Durum wheat productivity in Mediterranean regions faces growing challenges from drought and heat stress. Understanding the genetic architecture of diverse germplasm is therefore essential to support pre-breeding efforts and enhance stress adaptation. In this context, 125 durum wheat genotypes were evaluated for agro-morphological traits across two contrasting Algerian locations over two growing seasons. A subset of 94 genotypes, selected on the basis of phenotypic characterization, was genotyped using the Illumina 7K SNP array. Population structure analysis revealed two to four subgroups, with linkage disequilibrium decaying at 4.09 Mb. Genome-wide association analysis identified 27 distinct significant SNPs associated with eight traits, with most associations detected for spike length, thousand-kernel weight, and plant height. The marker TGWA25K-TG0010 on chromosome 4A showed pleiotropic effects on plant height and peduncle length and co-localized with the Dwarf8 and gibberellic-acid-insensitive genes. Additionally, wsnp_Ex_c2033_3814035 on chromosome 2A was associated with heading earliness and the number of fertile spikelets per spike, and wsnp_Ku_c51039_56457361 on chromosome 5A with plant height and peduncle length in a single site and season. Several other environment-specific associations were also identified. These results support future studies in which the identified markers may be deployed in breeding strategies aimed at improving yield stability and stress adaptability in durum wheat under Algerian conditions.

Polyphenol oxidase (PPO) activity is a key determinant of wheat quality, influencing enzymatic browning of end products while also contributing to biochemical defence against (a)biotic stresses. In this review, we present a comprehensive structural characterization of more than 25 distinct alleles across the Ppo-1 and Ppo-2 gene families, revealing extensive allelic diversity between bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum ssp. durum (Desf.) Husn.). Comparative analyses across the A, B, and D genomes reveal substantial structural polymorphisms that contribute to functional diversification of Ppo genes. Our synthesis indicates that this broad allelic repertoire provides a genetic toolkit for fine-tuning PPO activity across tissues and phenological stages. This regulation is important for environmental adaptation while maintaining high processing quality standards. Emerging evidence challenges the prevailing assumption that “low-PPO is always better.” Higher PPO activity levels in certain cultivars are often associated with more robust defence responses, potentially providing greater protection against pathogens and environmental stressors. However this relationship remains largely correlative and requires functional validation. These observations suggest that excessive suppression of PPO activity may inadvertently weaken plant resilience. Overall, the data support a paradigm shift toward strategic modulation of PPO activity, balancing the maintenance of plant defence across diverse agro-climatic environments with the preservation of end-use quality in wheat-derived products.

The Apulian wine industry, a cornerstone of Italian viticulture, benefits from the great genetic diversity of local grape varieties that are closely linked to the traditional and cultural heritage of Apulian landscape. The aim of this study is to investigate the genomic diversity of five representative Apulian grapevine varieties, ‘Negramaro’, ‘Malvasia Nera’, ‘Primitivo’, ‘Minutolo Bianco’ and ‘Uva di Troia’ using genotyping-by-sequencing. By analysing 59 183 high-quality single nucleotide polymorphism (SNP) markers across 75 clones, we were able to detect significant genetic variation within and between varieties. The fixation index was calculated for each individual SNP, identifying 5 363 non-redundant divergent SNPs. Of these, 1 785 were located within genes, including 887 in untranslated regions, 518 in introns, and 380 in coding sequences. The results highlighted divergent loci associated with genes crucial for secondary metabolism, stress resilience, and berry quality traits. Key genes identified in this study include WRKY transcription factors, MYB regulators, and enzymes such as glycosyltransferases and O-methyltransferases, all of which play an important role in the biosynthesis of secondary metabolites that influence wine flavour, aroma, and pigmentation. Additionally, six SNP loci were validated for varietal discrimination by PCR amplification and Sanger sequencing, confirming their potential for traceability. These results provide a solid genomic foundation for the preservation and valorisation of Apulia's rich wine heritage and for the development of targeted breeding programs to enhance the quality and resilience of Apulian wines in the face of changing consumer's preferences, market and climatic conditions.

