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Abiotic stress strongly affects yield-related traits in durum wheat, in particular drought is one of the main environmental factors that have effect on grain yield and plant architecture. In order to obtain new genotypes well adapted to stress conditions, the highest number of desirable traits needs to be combined in the same genotype. In this context, hundreds of quantitative trait loci (QTL) have been identified for yield-related traits in different genetic backgrounds and environments. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies for the reliability of their location and effects. MQTL analysis is a useful method to dissect the genetic architecture of complex traits, which provide an extensive allelic coverage, a higher mapping resolution and allow the identification of putative molecular markers useful for marker-assisted selection (MAS). In the present study, a complete and comprehensive MQTL analysis was carried out to identify genomic regions associated with grain-yield related traits in durum wheat under different water regimes. A total of 724 QTL on all 14 chromosomes (genomes A and B) were collected for the 19 yield-related traits selected, of which 468 were reported under rainfed conditions, and 256 under irrigated conditions. Out of the 590 QTL projected on the consensus map, 421 were grouped into 76 MQTL associated with yield components under both irrigated and rainfed conditions, 12 genomic regions containing stable MQTL on all chromosomes except 1A, 4A, 5A, and 6B. Candidate genes associated to MQTL were identified and an in-silico expression analysis was carried out for 15 genes selected among those that were differentially expressed under drought. These results can be used to increase durum wheat grain yields under different water regimes and to obtain new genotypes adapted to climate change.

Aims: Progressive chronic kidney disease represents a dreadful complication of type 2 diabetes mellitus (T2DM). We tested the pattern of use and the renal effects of old glucose-lowering drugs in T2DM patients cared for by Italian general practitioners (GPs). Methods: Data of 2606 T2DM patients were extracted from the databases of GPs, who do not have access to the most recent glucose-lowering drugs in Italy. The rate of kidney function decline was calculated by CKD-EPIcr, based on two consecutive creatinine values. Results: Metformin was used in 55% of cases, either alone or with sulfonylureas/repaglinide, across the whole spectrum of CKD (from 66% in stage G1 to only 8% in G4). Sulfonylurea use peaked at 21–22% in stage G2–G3a, whereas repaglinide use significantly increased from 8% in G1 to 22% in G4. The median rate of CKD decline was − 1.64mL/min/1.73m2 per year; it was higher in G1 (− 3.22 per year) and progressively lower with CKD severity. 826 cases (31.7%) were classified as fast progressors (eGFR decline more negative than − 5mL/min/1.73m2 per year). The risk of fast progressing CKD was associated with increasing BMI, albuminuria, and sulfonylurea use, alone (OR, 1.47; 95% confidence interval, 1.16–1.85), or in association with metformin (OR, 1.40; 95% CI 1.04–1.88). No associations were demonstrated for metformin, cardiovascular and lipid lowering drug use. Conclusion: In the setting of Italian family practice, sulfonylurea use is associated with progressive CKD in patients with T2DM. Metformin, at doses progressively reduced according to CKD stages, as recommended by guidelines, is not associated with fast progression.

Background Dental pulp stem cells (DPSCs) are low immunogenic and hold immunomodulatory properties that, along with their well-established multi-potency, might enhance their potential application in autoimmune and inflammatory diseases. The present study focused on the ability of DPSCs to modulate the inflammatory microenvironment through PD1/PD-L1 pathway. Methods Inflammatory microenvironment was created in vitro by the activation of T cells isolated from healthy donors and rheumatoid arthritis (RA) patients with anti-CD3 and anti-CD28 antibodies. Direct and indirect co-cultures between DPSCs and PBMCs were carried out to evaluate the activation of immunomodulatory checkpoints in DPSCs and the inflammatory pattern in PBMCs. Results Our data suggest that the inflammatory stimuli trigger DPSCs immunoregulatory functions that can be exerted by both direct and indirect contact. As demonstrated by using a selective PD-L1 inhibitor, DPSCs were able to activate compensatory pathways targeting to orchestrate the inflammatory process by modulating pro-inflammatory cytokines in pre-activated T lymphocytes. The involvement of PD-L1 mechanism was also observed in autologous inflammatory status (pulpitis) and after direct exposure to pre-activated T cells from RA patients suggesting that immunomodulatory/anti-inflammatory properties are strictly related to their stemness status. Conclusions Our findings point out that the communication with the inflammatory microenvironment is essential in licensing their immunomodulatory properties. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02664-4.

