Capsaicinoids, the molecules responsible for pungency in pepper (Capsicum spp.), and their non-pungent analogs, capsinoids, are synthesized through the interaction of two distinct metabolic pathways: the branched chain fatty acid pathway and the phenylpropanoid pathway. These two families of bioactive compounds are unique to the genus Capsicum and, besides their importance for pepper taste, are associated with several beneficial effects, such as weight management, antioxidant activity and prevention of various diseases. Although QTLs associated with capsaicinoid and capsinoid accumulation have been reported in several studies, these findings remain dispersed across different populations, limiting their direct comparison and practical use in breeding. In this study, we aim to collect, compare, integrate, and synthesize the available literature on capsaicinoid and capsinoid QTLs. A total of 155 QTLs associated with these traits were physically mapped onto the reference pepper genome (CM334 -v1.6) and analyzed within a common genomic framework. The physical integration of the selected regions allowed us to identify 23 Quantitative Genomic Regions (QGRs) and prioritize potential candidate genes located within them. This genome-based integration advances beyond previous descriptive summaries, providing a unified physical framework for comparing QTLs across studies and genetic backgrounds. This review provides a comprehensive resource for researchers aiming to understand the genetic mechanisms behind capsaicinoid and capsinoid biosynthesis and for breeders focused on improving the levels of these bioactive compounds in pepper. It enables the identification of key QTL regions through the integration of data from diverse populations, highlights potential donor genotypes reported in the literature for specific traits, and facilitates the discovery of candidate genes for future functional validation and marker-assisted breeding. Overall, this study provides a consolidated genomic framework for understanding the genetic architecture of capsaicinoid and capsinoid biosynthesis and for accelerating the development of pepper cultivars with improved profiles of these bioactive compounds.

BackgroundColor transitions from green to purple in eggplant (Solanum melongena L.) flowers and berries result from chlorophyll and anthocyanin accumulation. While structural genes (CHS, CHI, F3’H, DFR, ANS, UGT) and regulatory transcription factors (MYB, bHLH, WD40) in the anthocyanin pathway are well characterized, fine-scale transcriptional regulation is less understood. Long non-coding RNAs (lncRNAs) contribute to pre- and post-transcriptional regulation, whereas alternative splicing (AS) events control exclusively post-transcriptional modifications.MethodsHere we performed an integrated transcriptomic analysis of mRNAs, lncRNAs and AS events to investigate fine regulation of anthocyanin biosynthesis.ResultsA PacBio assembly of the eggplant cultivar “Black Beauty” genome allowed the computational prediction and expression analysis of all transcripts in fruit peel and flower corolla. We identified 4, 126 lncRNAs and 34, 745 novel transcript isoforms, and tissue-specific regulatory networks revealed multiple lncRNAs and protein-coding genes AS events associated with anthocyanin biosynthesis. Quantification of anthocyanins in both peel and corolla enabled the construction of putative tissue-specific models of anthocyanin transcriptional regulation.DiscussionThis study provides a starting point to improve the knowledge of fine-tuning anthocyanin regulation at the transcriptional level, highlighting tissue-specific lncRNAs and AS events linked to regulatory genes, and offering, to our knowledge, the first evidence of lncRNA involvement in anthocyanin biosynthesis in eggplant.

Salinity severely limits eggplant productivity, yet the transcriptional bases of tolerance to prolonged salt exposure remain incompletely understood. Here, we analyzed long-term salinity responses in two contrasting eggplant (Solanum melongena L.) genotypes from the G2P-SOL core collection, focusing on genotype-dependent transcriptional regulation under chronic stress. Plants were exposed to 200 mM NaCl for 23 days at the reproductive stage, and transcriptome profiling was performed at the end of the stress period. Physiological assessment and high-throughput phenotyping confirmed a strong divergence in water status and plant architecture between genotypes under salinity, providing a reference framework for transcriptomic interpretation. RNA-seq analysis revealed marked genotype-specific differences in transcriptional responses. While both genotypes activated a conserved salt-stress program involving redox homeostasis, proteostasis and growth repression, the tolerant genotype displayed a substantially broader and more coordinated transcriptional reprogramming. This response involved large-scale modulation of pathways related to translation and RNA metabolism, hormone signaling crosstalk, membrane transport, cell wall remodeling and oxidative stress management, together with the selective repression of growth- and signaling-related functions. In contrast, the sensitive genotype showed a more limited response dominated by defense- and damage-associated transcripts. Overall, these results indicate that long-term salt tolerance in eggplant is associated with genotype-specific transcriptional reprogramming superimposed on a shared basal stress response. This work highlights regulatory pathways and candidate genes potentially relevant for breeding strategies targeting salt resilience.