The bacterium Xylella fastidiosa subsp. pauca (Xfp) is the causal agent of Olive Quick Decline Syndrome (OQDS), a disease characterized by leaf scorch, irregular periderm development, branch desiccation, general growth arrest, and eventual plant death, leading to extensive damage to olive groves (Olea europaea L.) and severely impacting agricultural production in the Apulia region, Italy’s leading producer of olive oil. To date, no cure for the disease exists, and most olive germplasm is susceptible, with only a few varieties showing resistance. Among them, the Leccino cultivar displays resistance to the pathogen, exhibiting little to no symptoms after infection. In contrast, other varieties, such as Oliva Rossa, are highly susceptible, while cultivars like Donna Francesca exhibit an intermediate level of susceptibility. Only limited studies have investigated the genetic basis underlying these differential responses. Comparative transcriptomic analysis of the above-mentioned olive cultivars revealed distinct and divergent defence strategies. The susceptible Oliva Rossa showed a broad but largely ineffective transcriptional reprogramming, including the downregulation of cytoskeleton-related genes. In contrast, the resistant Leccino displayed a more targeted activation of sulphur assimilation pathways, antioxidant responses, and cell wall–associated proteins, enabling more effective pathogen containment. The cultivar Donna Francesca exhibited a reduced transcriptional response overall, consistent with its intermediate level of susceptibility. Only 5 of 1,758 differentially expressed genes were shared across all cultivars, highlighting highly cultivar-specific responses and the overall complexity of the host–pathogen interaction. Resistance appears to be associated with a focused and limited transcriptional activation, susceptibility with widespread but ineffective gene reprogramming, and intermediate susceptibility with modest yet efficient transcriptional adjustments. Each olive cultivar responds to Xfp infection by modulating a distinct set of genes, suggesting that resistance and susceptibility are governed by different molecular mechanisms. This cultivar-specific transcriptional behaviour highlights the complexity of host–pathogen interactions and expanding analyses to additional genotypes could provide further insights into the genetic and molecular bases of these diverse responses.

The success of the Primitivo variety underscores the critical need for the managing of clone genetic conservation, utilization, and improvement. By combining genomic and environmental data, breeders can better predict the performance of varieties, thereby improving breeding efficiency and enabling more targeted development of high-quality grapevine cultivars. In this study, 35 Primitivo clones were analysed, including selected and certified clones that have been propagated over several years in Apulia. Genetic variability among the Primitivo clones was assessed through genotyping by sequencing. Using 38,387 filtered SNPs, pairwise identity-by-state (IBS) analysis demonstrated the uniqueness of the 35 clones (IBS < 0.75), indicating a high degree of variability among the samples. Genetic diversity analysis revealed three primary groups, which were differentiated based on geographic origin. The clones from Gioia del Colle were grouped into two distinct clusters, which aligns with the observed variation in grape-related traits. The fixation index (FST > 0.50) identified numerous loci putatively associated with stress responses and developmental traits, including genes involved in key plant biological processes, stress response regulation, and adaptation to environmental conditions such as glutamate receptors, auxin, and ethylene signalling.

The olive tree (Olea europaea L.) holds exceptional ecological, cultural, and economic significance in the Mediterranean Basin. Understanding its genetic diversity is critical for conservation, breeding, and authentication of olive cultivars. While nuclear genome analyses have elucidated much of the species’ genetic structure, chloroplast genome sequencing provides complementary insights, particularly in tracing maternal lineages, uncovering domestication pathways, and identifying cryptic genetic variation. In this study, we investigated the plastome diversity of fifteen centuries-old olive trees from Jordan through reference-guided assembly and comparative analysis using the FARGA cultivar plastome as a reference. Despite overall genomic conservation, nucleotide diversity analyses revealed several polymorphic hotspots—most notably within the psbM and ycf1 genes and the atpB-rbcL intergenic spacer. Structural variation, including simple sequence repeats and tandem repeats, highlighted intra-population diversity. One sample (TF - 3) exhibited heteroplasmy, suggesting a biological origin that warrants further investigation. Phylogenetic reconstruction grouped most samples within the Mediterranean E1 lineage, with TF - 3 and a few others forming distinct clusters. Comparisons with nuclear genotyping data demonstrated both congruence and divergence, emphasizing the value of a dual-genome approach. This study reinforces the utility of plastome sequencing in varietal identification, conservation genetics, and evolutionary studies, and contributes novel genomic resources for Jordanian olive germplasm.

