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Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar 'Bouche de Bétizac' (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between 'Bouche de Bétizac' and the susceptible cultivar 'Madonna' (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of 'Bouche de Bétizac' consisted of 1459 loci and spanned 809.6 cM; the map of 'Madonna' consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the 'Bouche de Bétizac' map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes. [ABSTRACT FROM AUTHOR]

Due to global climate cooling and aridification since the Paleogene, members of the Neogene flora were extirpated from the Northern Hemisphere or were confined to a few refugial areas. For some species, the final reduction/extinction came in the Pleistocene, but some others have survived climatic transformations up to the present. This has occurred in Castanea sativa , a species of high commercial value in Europe and a significant component of the Caucasian forests' biodiversity. In contrast to the European range, neither the historical biogeography nor the population genetic structure of the species in its isolated Caucasian range has been clarified. Here, based on a survey of 21 natural populations from the Caucasus and a single one from Europe, we provide a likely biogeographic reconstruction and genetic diversity details. By applying Bayesian inference, species distribution modelling and fossil pollen data, we estimated (i) the time of the Caucasian—European divergence during the Middle Pleistocene, (ii) the time of divergence among Caucasian lineages and (iii) outlined the glacial refugia for species. The climate changes related to the Early–Middle Pleistocene Transition are proposed as the major drivers of the intraspecific divergence and European–Caucasian disjunction for the species, while the impact of the last glacial cycle was of marginal importance. [ABSTRACT FROM AUTHOR]

Evidence has been documented in Europe of introgression, the transfer of genetic material, between Asian chestnut species (Castanea crenata and C. mollissima) and the native C. sativa through spontaneous hybridization and subsequent backcrossing. However, the extent of this introgression has not been monitored in a particular forest stand or in adult and juvenile trees simultaneously. We assessed introgression in a natural C. sativa forest in northwest Spain and developed a reliable method to detect the presence of Asian germplasm of Castanea spp. A total of 34 adult trees and 42 saplings were genotyped at 13 SSRs in a forest where ink-disease-resistant C. crenata and C. mollissima seedlings had been planted in the 1940s. The 13 SSR loci selected were highly polymorphic and 115 different alleles were detected for the individuals sampled. Bayesian clustering identified two groups for C. sativa and one group each for C. mollissima and C. crenata. Within the forest, 70.6 per cent of adults and 28.6 per cent of juveniles were classified as pure C. sativa. Most juveniles were C. sativa × C. crenata (>40 per cent) and ca. 10 per cent were C. crenata × C. mollissima hybrids. Six new alleles private to C. crenata are reported here. The study quantifies, for the first time in Europe, introgression of Asian germplasm into a natural C. sativa forest. It also examines the extent of introgression in offspring and provides a method to detect exotic germplasm in C. sativa forests. We discuss why the forest studied may benefit from transfer of alleles involved in ink-disease resistance and why introgression will be detrimental to drought tolerance in offspring. [ABSTRACT FROM AUTHOR]

• Key message: Understanding the adaptive mechanisms of forest species is vital to ensure their survival in a climate change scenario. This study aimed at uncovering the relationship between genetic variability and environmental variables in naturalCastanea sativapopulations, unveiling how different climate scenarios drove local adaption processes using a landscape genomics approach. Our findings provide useful data for future management of this species. • Context: Temperate forest species, such as chestnut (Castanea sativa Mill.), are currently threatened by increasing temperature together with disruption and reduction of precipitation due to climate change. In this context, understanding the adaptation processes of species will help to manage and ensure the conservation of forests. • Aims: We studied the relationship between genetic variability and climate variables in natural populations of C. sativa using a landscape genomics approach aimed to identify local adaption processes. • Methods: Using five genomic SSRs and eight functional EST-SSRs markers, 268 individuals belonging to ten different natural European chestnut populations distributed in contrasting climatic sites were genotyped. In addition, associations between allelic variation and climatic variables (environmental association analyses approach) were performed using Samβada and LFMM. • Results: Results highlighted a strong inter-relationship between climate variables and evolutionary processes resulting in adaptive variation. STRUCTURE analysis based on functional markers split the populations in three separate gene pools (K = 3), mostly in agreement with the different climatic conditions existing in the studied areas. Divergent spatial patterns of genetic variation between rainy and arid areas were found. We detected a total of 202 associations with climate among 22 different alleles, 9% of which related with the outlier locus FIR059, known to be implicated in regulatory mechanisms during water stress adaptation processes. • Conclusion: Landscape genomics analyses revealed a pattern of adaptive variation, where specific climatic variables influenced the frequencies distribution and fixation of several alleles, resulting in local adaptation processes of the populations in the investigated areas. Our findings underline the close inter-relationship existing between climate and genetic variability and indicate how this approach could provide valuable information for the management of forest species in a rapidly changing environment. [ABSTRACT FROM AUTHOR]