A diagnostic non-invasive biomarker test for prostate cancer at an early stage, with high sensitivity and specificity, would improve diagnostic decision making. Extracellular RNAs present in seminal plasma might contain biomarker potential for the accurate detection of clinically significant prostate cancer. So far, the extracellular messenger RNA (mRNA) profile of seminal plasma has not been interrogated for its biomarker potential in the context of prostate cancer. Here, we investigate the mRNA transcriptome in seminal plasma samples obtained from prostate cancer patients (n=25), patients with benign prostate hyperplasia (n=26) and individuals without prostatic disease (n=6). Seminal plasma harbors a complex mRNA repertoire that reflects prostate as its tissue of origin. The endogenous RNA content is higher in the prostate cancer samples compared to the control samples. Prostate cancer antigen 3 (PCA3), a long non-coding RNA with prostate cancer-specific overexpression, and ATP-binding cassette transporter 1 (ABCA1), known to be involved in the prostate cancer pathogenesis, were more abundant in the prostate cancer group. In addition, twelve high confidence fusion transcripts could be detected in prostate cancer samples, including the bona-fide prostate cancer fusion transcript TMPRSS2-ERG. Our findings provide proof-of-principle that the extracellular transcriptome of seminal plasma can reveal information of an underlying prostate cancer.

A better understanding of the genetic basis of the plastic response of plants to drought will be instrumental to optimize management practices and breeding strategies in wheat. This study investigated a number of proxy traits i nfluencing the adaptive response to drought stress (NDVI and IRT by UAV and tractor, leaf and spike waxiness, leaf angle and leaf rolling) using a GWAS panel of 280 elite durum wheat accessions that were field - evaluated at Maricopa Agricultural Center, USA , under full irrigation and progressive drought stress. A genetic characterization of the durum panel was carried out using the Illumina iSelect wheat 90K SNP assay and a Genome Wide Association Study (GWAS) was performed using Mixed Linear Model (MLM) i n Tassel in order to identify the genetic intervals harboring loci controlling the investigated traits. For epicuticular leaf and spike waxiness, highly significant QTLs were detected for both traits (chromosomes 1B, 2A, 5B) while others were associated on ly to one of the two traits (chr. 1AS, 2AS and 7BL for ear waxiness, 6BS and 4BS for leaf waxiness). GWAS analysis pointed out other significant regions controlling leaf angle in chr. 1AL, 1BS, 3AS, 5AS, 5BL and 6BL chromosomes, two major QTLs in chr. 5BL and 6BS for leaf rolling and four in chr. 1AL, 5BL, 6BS and 7BL for SPAD. As to NDVI and IRT collected in different times and phenological phases, different results were obtained with the drone and tractor-mounted camera. Common QTLs were detected with both methods on chr.2BS, 5AL, 7AS and 7AL for NDVI. Additional QTLs were identified in chr. 1AL and 4BL for NDVI and in chr. 2AL and 5AS for IRT trait with tractor-mounted sensors.

In this study we report the characterization of 183 elite durum wheat ( Triticum turgidum ssp. durum Desf.) for root system architecture (RSA) and shoot developmental traits. Plants were grown in controlled conditions up to the 7th leaf appearance (late tillering) using the high throughput phenotyping platform GROWSCREEN Rhizo, a rhizo - box - based system consisting of deep (90 cm) rhizo - boxes integrated with automatic root RGB imaging. The following RSA traits were measured: seminal root length, noda l root length, lateral root length, root system convex hull, root system width and depth distribution (twice per week). Measurements of leaf area, leaf number and tiller number were performed twice per week and SPAD measurements were collected twice during the experiment. Root dry biomass and shoot fresh and dry biomass were collected at the end of the experiment. The dynamic collection of the above mentioned traits allowed us to model root and shoot growth and thus to disentangle the final point phenotypes in simpler and integrative phenes. A genome - wide association study (GWAS) based upon the Illumina Infinium 90K SNP assay identified many QTLs for RSA and/or shoot growth traits (P < 0.0001). GWAS confirmed a highly significant effect on adult plant root s ystem width due to two major QTLs on chromosomes 6AL and 7AC previously identified on seminal roots (Maccaferri et al. 2016). Notably, haplotype frequency of the QTL cluster on chromosome 7AC was found to be significantly associated with root depth, root s ystem width, root specific weight and shoot/root ratio. Notably, shoot/root ratio revealed a strong, contrasting selection pattern between the cultivars released by the rainfed and irrigated breeding programs conducted at ICARDA and CIMMYT, respectively, suggesting an indirect but major role of RSA features in durum wheat breeding and environmental adaptation. These results provide valuable insights toward a better understanding and more effective deployment of the RSA QTLome in durum wheat as related to di fferent environmental conditions.

