In the scenario of ongoing climate changes, the selection of plant genotypes with high salt tolerance is emerging as the most sustainable strategy to safeguard crop yield and quality and make productive use of salinized soils. Glassworts are annual and perennial halophytes found in inner and coastal wastelands, indistinctly consumed as high-nutritional green vegetables. Traditional taxonomic classification based on morphological traits can be very challenging in glasswort, due to phenotypic plasticity, reduced plant morphology, and inbreeding. In this work, we used DNA-based molecular tools to overcome such constraints and assess inter-generic and inter-specific genetic diversity in a collection of ecotypes from different Apulian areas. A fast and reliable Allele-Specific PCR assay was optimized to enable molecular detection of annual and perennial genera. Species-level classification was obtained through a similarity- and phylogeny-based approach relying on matK and rbcL DNA barcoding. Combined DNA tools identified perennial samples as Sarcocornia fruticosa and Arthrocaulon macrostachyum, along with annual Salicornia europaea, and phylogenetic trees unveiled genetic distances between glassworts, which clustered according to life cycle. The relationship between genotypes and nutritional profiles was finally investigated, suggesting that environmental factors may play a predominant role over taxonomic relatedness in shaping interspecific differences in nutrient composition of the analyzed samples.

Durum wheat, a globally significant crop for high-quality pasta production, remains vulnerable to unseasonal freezing events, a risk that is intensified with climate variability. To address this challenge, we combined genome-wide association studies (GWAS), genomic prediction, and marker-assisted selection to improve both freezing tolerance and grain quality in durum wheat. A panel of 250 diverse accessions, comprising cold-adapted lines from Eastern Europe and high-quality genotypes from Southern Europe, was genotyped using a 25K SNP array. Clear genetic differentiation by geographical origin and growth habit highlighted contrasting allelic patterns for adaptation and quality traits. Phenotypic evaluations were carried out in experimental field trials over two consecutive growing seasons in Italy and Russia to assess the freezing tolerance and quality performance of the genetic materials. GWAS identified five significant marker-trait associations (MTAs) for freezing tolerance on chromosomes 2A, 2B, 3B, 4A, and 5A. Notably, a strong MTA on chromosome 5A (physical position 488.2 Mb) individually explained up to 27% of the phenotypic variance (PVE), co-localizing with the critical Fr-A2 cold-stress regulatory locus. Significant associations for grain-quality traits were localized on a 1B chromosome hotspot (541-652 Mb). A multi-trait genomic selection model integrating freezing tolerance, grain weight, and gluten traits enabled the identification of optimal parental lines, resulting in measurable gains across simulated generations. From the top-ranked crosses, BC2F2 populations were developed and genotyped with KASP markers targeting validated MTAs. Lines carrying favorable alleles for both freezing tolerance and gluten strength were successfully selected, confirming the predictive accuracy of the model. The integration of GWAS, diversity-preserving genomic prediction, and functional marker validation offers a robust and scalable pipeline for breeding cold-resilient, high-quality durum wheat, providing tangible tools to adapt Mediterranean and similar wheat systems to increasing climate variability.

Strigolactones (SLs) are carotenoid-derived molecules that act as both rhizosphere signals and plant hormones. Although they play pivotal roles in plant development and signaling, our understanding of their functions, particularly in response to environmental stresses, remains limited. Moreover, the SL biosynthetic enzyme CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7) has been proposed to exert SL-independent biological roles, but experimental evidence is lacking. To address this, we analyzed root transcriptomic profiles of the wild type (WT) pea cultivar 'Tere`se' and the two near-isogenic mutants rms5, defective in CCD7, and rms1, defective in CCD8. Gene Ontology enrichment analysis revealed that SL deficiency suppresses stress-related processes, including responses to salt, heat, and hydrogen peroxide, as well as cellular functions related to cell cycle progression, cell division, and protein and amino acid metabolism. LC-MS/MS profiling revealed significant crosstalk with stress-related hormones, with SL levels positively correlated with abscisic acid and negatively correlated with jasmonic acid. Analysis of mutant-specific transcriptomic changes indicated that CCD7 contributes to several biological processes beyond its role in SL biosynthesis, including light-related functions, apocarotenoid metabolism, and mycorrhization. Colonization assays further demonstrated a SL-independent positive role of CCD7 in mycorrhization, as rms5 mutants exhibited reduced fungal colonization compared to rms1 and WT. Overall, our findings reveal a broad involvement of SLs in plant stress adaptation and uncover additional CCD7mediated pathways beyond canonical SL biosynthesis, which are potentially linked to the accumulation of 9-cis beta-carotene-derived apocarotenoids or alternative CCD7 substrates.

