aspects. In this study, we investigated these determinants using data from a large survey among Italian university students (15 Universities: 4778 filled questionnaires). Besides the health-related aspects, represented by environmental health risk perception and functional health literacy, we considered social and demographic characteristics (gender, area of residence, sources of information, trust in institutional and non-institutional subjects, and students' capacity of positive actions, indicated as internal locus of control). The attitudes towards pro-environmental behaviors were positive for more than 70% of students and positively related with health risk perception, internal locus of control, and health literacy. The correspondence between the positive attitudes towards pro-environmental behaviors and the real adoption of such behaviors was approximately 20% for most behaviors, except for the separate collection of waste (60%). Such a discrepancy can be attributable to external obstacles (i.e., lack of time, costs, lack of support). The health-related aspects were linked to the pro-environmental attitudes, but to a lesser extent to pro-environmental behaviors, owing to the complexity of their determinants. However, they should be taken in account in planning education interventions

Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Characterization of the international network FAIR 202 of provenance and progeny trials of cork oak on multiple sites for further use on forest sustainable management and conservation of genetic resources

The international network of provenance and progeny trials was established in 1998 in France, Italy, Portugal, Spain and Tunisia under the EU Commission financed concerted action FAIR 202 benefiting from homogeneous plant raising and standardize experimental design. The trials include 34 provenances that are being characterised using quantitative genetics and molecular genetics to study survival, growth, morphological and physiological traits in relation with geographical origin. France 2008– Provenance were assess using survival, growth (height) and vigour parameters. Provenance PT 23 and PT+ES 25 had the lowest survival rate respectively 79,2% and 77,8% while ES 8, ES 7, MA 31 and PT 19 had 94,4%. In 2008 the mean height at Les Maures was 48.73 cm and the form keeps plagiotropic. Italy- Sardinia, Grighine, 2010 The average mortality was 7%, ranging from 13-14% at the provenance IT LA-VT; IT SI-CT; MO I-1 and 0-2% for FRII, ES 3-V, ES F-PAR, PT IV-03, TU I; TU II. Mean height and trunk DBH over cork were respectively 273cm and 5.1cm. MO I-2, TU II, ES 4-CR are above mean on height (302-309 cm), and the Italian provenances are under mean (237-249cm). The maximum DBH was reached by MO I-2 (6 cm) followed by ES-4 CR and MO III-2 (5.8 cm) and the minimum is at IT PU-BR (3.8 cm), followed by the other Italian provenances (4-4.6cm) and PT V-01 (4.5 cm). Portugal Results from field trials show significant differences among populations on survival, growth and adaptive traits (phenology, water use efficiency - WUE). Mogadouro trial, 2011 -provenance variation was assessed using growth, vigour and survival. The bud burst as adaptive characteristic was observed during 2011-2013. The Moroccan provenances show good adaptive characteristics in terms of growth, vigour and stem form. There was no significant differences (p<0.05) in provenances bud burst. The mean height is not correlated with survival. Italian provenances present lower height but higher survival. The overall mortality is around 26%. The highest growth is being observed in the Moroccan provenances and French ones showed lowest survival. Results from field trials at Italy (continent), Spain and Tunisia are also referred. Genotype by environment interaction (G x E) is discussed. Due to the large variability of responses between cork oak provenances we emphasise the importance to use these results when considering the seed origin aiming for large scale planting programs for adaptation, cork quality, pest and diseases susceptibility and for conservation of genetic resources, Progeny trials provide key information for genetic improvement programmes on estimates of breeding values on economic characteristics such as cork quality and an approach on inbreeding problems. Perspectives Used in synergy the results from provenance and progeny trials are likely to provide insights for balancing the conflicting objectives such as maximising selection intensity while maintaining variation. Taking into consideration that the cork from the second striping made 3-4 years after the first gives information about the quality liable to be used on selection for afforestation guide lines we enhance the need of concerted criteria on debarking season and procedures. The results from these trials will contribute to the knowledge on genetic variation and are a privileged living material to study climate change effects and adaptation to biotic and abiotic factors and for sustainable management of this long living species.info:eu-repo/semantics/publishedVersio