The Apulian wine industry, a cornerstone of Italian viticulture, benefits from the great genetic diversity of local grape varieties that are closely linked to the traditional and cultural heritage of Apulian landscape. The aim of this study is to investigate the genomic diversity of five representative Apulian grapevine varieties, ‘Negramaro’, ‘Malvasia Nera’, ‘Primitivo’, ‘Minutolo Bianco’ and ‘Uva di Troia’ using genotyping-by-sequencing. By analysing 59 183 high-quality single nucleotide polymorphism (SNP) markers across 75 clones, we were able to detect significant genetic variation within and between varieties. The fixation index was calculated for each individual SNP, identifying 5 363 non-redundant divergent SNPs. Of these, 1 785 were located within genes, including 887 in untranslated regions, 518 in introns, and 380 in coding sequences. The results highlighted divergent loci associated with genes crucial for secondary metabolism, stress resilience, and berry quality traits. Key genes identified in this study include WRKY transcription factors, MYB regulators, and enzymes such as glycosyltransferases and O-methyltransferases, all of which play an important role in the biosynthesis of secondary metabolites that influence wine flavour, aroma, and pigmentation. Additionally, six SNP loci were validated for varietal discrimination by PCR amplification and Sanger sequencing, confirming their potential for traceability. These results provide a solid genomic foundation for the preservation and valorisation of Apulia's rich wine heritage and for the development of targeted breeding programs to enhance the quality and resilience of Apulian wines in the face of changing consumer’s preferences, market and climatic conditions.

Bulked segregant analysis (BSA) is a widely used method for identifying genomic loci associated with traits of interest in crops. However, conventional BSA is limited by its reliance on phenotype-driven bulk sampling, which restricts its scalability and confines its applicability to single-trait analysis. This study introduces a novel method, reverse BSA-QTLseq, which uses genotype-driven bulk reconstruction through bioinformatics, enabling the simultaneous mapping of multiple traits from the same genotypic dataset. Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci (QTLs). Using a bread wheat recombinant inbred line (RIL) population as a case study, we mapped loci associated with heading date and plant height , confirming approximately 95% of known QTLs, including both dwarfing genes (e.g., Rht-B1 and Rht-5) and flowering-time regulators (e.g., Vrn-A1), and identified novel QTLs and candidate loci with strong phenotypic effects. The phased genotyping strategy maximized genetic distance in the initial sampling, facilitating the in silico reconstruction of trait-specific contrasting bulks. Integration of transcriptional profiles from the parental lines of the RIL population, from which the bulks were derived, aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response, nutrient transport, and stress adaptation. The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping, with broad implications for marker-assisted breeding and selection programs. Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq, accelerating genetic improvement in crops.

BACKGROUND:Plant genetic resources (PGRs) are crucial for sustainable agriculture and food security, but the roadmap of the European Strategy Forum on Research Infrastructures (ESFRI) lacks a dedicated research infrastructure (RI) for their systematic cataloguing, safeguarding and improvement. To fill this gap, we propose a new RI concept specifically for PGRs in Europe. SCOPE:The proposed RI, called 'Plant Genetic Resources Community for Europe' (GRACE), is aimed to support current and future research projects on PGRs, enhance collaboration across European countries, unlock the adaptive potential of crop biodiversity preserved in PGR collections, and strengthen the current and future sustainability of the food chain in Europe. As part of the preparatory project 'Promoting a Plant Genetic Resource Community for Europe' (PRO-GRACE), we analysed the current landscape of European RIs supporting PGR-related research in complementary fields regarding research aims, research products and features/services. CONCLUSIONS:Through a robust quantitative approach, we have identified gaps and potential synergies among six RIs from the Health and Food and Environment domains of the ESFRI roadmap. These findings were discussed in the context of European PGR research priorities and current societal needs, and the implementation of GRACE was proposed as a strategic response to these challenges.

This study aimed to identify and evaluate the genetic diversity of olive trees in Jordan, a country located in the eastern Mediterranean, where olive domestication originated. For this purpose, a total of 386 olive trees were analyzed, including 338 collected from two surveys (JOCC-1 and JOCC-2) across seven regions, and 48 selected accessions from the Olive Germplasm Bank of Jordan (JGBOC). These trees underwent comprehensive phenotypic and molecular characterization using different tools. Significant differences in morphological traits were detected among tested regions using the Chi-square test. Principal components analysis revealed that fruit color change and growth habit as the most discriminating traits, segregating the trees into two groups, with the first group including the Kanabisi cultivar and the second group including the Kfari Baladi cultivar. Utilizing Kompetitive Allele Specific PCR assay, two sets of informative SNPs were used for the genetic diversity analysis. Cladograms were constructed using the maximum likelihood method, revealing a consistent pattern where two clades containing identical genotypes were observed to cluster with the Kfari Baladi or Kanabisi. In addition, the SNP data was used to perform a comparative analysis with the Worldwide Olive Germplasm Bank of Córdoba, which revealed 73 unreported olive genotypes from Jordan. Genetic structure analyses using Discriminant Analysis of Principal Components (DAPC) identified four clusters with distinctive patterns of relatedness among 149 unique accessions, including 52 olive accessions from various Mediterranean countries (IOCC-3). ADMIXTURE analysis revealed four genetic clusters, consistent with the clustering observed in DAPC and cladogram analysis, indicating a high level of genetic admixture among Jordanian olive germplasm. In conclusion, the results show that olive trees in Jordan are highly diverse, providing valuable information for future conservation and management plans.

