IntroductionIn Lombardia region of Italy, several collections of Phaseolus vulgaris and Phaseolus coccineus landraces are conserved in specialized repositories (germplasm banks), yet their morphological characterization and genetic potential remain poorly documented. Given the importance of common (P. vulgaris) and runner (P. coccineus) bean landraces as genetic resources for biodiversity conservation, resilience to biotic and abiotic stresses, and crop improvement, this study aimed to analyse threatened bean landraces from Lombardia that are at risk of extinction and genetic erosion.MethodsA total of eight common bean and seven runner bean accessions were sampled, morphologically characterized in-situ, and genetically analysed using a genotyping-by-sequencing approach to assess genetic diversity and population structure. The results showed no clear clustering of landraces based on geographic origin for either species.ResultsCommon bean landraces exhibited distinct genetic identities, characterized by high inbreeding coefficients and low observed heterozygosity, consistent with their predominantly autogamous mating system, and strong genetic differentiation was detected among landraces. In contrast, runner bean landraces showed clustering of individuals within populations, higher observed heterozygosity, low inbreeding coefficients, and limited genetic differentiation, reflecting their allogamous pollination system.DiscussionThese findings highlight contrasting genetic structures between the two species and provide a foundation for the conservation and valorisation of Lombardia bean landraces.

Climate change is the greatest challenge to modern agriculture. It significantly impacts agricultural systems through an increased frequency and intensity of extreme environmental events. Maize, a vital crop for global food security, is particularly vulnerable to these changes, highlighting the urgent need to develop resilient varieties. This study aims to identify significant genes for adaptation to environmental conditions in 140 individuals derived from 28 Italian maize landraces using a landscape genomics approach to support the development of resilient maize genotypes. Landraces were genotyped using genotyping-by-sequencing, and the resulting genetic matrix was used to characterize the collection's diversity. Population genetic studies were conducted to investigate the genetic diversity and structure of the collection. Partial redundancy analysis (pRDA) was subsequently employed to analyze the relationship between climate variables and genetic variation of the materials. Among the 12 ancestral populations identified, both well-defined populations and highly admixed groups were observed. This degree of admixture was reflected in the clustering analysis and principal component analysis (PCA), although clear differentiation of individual populations was still apparent. pRDA revealed that 30% of the genetic variance in the collection was explained together by climate (45%), geography (11%), and genetic structure (31%). Three potential genomic signals of adaptation were identified in relation to the environmental variability across the sampling sites. The results highlight significant intra-landrace variability within the examined germplasm and reveal unique landraces tied to ancestral lineages. Notably, we identify distinct genetic markers strongly correlated with environmental factors. This discovery opens new avenues for potential genetic improvement in maize cultivation. Landraces preserve vital traits for the adaptation of maize to environmental stresses, thereby serving as key sources for breeding programs aimed at improving stress tolerance and yield stability under climate change.

Maize (Zea mays L.) is one of the most productive crops worldwide. As a heterotic crop predominantly grown as F1 hybrid, maize exhibits challenges for genetic studies of complex traits, since homozygous genotypes, which are largely used in these studies, may not accurately reflect what happens in cultivated conditions. To map Fusarium Ear Rot (FER) resistance to Fusarium verticillioides and traits with potential impact on yield, including phenology, we constructed a recombinant intercross (RIX) population. This was achived by crossing pairs of recombinant inbred lines (RILs) derived from a multi-parent maize population. We characterized the RIX population over two growing seasons, employing artificial F. verticillioides inoculation. The heterozygous background of the material enabled the identification of QTL and candidate genes through in silico reconstruction of RIX genotype probabilities. A total of 37 loci were identified using single-year BLUPs while 29 with joint-year BLUPs. These, included several known QTL associated with days to tasseling, kernel row number and a QTL on the chromosome 9 associated with FER resistance. In this region, we could identify candidates based on their predicted functions and potential roles in plant-pathogen interactions and/or resistance mechanisms. These QTL represent potential breeding targets to FER resistance and yield components in commercial maize varieties.

