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• Premise of the study: Large-scale studies on the genetic diversity of forest trees are relevant for the inventory, conservation, and management of genetic resources and provide an insight into the geographical origins of the species. This approach is appropriate to use with Castanea sativa, a tree of great economic importance and the only species from the genus Castanea in Europe. The history of C. sativa was deduced from fossil pollen data, but the large-scale genetic structure of this species needs to be elucidated. We evaluated the genetic diversity of C. sativa to define previously unclarified genetic relationships among the populations from Turkey and those from Greece and western Europe. The influence of natural events such as glaciations and human impact in terms of species distribution are discussed.• Methods: Wild chestnut trees (779) were sampled in 31 European sites. Six polymorphic microsatellites were used for the analysis. A set of measures of intra- and interpopulation genetic statistics were calculated. The population structure was inferred by using a Bayesian approach.• Key results: The population structure showed a genetic divergence between the eastern (Greek and Turkish) and western (Italian and Spanish) populations. Two gene pools and a zone of gene introgression in Turkey were revealed.• Conclusions: The inferred population structure shows a strong geographical correspondence with the hypothesized glacial refugia and rules out the migration of the chestnut from Turkey and Greece to Italy. The homogeneous gene pool observed in Italy and Spain could have been originated from common refugia along with human-mediated colonization.

Genetic erosion, mainly caused by the replacement of local landraces with high yielding or exotic varieties is causing loss of agrobiodiversity. Landraces of horticultural species, grown by small producers, represent today an important value in the preservation of agrobiodiversity. Umbria, a region of central Italy, is characterized by agricultural systems linked to tradition and cultivation of local landraces. In this study, the genetic profile of some traditional Umbrian tomato landraces was characterized for the first time, and the landraces uniqueness was evaluated by comparison with commercial varieties. One-hundred and twenty-one plants provided by local farmers and seed companies, represented by local and commercial varieties were analyzed using 19 SSRs markers. A total of 60 alleles were found with moderate levels of diversity. The mean number of alleles per locus was 3.158 and the average polymorphism information content was 0.38. Unweighted UPGMA clustered the accessions into four groups. The gene pool of Umbrian landraces seems to be highly differentiated compared to commercial varieties, with landraces showing a genetic distinctiveness. Furthermore, an identifying fingerprinting code of each tomato landrace was generated and an innovative method for varietal identification based on the ‘QR code’ was proposed. The results obtained in this study will be useful for a better management, conservation and propagation of tomato genetic resources in Umbria region.

Alnus cordata is an endemic tree species native to the Southern Italian Apennines and north‐eastern Corsica, renowned for its ecological significance. Climate change projections for the Mediterranean basin indicate range shifts and increased fragmentation for many forest trees, including A. cordata. Hybridization with the sympatric A. glutinosa in the central part of its Italian native range may also influence the genetic structure and conservation priorities for A. cordata. A comprehensive conservation strategy is needed to preserve its genetic resources in Italy. We analyzed the genetic diversity, population structure, and extent of hybridization with A. glutinosa in 23 A. cordata forest stands across its native Italian range using nuclear microsatellites. Habitat suitability was modeled under current and future climate scenarios using an ensemble forecasting approach. Conservation prioritization was guided by a genetically informed Reserve Selection analysis in DIVA‐GIS to identify areas of high conservation value and address gaps in genetic resource representation. Italian alder populations exhibit low genetic diversity, which decreases towards the southern latitudinal margins of the peninsula. Hybridization and introgression with Alnus glutinosa have a geographically localized impact on the genetic variation within A. cordata populations. Local increases in private allelic richness do not alter the spatial genetic structure of A. cordata, but they help mitigate the risk of severe genetic erosion. A significant proportion of the species' genetic diversity is effectively preserved through in situ conservation. Model projections under future climate scenarios indicate a substantial decline in habitat suitability for A. cordata stands with high priority for in situ conservation. This highlights the need for complementary strategies, including ex situ conservation measures. Our study highlights the importance of integrating genetic analyses, habitat suitability modeling, and spatial prioritization techniques for effective conservation planning of A. cordata in the face of climate change across the Mediterranean. Alnus cordata is an endemic tree species native to the Southern Italian Apennines and north‐eastern Corsica, renowned for its ecological significance. We analyzed the genetic diversity, population structure, and extent of hybridization with A. glutinosa in 23 A. cordata forest stands across its native Italian range. Conservation prioritization was guided by a genetically informed Reserve Selection analysis in DIVA‐GIS to identify areas of high conservation value and address gaps in genetic resource representation.