ABSTRACT Globe artichoke ( Cynara cardunculus var. scolymus L.) comprises a broad range of local ecotypes and varietal groups whose genetic diversity has been investigated through different molecular markers. However, recent advances in next-generation sequencing and pangenomics approaches provide new opportunities to capture genome-wide variation at higher resolution and to develop practical tools for varietal discrimination, traceability, and germplasm conservation. In this study, we developed the first pangenomic framework for cultivated artichoke and evaluated pangenome-informed SNP markers for varietal fingerprinting. Whole-genome resequencing data from the Italian local ecotype ‘Asti Sorì’ were integrated with publicly available genomic data from representative globe artichoke and cultivated cardoon accessions to construct and annotate a pangenome. Genome-wide SNP and presence/absence variation (PAV) analyses were combined with pangenome-anchored genotyping-by-sequencing (GBS) data from 45 accessions representing the main cultivated varietal groups. The pangenome revealed a largely conserved core gene repertoire alongside a smaller accessory component, with gene accumulation curves suggesting a tendency toward saturation within the sampled cultivated germplasm. SNP- and PAV-based analyses provided complementary views of accession relationships and consistently resolved the principal cultivated groups. Across the broader germplasm panel, pangenome-anchored GBS-derived SNPs identified well-supported phylogenetic clusters corresponding to recognized varietal types. A reduced panel of 50 SNPs, selected through iterative random subsampling, retained at least 90% of the genetic diversity captured by the full dataset and reproduced its main population structure. This compact pangenome-anchored marker set provides a practical foundation for varietal fingerprinting, DUS-oriented applications, traceability, and conservation of traditional globe artichoke germplasm. Validation across independent collections will be required before routine deployment.

IntroductionRye (Secale cereale L.) is a cereal crop well adapted to marginal environments, where traditional populations represent valuable reservoirs of genetic diversity. In the Aosta Valley (NW Italy), several local rye populations have historically been maintained under small-scale farming systems, but their genetic structure has not yet been investigated using genome-wide approaches.MethodsWe performed a high-resolution population genomic analysis of twelve rye populations using a K-seq genotyping approach. A genome-wide SNP dataset was generated and used to assess genetic diversity and population structure through complementary multivariate, distance-based, and model-based analyses.ResultsSubstantial genetic variation was detected within populations (HT = 0.354), together with a moderate level of genetic differentiation among populations (GST = 0.254). Populations collected in the 1980s showed consistently higher genetic diversity and differentiation (HT = 0.392; GST = 0.311) than populations collected in 2000 (HT = 0.306; GST = 0.180), suggesting a reduction in genetic variability in more recent germplasm. Multivariate and clustering analyses identified distinct genetic groups and clusters of closely related populations, revealing a complex genetic structure shaped by both differentiation and admixture.DiscussionThese findings provide an updated view of the genetic architecture of Aosta Valley rye populations and underline the importance of conserving genetically diverse and differentiated populations. More broadly, the study demonstrates the utility of K-seq for generating informative SNP datasets and investigating population structure in rye, supporting its application to the characterization and management of plant genetic resources.

Heat stress is one of the most damaging abiotic constraints on crop productivity, and its consequences are expected to intensify as extreme temperature events become more frequent and severe. Pepper (Capsicum annuum L.) is particularly vulnerable to sustained high temperatures, which can disrupt photosynthetic performance, cellular homeostasis, and redox regulation. However, the physiological and transcriptional dynamics underlying genotype-dependent responses to prolonged heat exposure remain insufficiently understood. We combined repeated physiological measurements with time-course RNA sequencing to compare GPC003240, previously identified as a candidate heat-tolerant accession, with two non-elite accessions, GPC010350 and GPC014930, which are phenotypically divergent from each other, under 40/30 Celsius degrees Day/night temperatures for up to six days. GPC010350 maintained comparatively stable photosystem II performance and higher stomatal conductance, whereas GPC014930 showed progressive photochemical impairment and lower conductance; GPC003240 displayed a distinct, moderately responsive profile. Transcriptomic responses showed partial functional convergence during the early phase of stress exposure but diverged markedly after six days. When gene expression at day 6 was compared with the pre-treatment baseline separately within each genotype, 4,436 differentially expressed genes were detected in GPC010350, compared with 680 in GPC003240 and only 78 in GPC014930. The late response of GPC010350 was associated with enrichment of RNA- and ribosome-related, biosynthetic, DNA-repair, and genome-maintenance functions. By contrast, GPC014930 showed negative enrichment of photosynthesis, plastid organization, redox homeostasis, and translation-related processes. Global co-expression analysis identified a time-decreasing photosynthesis-associated module (ME5) and two time-increasing modules, ME12 and ME19, that were enriched in genes contributing to the late GPC010350 response. Integration of differential expressions, module membership, and functional annotation highlighted a heat shock transcription factor (Caz03g27980), HSP101 (Caz03g07770), and a dual-specificity phosphatase (Caz05g20970) as candidates for further investigation. Overall, the results suggest that genotype-dependent responses to prolonged heat exposure were associated not only with the magnitude of early transcriptional change, but also with differences in the temporal organization of stress-response, maintenance, and metabolic processes. The contrasting responses of the non-elite accessions GPC010350 and GPC014930 further highlight the value of phenotypically diverse germplasm for uncovering mechanisms relevant to future heat-tolerance breeding.