BACKGROUND: Orobanchaceae are parasitic weeds causing substantial yield losses in many crops, including pea (Pisum sativum L.). Within host species, genotypes that display enhanced resistance to Orobanchaceae often exude low levels of strigolactones (SLs) from their roots, in line with evidence that SLs stimulate the germination of Orobanchaceae. However, to which extent genetically determined low SL exudation contributes to field resistance to Orobanchaceae was poorly investigated. Here, we studied the relation between SL exudation and field response to Orobanche crenata Forsk. (Oc) in pea. RESULTS: The screening of a germplasm panel identified three novel sources of field resistance to Oc and revealed an association between field resistance and low SL exudation. Although the SL-deficient mutants rms1 and rms5 were more resistant than their wild-type backgrounds, they still suffered substantial Oc parasitization. Genetic analysis and RNA-seq of recombinant inbred lines uncovered both SL-dependent and SL-independent mechanisms contributing to the near-complete resistance to Oc previously reported in the breeding line ROR12, and identified candidate genes possibly underlying resistance loci. CONCLUSIONS: Besides identifying novel sources of resistance to Oc, our study indicates that reduced or absent SL exudation alone is not sufficient to confer complete field resistance to Oc in pea. This suggests the necessity of exploring SL-independent resistance mechanisms for breeding purposes. Further investigations are needed to clarify whether a similar scenario applies to other crops affected by Orobanchaceae, and to characterize genes causally related to Oc resistance.

The species Cucumis melo L. includes two neglected and underutilized vegetable crops, cucumber melon (C. melo subsp. melo var. chate) and snake melon (C. melo subsp. melo var. flexuosus). In particular, cucumber melon was highly popular in Mediterranean civilizations during Antiquity and the Middle Ages, whereas today its cultivation is mostly confined to the Salento area of southern Italy. Here, we describe the collection and characterization of thirteen cucumber melon and two snake melon populations from Salento. Whole-genome resequencing of DNA pools was performed to investigate genetic diversity within and among populations. The cucumber melon population UBGCMC111, most widely cultivated and marketed, exhibited the lowest heterozygosity, possibly reflecting more intense selection by farmers. Hierarchical clustering revealed genetic divergence of UBGCMC111 and UBGCMC053, the latter originating from a unique area of Salento with linguistic and cultural ties to Greek heritage. Despite some unique patterns of variation, snake melons clustered together with cucumber melons, suggesting overall genetic similarity. A total of 1,307 alleles were fixed and private to different populations under study, potentially valuable for their traceability. Some of them were associated with genes possibly underlying deeply grooved and pale green pepo phenotypes of the populations UBGCMC111 and UBGCMC124, respectively. Replicated field trials enabled germplasm characterization and the selection of agronomically superior populations. Overall, this study safeguards valuable C. melo genetic diversity from further genetic erosion. Additionally, it provides genomic and phenotypic data laying a foundation for integrating unexplored genetic resources into mainstream agrifood systems and breeding programs.

Almond [Prunus dulcis Miller (D. A. Webb), syn. Prunus amygdalus L.)] is the major tree nut crop worldwide in terms of production and cultivated area. Almond domestication was enabled by the selection of individuals bearing sweet kernels, which do not accumulate high levels of the toxic cyanogenic glucoside amygdalin. Previously, we showed that the Sweet kernel (Sk) gene, controlling the kernel taste in almond, encodes a basic helix loop helix (bHLH) transcription factor regulating the amygdalin biosynthetic pathway. In addition, we characterized a dominant allele of this gene, further referred to as Sk-1, which originates from a C1036→T missense mutation and confers the sweet kernel phenotype. Here we provide evidence indicating that the allele further referred to as Sk-2, originally detected in the cultivar "Atocha" and arising from a T989→G missense mutation, is also dominantly inherited and confers the sweet kernel phenotype in almond cultivated germplasm. The use of single nucleotide polymorphism (SNP) data from genotyping by sequencing (GBS) for population structure and hierarchical clustering analyses indicated that Sk-2 occurs in a group of related genotypes, including the widespread cultivar "Texas", descending from the same ancestral population. KASP and dual label functional markers were developed for the accurate and high-throughput selection of the Sk-1 and Sk-2 alleles, and the genotyping of a panel of 134 almond cultivars. Overall, our results provide further insights on the understanding of the almond cultivation history. In addition, molecular marker assays and genotypic data presented in this study are expected to be of major interest for the conduction of almond breeding programs, which often need to select sweet kernel individuals in segregant populations.