Castanea sativa is classified as non-indigenous in Britain and Ireland. It was long held that it was first introduced into Britain by the Romans, until a recent study found no corroborative evidence of its growing here before c. AD 650. This paper presents new data on the genetic diversity of C. sativa in Britain and Ireland and potential ancestral sources in continental Europe. Microsatellite markers and analytical methods tested in previous European studies were used to genotype over 600 C. sativa trees and coppice stools, sampled from ancient semi-natural woodlands, secondary woodlands and historic cultural sites across Britain and Ireland. A single overall genepool with a diverse admixture of genotypes was found, containing two sub groups differentiating Wales from Ireland, with discrete geographical and typological clusters. C. sativa genotypes in Britain and Ireland were found to relate predominantly to some sites in Portugal, Spain, France, Italy and Romania, but not to Greece, Turkey or eastern parts of Europe. C. sativa has come to Britain and Ireland from these western European areas, which had acted as refugia in the Last Glacial Maximum; we compare its introduction with the colonization/translocation of oak, ash, beech and hazel into Britain and Ireland. Clones of C. sativa were identified in Britain, defining for the first time the antiquity of some ancient trees and coppice stools, evincing both natural regeneration and anthropogenic propagation over many centuries and informing the chronology of the species' arrival in Britain. This new evidence on the origins and antiquity of British and Irish C. sativa trees enhances their conservation and economic significance, important in the context of increasing threats from environmental change, pests and pathogens.

The Asian chestnut gall wasp (ACGW) (Hymenoptera Dryocosmus kuriphilus Yasumatsu) is a severe pest of sweet chestnut (Castanea sativa Mill.) with a strong impact on growth and nut production. A comparative field trial in Central Italy, including provenances from Spain, Italy, and Greece, was screened for ACGW infestation over consecutive years. The Greek provenance Hortiatis expressed a high proportion of immune plants and was used to perform a genome-wide association study based on DNA pool sequencing (Pool-GWAS) by comparing two DNA pools from 25 susceptible and 25 resistant plants. DNA pools were sequenced with 50X coverage depth. Sequence reads were aligned to a C. mollissima reference genome and the pools were compared to identify SNPs associated with resistance. Twenty-one significant SNPs were identified and highlighted a small genomic region on pseudochromosome 3 (Chr 3), containing 12 candidate genes of three gene families: Cytochrome P450, UDP-glycosyltransferase, and Rac-like GTP-binding protein. Functional analyses revealed a putative metabolic gene cluster related to saccharide biosynthesis in the genomic regions associated with resistance that could be involved in the production of a toxic metabolite against parasites. The comparison with previous genetic studies confirmed the involvement of Chr 3 in the control of resistance to ACGW.

Sweet chestnut is a tree of great economic (fruit and wood production), ecological, and cultural importance in Europe. A large-scale landscape genetic analysis of natural populations of sweet chestnut across Europe is applied to (1) evaluate the geographic patterns of genetic diversity, (2) identify spatial coincidences between genetic discontinuities and geographic barriers, and (3) propose certain chestnut populations as reservoirs of genetic diversity for conservation and breeding programs. Six polymorphic microsatellite markers were used for genotyping 1608 wild trees sampled in 73 European sites. The Geostatistical IDW technique (ArcGIS 9.3) was used to produce maps of genetic diversity parameters (He, Ar, PAr) and a synthetic map of the population membership (Q value) to the different gene pools. Genetic barriers were investigated using BARRIER 2.2 software and their locations were overlaid on a Digital Elevation Model (GTOPO30). The DIVA-GIS software was used to propose priority areas for conservation. High values of genetic diversity (He) and allelic richness (Ar) were observed in the central area of C. sativa ’s European distribution range. The highest values of private allelic richness (PAr) were found in the eastern area. Three main gene pools and a significant genetic barrier separating the eastern from the central and western populations were identified. Areas with high priority for genetic conservation were indicated in Georgia, eastern Turkey, and Italy. Our results increase knowledge of the biogeographic history of C. sativa in Europe, indicate the geographic location of different gene pools, and identify potential priority reservoirs of genetic diversity.