Italian sweet pepper landraces represent an important reservoir of genetic diversity, although their practical exploitation in breeding programmes remains limited. Historical germplasm collections preserve variation accumulated through centuries of farmer selection, but their organization into resources suitable for pre-breeding and parental selection has rarely been investigated. In this study, 35 historical Piedmont sweet pepper accessions conserved in the DISAFA Genebank and five historical breeding reference lines were characterized through quantitative fruit phenotyping and genome-wide SNP genotyping. A total of 190 individuals were genotyped by ddRADseq, yielding a final dataset of 1925 filtered SNP markers. Phenotypic characterization confirmed the major historical fruit morphotypes, while genome-wide analyses revealed genetic relationships broadly consistent with traditional morphotype classification and the history of conservative selection. Comparison between historical accessions and the corresponding sampled reference lines identified complementary private variation in all comparable genomic groups, although private variation was also detected in the reference materials. On this basis, we propose Historical Breeding Pools as a breeding-oriented interpretive framework integrating genomic relationships, traditional morphotypes and historical breeding reference lines to organize conserved diversity for future pre-breeding and parental selection. These results show how historical genebank collections can be characterized beyond conservation alone and used to prioritize genetic resources for further breeding-oriented evaluation.

Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the genome-wide association of historical genebank phenotypic data on a genotyped worldwide collection of 3449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a genotype-environment association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.

Eggplant (Solanum melongena L.) is a major Solanaceous crop of Asian origin, but genomic resources remain limited compared to related species. Here, a core collection of 368 accessions spanning global diversity of S. melongena and wild relatives is phenotyped for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, 40 chromosome-level assemblies of S. melongena, its progenitor S. insanum and the allied species S. incanum enable the construction of two graph-based pangenomes, capturing broad genetic variation. We demonstrate the power of these datasets by identifying major loci controlling prickliness and resistance to Fusarium oxysporum f. sp. melongenae, driven by SVs affecting the LONELY GUY 3 gene and a resistance gene cluster, respectively, as well as a mutation in a GDSL-like esterase/lipase gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, enabling detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.

Sweet pepper (Capsicum annuum L.) holds significant economic and nutritional value, with fruit shape being a key trait influencing marketability and consumer preferences. Traditional breeding approaches for improving fruit morphology are labor-intensive, requiring novel strategies to accelerate genetic gains. A Multiparent Advanced Generation Inter-Cross (MAGIC) population was developed from eight diverse C. annuum accessions to capture extensive genetic diversity. At present, the population is in the G6 developmental stage. To characterize the variability captured by the crossings, whole-genome sequencing of parental lines was performed, identifying similar to 39.3 million polymorphisms, including single nucleotide polymorphisms (SNPs) and structural variants (SVs). A preliminary selective sweep (SS) analysis based on sequencing data of the 8 parentals lines, together with 8 Italian landraces, was conducted, leading to the identification of genomic regions associated with fruit morphology. In these regions, candidate genes involved in transcription regulation and hormone response pathways were highlighted, and SNP variants across the genotypes identified. Among them, a set of polymorphisms on CaOFP20 (Caz10g08850), a transcriptional repressor associated with fruit elongation, phylogenetically clustered together the elongated-fruit accessions, reinforcing the putative role of the ovate-family transcription factor in fruit morphology regulation. Additional candidate genes, auxin response factors, and NAC domain proteins, were present in the selective sweep regions related to fruit weight, diameter, and length. These findings provide a valuable genomic framework that can be leveraged in marker-assisted selection to improve fruit shape traits in sweet pepper, contributing to more efficient and targeted breeding strategies.