Popcorn (Zea mays spp. mays - Everta) is an ancient and widely recognized maize type, of American origin, enjoyed for centuries worldwide and still highly valued for its unique popping trait. Italy, considered a secondary center of maize differentiation, still holds a rich diversity of local maize landraces survived on farm and also ex situ stored. Despite this genetic wealth, Italian popcorn varieties have largely been neglected in modern breeding programs and remain poorly characterized, with only fragmented and incomplete data available. Recent studies have confirmed the widespread presence of traditional popcorn landraces across Italy, also if relegate to small garden cultivations, yet a comprehensive understanding of their genetic and agronomic traits remains lacking. This underscores the urgent need to preserve and document these landraces to conserve biodiversity and protect Italy’s cultural heritage. In response to this gap, in this study, ten Italian popcorn landraces were collected and morphological characterization was performed. Moreover, a genetic characterization of 282 individuals was conducted using a GBS approach. The morphological characterization revealed significant phenotypic and agronomic variability for a total of 13 traits including susceptibility to fungal infection and popping traits, whereas the genetic one identified 313,342 SNP variants, uncovering evidence of local adaptation and provided insights into population structure by Admixture analysis, which revealed the presence of 8 ancestral populations consistently with morphological and historical data. This work sheds light on these neglected landraces, offering valuable information for biodiversity conservation and future breeding efforts, particularly in marginal areas where smallholder cultivation remains crucial.

Context Maize is a major crop in Italy and is constantly affected by the fungus Fusarium verticillioides, producing ear rot and grain contamination by fumonisins. Finding new genotypes resistant to Fusarium infection is an important goal for the improvement of maize cultivation. Aims The objective of this work was to test a collection of 33 traditional landraces from the Emilia-Romagna (Italy) region for Fusarium ear rot (FER) severity, fumonisin content, and their agronomic performance. Methods Primary ears were artificially inoculated with a toxigenic strain of F. verticillioides in a 2-year experimental trial. The landrace ‘Nostrano di Storo’ and a commercial hybrid of FAO maturity class 300 were also included and used as comparisons representing a well-known and highly valued landrace and a modern flint hybrid, respectively. Key results The collection showed great phenotypic variability for all the agronomic traits assessed and responded differently to the Fusarium infection with percentages of FER ranging from 6.6% to 49.3%, and fumonisins from 4.3 mg/kg to 34.5 mg/kg. Thirteen and six landraces displayed FER percentages and fumonisin content very similar to the hybrid, respectively. Moreover, eight landraces exhibited grain yield values comparable to the hybrid. Interestingly, Va221, Va227 and EMR03 showed the best combination among these three traits. Conclusions This local material can be considered suitable for breeding purposes targeting the development of FER and fumonisin resistant germplasm. Implications The collection may represent a resource for future research aimed at evaluating the response to multiple pathogens and their associated mycotoxins.

BackgroundThe increased attention in agri-food quality and safety has led to the progress of DNA-based tools aimed to fight adulteration issues. Among the various molecular approaches, those ones based on molecular markers and DNA barcoding have been adequately validated, whereas new tools such as droplet digital PCR (ddPCR), isothermal amplification and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) (CRISPR/Cas) system are starting to overtake the performances of the former ones and to be applied in the agri-food sector.Scope and approachHerein, an overview of the recent advances and exploitations of the DNA-based techniques for the authenticity and traceability of fresh and processed plant-derived food, feed and medicinal products is provided, including research about the monitoring of contaminant and allergen presence. Moreover, the potentials and flaws of these molecular tools are also discussed.Key finding and conclusions: DNA-based technologies represent valuable tools for preventing agri-food frauds and adulteration of several vegetable products present on the market such as spices, extra virgin olive oil, wine, cocoa, and medicinal plants. The application of these methods can contribute to the protection of consumers and all stakeholders involved in the agri-food production and distribution.

The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a FST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area.