Although you may have visited a bank in your lifetime, maybe to deposit or withdraw money, it is likely that you have never been to a seed bank. These buildings do not contain money or gold bars but instead hold something even more precious: the seeds or other materials of plants belonging to over 50,000 species—~12.5% of all known plant species. Human pressures on natural ecosystems threaten many plants, and protecting the vast array of plant life on Earth is critical for assuring that we can grow enough food for everyone on the planet in the years to come. For this reason, scientists have thought of freezing seeds and/or other parts of plants to preserve them and make them available for the future. Seed banks also allow scientists to study the history of certain plants, and these banks can provide them with the resources needed to change some plant traits in helpful ways.

Two allelic variants of Pp-A3 and Pp-B1 were identified in purple durum wheat. Molecular markers at both loci were developed and validated on an independent panel, offering a breakthrough for wheat improvement. Purple wheats are a class of cereals with pigmented kernels of particular interest for their antioxidant and anti-inflammatory properties. Although two complementary loci (Pp-B1 and Pp-A3), responsible for purple pericarp have been pinpointed in bread wheat (Triticum aestivum L.), in durum wheat (Triticum durum Desf.) the causative genes along with functional and non-functional alleles are still unknown. Here, using a quantitative trait loci (QTL) mapping approach on a RIL population derived from purple and non-purple durum wheat genotypes, we identified three major regions on chromosomes 2A, 3A, and 7B explaining the highest phenotypic variation (> 50

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.

Key message Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Abstract Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values ( p -values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.

Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.

Durum wheat is a worldwide staple crop cultivated mainly in the Mediterranean basin. Progress in durum wheat breeding requires the exploitation of genetic variation among the gene pool enclosed in landraces, old cultivars and modern cultivars. The aim of this study was to provide a more comprehensive view of the genetic architecture evolution among 123 durum wheat accessions (41 landraces, 41 old cultivars and 41 modern cultivars), grown in replicated randomized complete block in two areas, Metaponto (Basilicata) and Foggia (Apulia), using the Illumina iSelect 15K wheat SNP array and 33 plant and kernel traits including the International Union for the Protection of new Varieties of Plants (UPOV) descriptors. Through DAPC and Bayesian population structure five groups were identified according to type of material data and reflecting the genetic basis and breeding strategies involved in their development. Phenotypic and genotypic coefficient of variation were low for kernel width (6.43%) and for grain protein content (1.03%). Highly significant differences between environments, genotypes and GEI (Genotype x Environment Interaction) were detected by mixed ANOVAs for agro-morphological-quality traits. Number of kernels per spike (h2 = 0.02) and grain protein content (h2 = 0.03) were not a heritability character and highly influenced by the environment. Nested ANOVAs revealed highly significant differences between DAPC clusters within environments for all traits except kernel roundness. Ten UPOV traits showed significant diversity for their frequencies in the two environments. By PCAmix multivariate analysis, plant height, heading time, spike length, weight of kernels per spike, thousand kernel weight, and the seed related traits had heavy weight on the differentiation of the groups, while UPOV traits discriminated moderately or to a little extent. The data collected in this study provide useful resources to facilitate management and use of wheat genetic diversity that has been lost due to selection in the last decades.

The olive tree (Olea europaea subsp. europaea var. europaea) represents the cornerstone crop of Apulian agriculture, which is based on the production of oil and table olives. The high genetic variability of the Apulian olive germplasm is at risk of genetic erosion due to social, economic, and climatic changes. Furthermore, since 2013, the spread of the Gram-negative bacterium Xylella fastidiosa subsp. pauca responsible for the olive quick decline syndrome (OQDS) has been threatening olive biodiversity in Apulia, damaging the regional economy and landscape heritage. The aim of this study was to investigate the differential response to X. fastidiosa infection in a collection of 100 autochthonous Apulian olive genotypes, including minor varieties, F1 genotypes, and reference cultivars. They were genotyped using 10 SSR markers and grown for 5 years in an experimental field; then, they were inoculated with the bacterium. Symptom assessments and the quantification of bacterium using a qPCR assay and colony forming units (CFUs) were carried out three and five years after inoculation. The study allowed the identification of nine putatively resistant genotypes that represent a first panel of olive germplasm resources that are useful both for studying the mechanisms of response to the pathogen and as a reserve for replanting in infected areas.