The genetic structure of sweet chestnut (Castanea sativa Mill.) across Europe was assessed using 73 inter-simple sequence repeat markers to screen 1,768 individuals from 68 stands distributed across 29 sites in five European countries (Italy, France, Spain, Greece, and UK). At each site, trees were sampled from three distinct management types (domestication levels): naturalized stands, managed coppice, and grafted fruit orchards. In more than a third of the orchards, nonlocal genetic material (grafted clones) were evident, showing (as predicted) large differences from the other two domestication levels for most of the within-population genetic diversity parameters estimated. Randomly generated linkage disequilibrium analysis revealed weak though significant differences in two-locus allelic correlations between naturalized stands and coppice, suggesting that long-term management techniques may influence the genetic makeup of the populations. Multivariate analysis revealed the existence of five distinct gene pools across the study area; three were located in Greece, one on the northwestern coast of the Iberian peninsula and a large gene pool covering the rest of the Mediterranean basin. The implications of the results are discussed in relation to developing conservation strategies for chestnut genetic resources in Europe.

Microsatellite or simple sequence repeats (SSRs) are one of the most used markers in population genetic studies. SSR markers developed from expressed sequence tags (EST) have proved useful to examine functional diversity in relation to adaptive variation. The information provided by both genomic and genic microsatellite markers could offer more accurate indication on the distribution of the genetic diversity among and within populations assuming different evolutionary drivers. This is the first study on chestnut (Castanea sativa Mill.) in which the genetic diversity was evaluated by means of genomic (SSRs) and genic (EST-SSRs) microsatellite markers. We genotyped nine natural European chestnut populations distributed throughout representative areas of contrasting climatic conditions in the Mediterranean basin. Genomic SSRs showed significantly higher levels of diversity in terms of number of alleles, effective number of alleles, expected heterozygosity and level of polymorphism. Furthermore, there were significant differences in the level of differentiation among populations. The UPGMA analysis revealed different clustering pattern between populations, being the grouping according to geographic distances in the case of genomic SSRs and two differentiated groups based on the northern-southern distribution of the populations for EST-SSRs. Furthermore, the EST-SSR transferability among related Castanea and Quercus species was stated. Our results confirm that combining genomic SSRs and EST-SSRs is a useful tool to give complementary information to explain the genetic and adaptive diversity in chestnut.

The current need for forest conservation and management has driven a rapid expansion of landscape genetics approach. This discipline combines tools from molecular genetics, landscape ecology and spatial statistics and is decisive for improving not only ecological knowledge but also for properly managing population genetic resources. This approach could be appropriate to sweet chestnut ( Castanea sativa Mill.), a multipurpose species of great economic importance in the Mediterranean basin and a species considered to be a good model of integration between natural and human-driven distribution of diversity. Sixteen chestnut populations, covering the distribution range of the species in Spain, were analysed using seven microsatellite markers. Results revealed a high level of genetic diversity in Spanish chestnut populations, which in part followed a geographical pattern, although distribution was not homogeneous. Likewise, areas particularly rich in diversity were detected, facilitating the development of a hypothesis about the history of chestnut in Spain. In conclusion, these results provide valuable baseline data for more in-depth studies on chestnut landscape genetics that can contribute to its conservation.

The Asian chestnut gall wasp (ACGW) (Hymenoptera Dryocosmus kuriphilus Yasumatsu) is a severe pest of sweet chestnut (Castanea sativa Mill.) with a strong impact on growth and nut production. A comparative field trial in Central Italy, including provenances from Spain, Italy, and Greece, was screened for ACGW infestation over consecutive years. The Greek provenance Hortiatis expressed a high proportion of immune plants and was used to perform a genome-wide association study based on DNA pool sequencing (Pool-GWAS) by comparing two DNA pools from 25 susceptible and 25 resistant plants. DNA pools were sequenced with 50X coverage depth. Sequence reads were aligned to a C. mollissima reference genome and the pools were compared to identify SNPs associated with resistance. Twenty-one significant SNPs were identified and highlighted a small genomic region on pseudochromosome 3 (Chr 3), containing 12 candidate genes of three gene families: Cytochrome P450 , UDP-glycosyltransferase , and Rac-like GTP-binding protein . Functional analyses revealed a putative metabolic gene cluster related to saccharide biosynthesis in the genomic regions associated with resistance that could be involved in the production of a toxic metabolite against parasites. The comparison with previous genetic studies confirmed the involvement of Chr 3 in the control of resistance to ACGW.