Variation of gene content and gene expression in terms of relative quantitative expression and tissue/organ specificity is a substantial factor affecting phenotypic diversity. In crops, particularly in cereals, the pantran scriptome and pan - genome concepts raised soon after the reference genomes were made available. Characterizing the gene expression presence - absence variation (ePAV) of tetraploid durum wheat ( Triticum turgidum ssp. durum) enables to investigate the associat ion between the genotypic and phenotypic variation at an unprecedented level of precision. The current study presents the transcriptome analysis for 13 elite varieties from worldwide germplasm spanning from 1969 up to 2005. We aim to describe the gene expr ession variation in relation to a high - quality reference genome sequence assembly of durum wheat cv. Svevo (c/o International Durum Wheat Genome Sequencing Consortium). cDNA libraries for the 13 varieties were produced from roots and leaves at the seedling stage, and developing grains. In order to study the gene expression pattern, RNA - seq libraries of 13 varieties were aligned to the durum wheat genome using HISAT2. The transcript abundance was calculated using StringTie and Ballgown. Expression matrix was then normalized using R package DESeq2 for further clustering and variance analysis. The annotation of the Svevo assembled genome resulted in 66,559 high confidence gene models. Overall, 75.0% (48,007 genes), 70.5% (45,142) and 74.5% (47,702) of genes wer e expressed in grain, leaf and roots, respectively. Considering the cultivars and the tissue/organ libraries overall, the percentage of genes mapped to the Svevo genome reference varied from 48.0% (Altar84, Capeiti 8, Claudio, Saragolla leaves) to a maximu m of 61.0% (Meridiano, Strongfield roots and grains). Principal Component Analysis (PCA) analysis showed a clear gene expression clustering lead by organs (leaves, grains and roots accounting for 33.0 % variance). Hierarchical clustering based on the stron gest PC1 – PC2 scores clearly differentiated up - and down - regulated gene clusters based on tissues and varieties. Variance expression analysis projected on the Svevo assembly allowed us to identify the chromosome regions that drove the major expression varia tion patterns. Presence/absence of expression polymorphism could also be observed for several of the genes sorted by PCA. Interestingly, by clustering the gene expression profiles and the cultivar’s expression profiles several gene expression patterns rela ted to the ancestry relationship among cultivars were evidenced, particularly for the grains. The functional annotation of these gene clusters is ongoing. Towards assembly of a pan - transcriptome in durum, the cultivar - specific reads that could not be mappe d on the Svevo genome (4 - 30% referred to the Svevo Illumina sequencing data) are being de novo assembled. This expression pattern database could also be useful to identify genes regulated by eQTLs and to elucidate the function of candidate genes