Buttafuoco dell'Oltrepo' Pavese (or Buttafuoco) is an important and renowned red wine, protected by a Denominazione di Origine Controllata (DOC) designation established in 2010, produced in the Northern Italy in the province of Pavia (Italy). The knowledge of factors as the typical microbial terroir and the metabolite composition of the wine is fundamental for producing excellent wines. In this work, two productions of Butta-fuoco Storico dell'Oltrep`o Pavese were followed in order to assess the microbial populations through different stages of the wine production chain and the metabolomic composition of the final wines. Microbial terroir was investigated through a metagenomic analysis that revealed a wide microbial consortium which is, for the major taxonomic groups, affected by sampling time over location. Before the metagenomic analysis, being DNA extraction from wine a difficult task, two different approaches were compared for a precise quantification of microbial DNA (bacteria and yeast): digital and real time PCR. Obtained results clearly evi-denced that digital PCR being was more sensitive than real time PCR and likely the method of choice for quantifying DNA extracted from processed matrices. Metabolomic profiling, focused on phenolic compounds, was able to clearly distinguish among vineyards and to highlight the presence of discriminating molecules that can be related to the different edaphic conditions.

While there is a rich collection of maize germplasm from Italy, it lacks genetic resources from the Aosta Valley, an isolated mountain region where landraces have been preserved in the absence of modern germplasm introductions. These local materials, which are still cultivated mainly at household level, can have high importance from a genetic and historical point of view. In the present study, five landraces named, after the collecting sites, Arnad, Arnad-Crest, Châtillon, Entrebin and Perloz, were sampled in Aosta Valley and subjected to historic, morphologic and genetic characterization. This study provided evidence for the landraces' long presence in Aosta Valley, a significant genetic variability and differentiation among the investigated landraces. Globally, 67 different alleles were detected ranging from 4 for markers phi127 and p-bnlg176 to 10 for phi031, with a mean of 6.7 alleles per locus. Observed heterozygosity levels were comprised from 0.16 to 0.51 and are generalkly lower than expected heterozigosity supporting fixation at some loci. STRUCTURE analysis revealed clear separation between accessions revealing the presence of four ancestral populations. This may be explained by the long reproductive isolation experienced by these materials. Finally, morphological observations confirm the high diversity between landraces revealing that they generally have flint kernels, variable color from yellow to dark red (Châtillon) while Perloz showed kernels with an apical beak. The present work confirms the importance of mountain areas in conserving biodiversity and increases the rich Italian maize germplasm with materials well adapted to marginal areas. Such new genetic variability may be used to breed new materials for more resilient agriculture.

Nowadays, agriculture is under the pressure of climate change and new pathogen outbreaks while farmers are requiring breeders to develop more resistant and resilient genotypes. The genetic base for breeding may be increased through appropriate conservation, description and characterization of local varieties and germplasm collections that have never been used in breeding, and which could be sources of useful alleles. In this framework, the present paper focuses on eight maize landraces of the eastern part of Emilia-Romagna, derived from the Italian maize collection sampled in 1954. Landraces are characterized by a short cycle length and different kernel types—mainly flint-like or an intermediate type of yellow or yellow–orange color—while dent landraces are less represented. Pigmented and white corns are absent even though one landrace (Va213) showed the presence of scattered blue kernels on yellow ears. Ear shape is frequently conical, a trait associated with drought-resistance and common in Italian traditional landraces. Genetic characterization was carried out on 529 individuals by using 10 SSR markers. A total of 68 different alleles, ranging from 4 for markers (phi084 and umc1401) to 11 (phi031) and from 27 (Va217) to 50 (Va211), were evidenced at the individual and population level. AMOVA analysis revealed a small amount (19%) of variability between populations, as supported also by PCoA, with the only exception of Va217, which is different from the others, as evidenced also by phylogenetic analysis. Population structure analysis resulted in the identification of three and four population levels, which are consistent with previous results.