Pea (Pisum sativum L.) is a widely cultivated legume of major importance for global food security and agricultural sustainability. Crenate broomrape (Orobanche crenata Forsk.) (Oc) is a parasitic weed severely affecting legumes, including pea, in the Mediterranean Basin and the Middle East. Previously, the identification of the pea line "ROR12", displaying resistance to Oc, was reported. Two-year field trials on a segregant population of 148 F7 recombinant inbred lines (RILs), originating from a cross between "ROR12" and the susceptible cultivar "Sprinter", revealed high heritability (0.84) of the "ROR12" resistance source. Genotyping-by-sequencing (GBS) on the same RIL population allowed the construction of a high-density pea linkage map, which was compared with the pea reference genome and used for quantitative trait locus (QTL) mapping. Three QTLs associated with the response to Oc infection, named PsOcr-1, PsOcr-2, and PsOcr-3, were identified, with PsOcr-1 explaining 69.3% of the genotypic variance. Evaluation of the effects of different genotypic combinations indicated additivity between PsOcr-1 and PsOcr-2, and between PsOcr-1 and PsOcr-3, and epistasis between PsOcr-2 and PsOcr-3. Finally, three Kompetitive Allele Specific PCR (KASP) marker assays were designed on the single-nucleotide polymorphisms (SNPs) associated with the QTL significance peaks. Besides contributing to the development of pea genomic resources, this work lays the foundation for the obtainment of pea cultivars resistant to Oc and the identification of genes involved in resistance to parasitic Orobanchaceae.

Filtered SNP variants of 53 onion accessions in VCF v4.0 format. For details on SNP calling and filtering, please see M&M of the manuscript titled: "Genotyping by sequencing defines genetic structure within the “Acquaviva” red onion landrace".

Abstract Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.

Genetic structure and distinctive features of landraces, such as adaptability to local agro-ecosystems and specific qualitative profiles, can be substantially altered by the massive introduction of allochthonous germplasm. The landrace known as "Cipolla rossa di Acquaviva" (Acquaviva red onion, further referred to as ARO) is traditionally cultivated and propagated in a small area of the Apulia region (southern Italy). However, the recent rise of its market value and cultivation area is possibly causing genetic contamination with foreign propagating material. In this work, genotyping-by-sequencing (GBS) was used to characterize genetic variation of seven onion populations commercialized as ARO, as well as one population of the landrace "Montoro" (M), which is phenotypically similar, but originates from another cultivation area and displays different qualitative features. A panel of 5011 SNP markers was used to perform parametric and non-parametric genetic structure analyses, which supported the hypothesis of genetic contamination of germplasm commercialized as ARO with a gene pool including the M landrace. Four ARO populations formed a core genetic group, homogeneous and clearly distinct from the other ARO and M populations. Conversely, the remaining three ARO populations did not display significant differences with the M population. A set of private alleles for the ARO core genetic group was identified, indicating the possibility to trace the ARO landrace by means of a SNP-based molecular barcode. Overall, the results of this study provide a framework for further breeding activities and the traceability of the ARO landrace.

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.

This dataset is referred to a collection of 41 faba bean (Vicia faba L.) and 15 lentil (Lens culinaris Medik.) accessions from the ex situ repository of the Institute of Biosciences and Bioresources of the Italian National Research Council (CNR-IBBR). All the accessions were grown at the experimental farm "P. Martucci" of the University of Bari "Aldo Moro" (41°01′22.1′′ N 16°54′21.0′′ E) during the growing season 2017–2018, according to a randomized block design with two replicates, each constituted by 10 individual plants. The dataset reports raw and elaborated analytical data determined on the flour produced from individual accessions, concerning proximate composition, bioactive compounds, antioxidant activity, fatty acid composition, and physicochemical and functional properties. Elaborated data might be used to understand the compositional variability within the species and, together with raw data, to highlight peculiar accessions characterized by valuable nutritional and/or technological attitude useful in research institutions and food industries. Furthermore, the data can be used for genetic studies aimed at identifying genomic regions underlying nutritional and technological traits.

The study was carried out on 23 entries of Origanumcollected from different areas of south Italy. The 23 entries were characterizedvia determining the chemical composition of their essential oils and genetic variability. The gas-chromatography of the essential oils of oregano accessions allowed the detection of 44 components with the predominance of carvacrol, thymol, linalyl acetate, γ-terpinene, o-cimene, s-caryophylleneand cis-ocimene. A high variability in the main components concentration was revealed except in the case of the accessions 13, 14 and 15 where the linalyl acetate ranging between 51.27 and 60.93%, outlining a new oregano chemotype.Using hierarchical cluster analysis, four main groups of samples were observed. Genetic variability using the RAPD analysis was not able to reveal clear polymorphism PCR patterns useful to distinguish the entries.So that, we decided to conduct further molecular analyses to determine the genetic variation among the entries under investigation, using AFLPs a powerful tool to perform phylogenetic analysis. This technique shows a high capability in detecting genetic variation. Combination between fluorescent system and polyacrylamide gels allows obtaining large number of bands (225 to 557). Finally, thecurrent study shows thatthe Dendrogram of genetic similarity of Origanum is widely variable amongst genotypes of this plant.

Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the "Acquaviva red onion" (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders.

High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype-phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.

Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index F-ST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.

A comprehensive study to assess and compare physico-chemical, nutritional and functional properties of a chickpea germplasm collection was carried out. The collection, composed of 57 accessions, also included black chickpeas from Apulia (Southern Italy), previously shown to display peculiar phenotypic and genetic features with respect to desi and kabuli chickpeas, and for which no information is currently available. Associations of genetic and phenotypic traits with nutritional and functional properties were assessed. Black (including Apulian types) and brown chickpeas showed a dietary fiber content ranging from 18.0 to 22.1 g 100 g(-1), high bioactive compound contents, and levels of PUFA that reached 64.4 and 67.0 g 100 g(-1) of total fatty acids, respectively. Brown accessions were characterized by high values of water absorption capacity (1.9 g water g(-1) of flour), therefore could be suitable for mixing with cereal flours to produce cereal-pulse foods. Our findings highlight the nutritional and technological potential of local landraces which are being replaced by modem cultivars and are therefore, at risk of genetic erosion.

Background: The variation on morphological, biochemical, and genetic characters is very important in germplasm management and conservation strategies. Objective: To determine the diversity of 23 accessions from Origanum vulgare L. and a commercial cultivar on the basis of agronomical, biochemical and genetic features. Methods: Different characters related to vegetative growth and essential oil production were studied while the genetic relationships between the individuals were evaluated with the use of Amplified Fragment Length Polymorphism. Results: Despite the accessions exhibited cymyl- and acyclic-compounds, all the essential oil chemotypes according to the prevalence of essential oil fractions were phenotypically varied. A considerable amount of biomass with maximum values in plant height was achieved by thymol/γ-terpinene chemotype and carvacrol chemotype making them of particular interest for the production of high-quality plant material and further for the mechanical harvest. The AFLP analysis, performed using 10 primer combinations, to obtain a dendrogram of genetic similarity, revealed a genetic variability that could be useful for the selection of the proper genetic groups in future breeding programs. Conclusion: We identified two chemotypes thymol/γ-terpinene and carvacrol with their suitability for the production of biomass and essential oil and for the mechanical harvest. The results of the molecular characterization of the species may support and contribute to breeding programmes for agronomic and biochemical traits.

The data article refers to the paper "Nutritional, physico-chemical and functional characterization of a global chickpea collection" [1]. The data are referred to a germplasm collection of 57 chickpea accessions from the ex situ repositories of the United States Department of Agriculture (USDA), the Department of Plant, Soil and Food Science of the University of Bari, Italy (DiSSPA), and the Institute of Biosciences and Bioresources of the Italian National Research Council (CNR-IBBR). Thirty-six accessions, belonging to desi and kabuli types, were representative of the geographic distribution of chickpea global cultivation, whereas twenty-one accessions, referable to the Apulian black type, derived from different area of the Apulian region, south of Italy. All the accessions were grown at the experimental farm "P. Martucci" of the University of Bari "Aldo Moro" (41°01'22.1″ N 16°54'21.0″ E) during the growing season 2017-2018, according to a randomized block design with two replicates, each replicate formed by 30 individual plants. This article reports the data of the proximate composition, the total bioactive compounds content, the fatty acid composition and the physico-chemical and functional properties of chickpea flour. Information provided in this article can be used by food industry to develop chickpea-based foods and by geneticists for studies of association mapping aimed at the identification of genomic regions controlling the nutritional and technological traits.

Wild almond species accumulate the bitter and toxic cyanogenic diglucoside amygdalin. Almond domestication was enabled by the selection of genotypes harboring sweet kernels. We report the completion of the almond reference genome. Map-based cloning using an F-1 population segregating for kernel taste led to the identification of a 46-kilobase gene cluster encoding five basic helix-loop-helix transcription factors, bHLH1 to bHLH5. Functional characterization demonstrated that bHLH2 controls transcription of the P450 monooxygenase-encoding genes PdCYP79D16 and PdCYP71AN24, which are involved in the amygdalin biosynthetic pathway. A nonsynonymous point mutation (Leu to Phe) in the dimerization domain of bHLH2 prevents transcription of the two cytochrome P450 genes, resulting in the sweet kernel trait.