This study investigates the genetic basis of fruit traits in European hazelnut ( Corylus avellana L.), with a focus on identifying the genetic determinants that influence nut and kernel traits as well as the genes associated with flowering time. The research aims to shorten hazelnut breeding cycles and understand the genetic interplay affecting these traits. Using a mapping population from 'Tonda Gentile delle Langhe' (TGdL) and 'Merveille de Bollwiller' (MB) cultivars (175 F1 progeny), extensive phenotyping and genotypic analysis were conducted. Quantitative trait loci (QTL) analysis identified 131 QTLs (52 major) associated with 12 nut and kernel traits were identified across the 11 LGs with 68 on the TGdL map and 63 on the MB map. Among them stable QTLs over the three years were detected on TGdL map (nine QTLs on five LGs) and MB map (13 QTLs on four LGs). The most interesting were on MB_04 and MB_05 LGs for fruit size traits, on TGdL_04 and TGdL_11 for fruit shape traits and on MB_02 for cluster traits. Through exploration of candidate genes within these regions a linkage between nut and kernel traits and flowering time were identified, along with candidate genes involved in key developmental processes such as cell proliferation and circadian clock regulation. Notably, genes affecting flowering time were also linked to fruit development traits, suggesting a genetic connection. Our findings highlight a significant genetic overlap between nut and kernel traits and flowering time, providing valuable genetic markers for use in hazelnut breeding programs. This research underlines the potential for using molecular breeding techniques to enhance trait selection efficiency, thereby supporting the development of new hazelnut varieties with improved quality and adaptability to changing environmental conditions. These insights are crucial for advancing sustainable agricultural practices and meeting the increasing global demand for hazelnuts.

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

The distribution of chlorophylls in eggplant (Solanum melongena) peel exhibits either a uniform pattern or an irregular green netting pattern. The latter, manifested as a gradient of dark green netting that is intensified in the proximal part of the fruit on a pale green background, is common in wild relatives and some eggplant landraces. Despite the selection of uniform chlorophylls during domestication, the netting pattern contributes to a greater diversity of fruit colours. Here, we used over 2300 individuals from different populations, including a multi-parent advanced generation inter-cross population for candidate genomic region identification, an F2 population for bulked segregant analysis by sequencing, and advanced backcrosses for edges-to-core fine-mapping, to identify SmGLK2 gene as responsible for the irregular netting in eggplant fruits. We also analysed the gene sequence of 178 S. melongena accessions and 22 wild relative species for tracing the evolutionary changes that the gene has undergone during domestication. Three different mutations were identified leading to the absence of netting. The main causative indel induces a premature stop codon disrupting the protein conformation and function, which was confirmed by western blot analysis and confocal microscopy observations. SmGLK2 has a major role in regulating chlorophyll biosynthesis in eggplant fruit peel.

Globe artichoke (Cynara cardunculus var. scolymus; 2n = 2x = 34) is a food crop consumed for its immature flower heads. Traditionally, globe artichoke varietal types are vegetatively propagated. However, seed propagation makes it possible to treat the crop as annual, increasing field uniformity and reducing farmers costs, as well as pathogens diffusion. Despite globe artichoke’s significant agricultural value and the critical role of heterosis in the development of superior varieties, the production of hybrids remains challenging without a reliable system for large-scale industrial seed production. Male sterility (MS) presents a promising avenue for overcoming these challenges by simplifying the hybridization process and enabling cost-effective seed production. However, within the Cynara genus, genic male sterility has been linked to three recessive loci in globe artichoke, with no definitive genetic mechanism elucidated to date. A 250 offsprings F2 population, derived from a cross between a MS globe artichoke and a male fertile (MF) cultivated cardoon (C. cardunculus var. altilis) and fitting a monogenic segregation model (3:1), was analyzed through BSA-seq, aiming at the identification of genomic regions/genes affecting male sterility. Four QTL regions were identified on chromosomes 4, 12, and 14. By analyzing the sequence around the highest pick on chromosome 14, a cytochrome P450 (CYP703A2) was identified, carrying a deleterious substitution (R/Q) fixed in the male sterile parent. A single dCAPS marker was developed around this SNP, allowing the discrimination between MS and MF genotypes within the population, suitable for applications in plant breeding programs. A 3D model of the protein was generated by homology modeling, revealing that the mutated amino acid is part of a highly conserved motif crucial for protein folding. Globe artichoke (Cynara cardunculus var. scolymus L.) is a mediterranean allogamous, mainly cultivated for human consumption. The establishment of superior varieties through heterosis has been applied in this species, but their production is complex, and the development of male sterile varieties has been of interest among plant scientists and breeders as a cost-effective solution for hybrid seeds production. Here, we report the use of the BSA-seq approach for the identification of a SNP strictly associated with male sterility in an F2 mapping population, we developed a single dCAPS marker allowing the discrimination between MS and MF genotypes within the population, and we discussed a potential role for a candidate gene (CYP702A3), involved in pollen grain vitality, present in the candidate region.

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.