Italian maize germplasm is particularly rich in local materials and each region is characterized by the presence of peculiar local varieties deriving from centuries of adaptation, selection and cultivation. While the introduction of hybrids, during the 1950s, led to the disappearing of many of these varieties, some have been maintained in cultivation by farmers, frequently in marginal areas, as a kind of family heritage. Local varieties were identified throughout field surveys carried out in recent years. The discovery of a traditional popcorn variety over the most common flint and semi-flint materials used for production of polenta was interesting. Since these varieties have never been adequately described and reported in scientific literature, this study was aimed to solve this lack of knowledge on recently discovered local maize populations. Characterization represents the first step of a process focused on the preservation and possible exploitation of important genetic resources. Traditional materials are a useful reservoir of genes for adaptation to local conditions and climate changes. Adequate breeding programs can use such germplasm for developing new and more resilient varieties. These local materials have been characterized at the morphological level highlighting plant, ear and kernel differences. Genetic characterization, carried out on 455 individuals by the use of 10 SSR markers, revealed 62 different alleles ranging from four for markers phi127, phi076 and phi084 to nine for marker p-bnlg176. The landraces are well distinguishable at genetic level since 40% of genetic variability is present among accessions. Five landraces are characterized by the presence of private alleles and heterozygosity levels are generally good. These findings support the possibility to correctly preserve local materials through in situ conservation. Phylogenetic analysis evidenced the presence of varietal clusters, the clearest one formed by three red-pigmented accessions. STRUCTURE analysis revealed that five landraces have a well-defined genetic attribution while the remaining two (EMR04-Mais Rosso di Rasora and EMR10-Mais del Principe di Scavolino) are both constituted by two different backgrounds.

Wine traceability based on DNA analysis has been reported in several previous studies but no one until now had monitored how far molecular traceability was possible during wine storage, before and after bottling. The present study tries to fill this gap of knowledge by following, in the real case of a large wine cooperative, the possibility to trace wine production through DNA analysis during storage period. Two monovarietal productions: red sparkling Bonarda PDO and white Pinot gris PDO, were followed starting from the end of oenological practices until 1 year after bottling. During the pre-bottling period, samples were collected every 10 days during four consecutive months, after bottling samples were collected at day 1 and after 2, 8 and 12 months. DNA analysis evidences that for both wines, traceability by applying SSR analysis on the extracted DNA is possible, at least, until month 8, after that DNA degradation increases hindering, mainly for the red wine, the possibility to a correct varietal identification.

Species of the genus Crocus are found over a wide range of climatic areas. In natural habitats, these geophytes diverge in the flowering strategies. This variability was assessed by analyzing the flowering traits of the Spanish collection of wild crocuses, preserved in the Bank of Plant Germplasm of Cuenca. Plants of the seven Spanish species were analyzed both in their natural environments (58 native populations) and in common garden experiments (112 accessions). Differences among species observed in the native habitats were maintained under uniform environmental conditions, suggesting a genetic basis for flowering mechanisms. Two eco-morphological types, autumn- and spring-flowering species, share similar patterns of floral induction and differentiation period in summer. The optimal temperature for this process was 23 °C for both types. Unlike Irano-Turanian crocuses, spring-flowering Spanish species do not require low winter temperatures for flower elongation. Hysteranthous crocuses flower in autumn prior to leaf elongation. We conclude that the variability in flowering traits in crocuses is related to the genetic and environmental regulation of flower primordia differentiation and elongation prior to emergence above the soil surface. The elucidation of the physiological differences between eco-morphological types of crocuses: synanthous with cold requirements and synanthous and hysteranthous without cold requirements, unlocks a new approach to the flowering evolution of geophytes in Mediterranean regions. Crocus species can serve both as a new model in the study of the molecular basis of hysteranthy and for the purposes of developing the molecular markers for desirable flowering traits.

Fusarium verticillioides is one of the most relevant fungal species in maize responsible for ear, stalk and seedling rot, as well as the fumonisin contamination of kernels. Plant lipoxygenases (LOX) synthesize oxylipins that play a crucial role in the regulation of defense mechanisms against pathogens and influence the outcome of pathogenesis. To better uncover the role of these signaling molecules in maize resistance against F. verticillioides, the functional characterization of the 9-LOX gene, ZmLOX4, was carried out in this study by employing mutants carrying Mu insertions in this gene (named as UFMulox4). In this regard, the genotyping of five UFMulox4 identified the mutant UFMu10924 as the only one having an insertion in the coding region of the gene. The impact of ZmLOX4 mutagenesis on kernel defense against F. verticillioides and fumonisin accumulation were investigated, resulting in an increased fungal susceptibility compared to the inbred lines W22 and Tzi18. Moreover, the expression of most of the genes involved in the LOX, jasmonic acid (JA) and green leaf volatiles (GLV) pathways, as well as LOX enzymatic activity, decreased or were unaffected by fungal inoculation in the mutant UFMu10924. These results confirm the strategic role of ZmLOX4 in controlling defense against F. verticillioides and its influence on the expression of several LOX, JA and GLV genes.