QSbm.ubo - 2BS=Sbm2, a major QTL controlling the response to Soil - Borne Cereal Mosaic Virus (SB CMV) in durum wheat, was c haracterized in two recombinant inbred line populations, namely Meridiano (resistant, R) x Claudio (moderately susceptible, MS) and Simeto (susceptible, S) x Levante (R). B y means of meta - QTL analysis QSbm.ubo - 2BS was mapped as a unique QTL within a 2 cM - wide interval (LOD - 2) in the distal region of chromosome arm 2BS (Maccaferri et al., 2012) . The addition of the Illumina 90K SNPs array to the durum linkage maps allowed to identify 36 transcripts - associated SNPs tightly associated with the Mendelized QTL (Maccaferri et al., 2014) . Nine SNPs from the Illumina 90K wheat array were converted to KASP markers, which provided fluorescent high - throughput assays spanning the QTL region. Marker - assisted selection (MAS) was performed on ∼ 2,000 RILs from the Svevo (R) x Ciccio (S) population (Gadaleta et al., 2009) with two KAS P markers flanking the QTL interval , KUBO 9 and KUBO 13. MAS identified 291 lines recombinant between the two markers. These lines were characterized for SBCMV response in the 2016 field nursery under severe and uniform SBCMV infection. The lines were scor ed for symptom severity (SS) on a 0 to 4 scale , where 0 = very res istant and 4 = very susceptible (Vallega and Rubies Autonell, 1985). They were also genotyped with seven KASP markers distributed along the QTL interval ( KUBO 1 , KUBO 3 , KUBO 27 , KUBO 29 , KU BO 38, KUBO 40 and KUBO 41 ) and with the DArT marker wPt - 2106 , the marker most associated with the phenotype in the Meridiano x Claudio RIL population (Maccaferri et al., 2012). The bimodal distribution of SS reflects the segregation of the resistance trai t in the QTL interval: frequency peaks were observed around values of 1.7 and 3.8. The fine - mapping allowed to narrow the most probable support interval to 0,2 cM between KUBO 27 and KUBO 1 based on the Svevo x Ciccio RILs population. Work is in progress to analyze other - 1,000 RILs of the same population in order to confirm the results obtained with the first part of the study and to improve the ongoing fine - mapping of the gene responsible for the resistance.

Genetic analysis of Soil-Borne Cereal Mosaic Virus (SBCMV) resistance in durum wheat was carried out on two recombinant inbred line (RIL) mapping populations obtained from Meridiano (resistant) x Claudio (susceptible) and Simeto (susceptible) x Levante (resistant) Italian elite cultivars. The RILs were characterized for SBCMV response under severe infection conditions over three consecutive years (2007-2009), as reported in Maccaferri et al. (2008 and 2011). Heritability of the disease response was high, with h2 values always above 80%. Joined quantitative trait locus (QTL) analysis pointed out the presence of a major quantitative trait locus (QSbm.ubo-2BS) in the distal chromosome 2BS accounting for 60–90% of the phenotypic variation for symptom severity, 40–70% for virus concentration and 30-60% for grain yield. By means of meta-QTL analysis QSbm.ubo-2BS was mapped as a unique QTL within a 2 cM-wide interval (LOD-2) close to the DArT marker wPt-2106 and tagged by wmc661-gwm210-barc35. The addition of the Illumina 90K SNPs array to the durum linkage maps allowed to map 36 gene-associated SNP markers flanking 1 cM on both sides the Mendelized QTL. The sequence of the wPt-2106 DArT clone was used to obtain a diagnostic PCR-based assay based on both high resolution melting (HRM) analysis and simple agarose gel electrophoresis (assay based on a 4 bp-indel) while the SNPs are being transformed into fluorescent Kasp® marker assays. Up to now, seven functional Kasp® markers have been obtained and re-mapped on the initial mapping populations. The distribution and frequency of the resistant haplotype is being investigated in panels of elite durum wheat (Triticum turgidum ssp. durum), cultivated emmer (Triticum dicoccum) and wild emmer wheat (Triticum dicoccoides). Collectively, these results provide the basis for efficient marker-assisted selection of resistance to SBCMV as well as the positional cloning of QSbm.ubo-2BS.

Key message: SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Abstract: Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.

In major crops, panels of germplasm accessions have been assembled for allele mining at targeted candidate genes and for whole-genome association mapping studies. A germplasm collection of 189 cultivated durum wheat accessions representing the major breeding groups was tested in a broad range of Mediterranean environments under rainfed and irrigated conditions with an average yield ranging from 0.9 to 6.8 t/ha. Yield, yield components, agronomic and physiological traits were recorded in 15 trials and tested for significant association with the allelic profile of 180 microsatellite markers (simple sequence repeats, SSRs). Population structure was evaluated and the clustering data were used as covariates in the association test. SSRs showing significant associations in several environments were identified for the traits with the highest heritability values, i.e. plant height, heading date, peduncle length and kernel weight, with R2 values ranging from 5 to 10%. As to yield and yield components, most associations were detected only in two to four environments, with an average R2 value lower than 5%.