This work represents the first epigenomic study carried out on saffron crocus. Five accessions of saffron, showing differences in tepal pigmentation, yield of saffron and flowering time, were analyzed at the epigenetic level by applying a methylation-sensitive restriction enzyme-sequencing (MRE-seq) approach. Five accession-specific hypomethylomes plus a reference hypomethylome, generated by combining the sequence data from the single accessions, were obtained. Assembled sequences were annotated against existing online databases. In the absence of the Crocus genome, the rice genome was mainly used as the reference as it is the best annotated genome among monocot plants. Comparison of the hypomethylomes revealed many differentially methylated regions, confirming the high epigenetic variability present among saffron accessions, including sequences encoding for proteins that could be good candidates to explain the accessions' alternative phenotypes. In particular, transcription factors involved in flowering process (MADS-box and TFL) and for the production of pigments (MYB) were detected. Finally, by comparing the generated sequences of the different accessions, a high number of SNPs, likely having arisen as a consequence of the prolonged vegetative propagation, were detected, demonstrating surprisingly high genetic variability. Gene ontology (GO) was performed to map and visualize sequence polymorphisms located within the GOs and to compare their distributions among different accessions. As well as suggesting the possible existence of alternative phenotypes with a genetic basis, a clear difference in polymorphic GO is present among accessions based on their geographic origin, supporting a possible signature of selection in the Indian accession with respect to the Spanish ones.

Wine is frequently reported as one of the most adulterated agro-food products worldwide. Among the traceability methods available, DNA is of particular interest providing the possibility to recognize uniquely the wine production cultivar/cultivars. Several studies carried out in controlled conditions (laboratory level or small production wineries) support the use of DNA in wine traceability, but the situation can change completely when moving from controlled to uncontrolled realities. In the present study, the entire production chain, in a large cooperative Italian winery, was followed, for a monovarietal (Pinot noir PDO) and a polyvarietal (Rosso Oltrepò TGI) production. Results support the feasibility of DNA traceability from grape delivering to the whole fermentation process and through the most common oenological operations as racking and filtration. The application of most aggressive methods (as the thermovinification process) can increase DNA degradation reducing but not hampering the possibility to apply DNA for traceability purposes. A different situation concerns the storage of wine in tanks, despite the controlled temperature and light conditions, or in bottles where DNA degradation continues strongly influencing the possibility to apply traceability.

Beaked corn represents one of the most characteristics and neglected group of Italian maize landraces. These genotypes, classified in the “Rostrata” group, were mostly grown in northern Italy, on the left bank of the Pò river, until the end of the Second World War and then subjected to strong genetic erosion because of the subsequent introduction of improved genotypes and hybrids of US origin. These materials are experiencing a revival period for cultivation, commercial exploitation and an increased number of farmers is seeking particular genotypes for the production of niche products. In Valchiavenna (Sondrio, Lombardia, Italy) maize cultivation has historical importance for polenta preparation and is characterized by the presence of at least three accessions of “Mais Rostrato Val Chiavenna”, one conserved since 1982 in germplasm bank ( here named as R17_BG) and two in situ (here named as R17_M; R17_T), with distinctive morphological traits at both ear and plant level. In the present study, these accessions have been characterized at the morphological and genetic level with 10 SSR markers and compared to other landraces of the Rostrata group. SSR analysis revealed from 3 to 11 alleles per locus evidencing a good level of heterosis and absence of allele fixation for landraces. Both phylogenetic and STRUCTURE analysis evidence that the three “Mais Rostrato Val Chiavenna” are different entities with a distinct genetic origin. Historical investigation revealed that the morphology most close to the “original” Mais Rostrato di Val Chiavenna is that of R17_T, dating back to the XIX century. These observations, coupled with morphological and genetic results may corroborate that R17_T corresponds to the original “Mais Rostrato Val Chiavenna”.