The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid 'Bouche de Bétizac' (BB) and the susceptible cultivar 'Madonna' (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as "response to stimulus" (GO:0050896), and "developmental processes" (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in "post-embryonic development". Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives. [ABSTRACT FROM AUTHOR]

Phoenix theophrasti is one of the few tree species tertiary relict endemic to the eastern Mediterranean, and it is one of the two palm species native to continental Europe. It has local populations both in Crete-Greece and in southwest Turkey. Like most of the relict endemics, it has a restricted distribution and it is at risk of extinction. The primary goal of this study was the genetic characterization of Turkish P. theophrasti populations by using SSR markers. The secondary goal was to detect the phylogenetic relations of P. theophrasti with nine different palm species which are P. dactylifera, P. reclinata, P. rupicola, P. roebelenii, P. canariensis, P. loureiri, P. acaulis, P. sylvestris from Phoenix genus and Chamaerops humilis from Chamaerops genus by the same markers. Chamaerops humilis was included in the study as the second natural palm species of the Europe. The genetic differentiation coefficient (FST) was found as 0.34, and the level of gene flow (Nm) within a generation among populations was found as 0.49. In general, excess of homozygotes relative to that expected with random mating was detected in the populations. The lowest differentiation of P. theophrasti was from P. dactylifera (FST = 0.1932), and the highest differentiation of P. theophrasti was from C. humilis (FST= 0.4261). We propose that P. theophrasti must urgently be included in the Red List of IUCN under the critically endangered (CR) category. Phylogenetic relations determined among the palm species indicated the necessity of re-evaluation of the taxonomy of palms. [ABSTRACT FROM AUTHOR]

The genetic structure of 15 wild populations of Castanea sativa located in Galicia (northwest of Spain) were compared with another 10 Spanish, 2 Italian, and 2 Greek populations using 9 nuclear microsatellites. Additionally, 41 Castanea crenata, 19 Castanea mollissima and 54 accessions of varieties were used to detect the presence of Asiatic germplasm and grafted varieties in wild stands. Bayesian methods detected two main clusters in the European populations of sweet chestnut: a Northern Iberian Peninsula cluster included the northern and northwestern Spanish populations and a Mediterranean cluster contained central and southern Spanish, Italian and Greek populations. Further subdivisions were also detected. The Northern Iberian Peninsula cluster was divided into Cantabrian and Atlantic clusters and the Mediterranean cluster was divided into western and eastern Mediterranean clusters. Several populations were highly affected by domestication because they were classified as admixed among the four defined groups. Negative values for the fixation index were detected in northern and northwestern Spain showing an excess of heterozygotes that could be explained by the introduction of grafted varieties and its introgression with local populations or by natural selection in favor of heterozygotes produced by ink disease. The combined analysis with the Asiatic species also indicated their presence and possible introgression in the wild populations of northwestern Spain. The results of this study suggest that the current genetic structure of sweet chestnut can be explained by existence of several refugia during Pleistocene and also by human activity that changes the structure of the populations. [ABSTRACT FROM AUTHOR]

Hazelnut ( Corylus avellana L.), a member of the family Betulaceae and the order Fagales, is native to Europe, Turkey, and the Caucasus. It has been cultivated for more than 5000 years. The majority of cultivars were selected from local wild populations over the past few centuries. Hazelnut is native to northern Portugal, with local production from landrace clonal selections. In recent years, hazelnut production has declined, and landraces are in danger of being lost. In this study, we used 16 microsatellite markers to investigate genetic diversity in wild populations, Portuguese landraces, and reference cultivars. A high level of polymorphism was found, as indicated by mean values for expected heterozygosity (0.74), observed heterozygosity (0.71), and polymorphism information content (0.78). A neighbor-joining dendrogram showed a clear separation of the wild genotypes from the landraces and reference cultivars. Bayesian analysis placed individuals in three groups, showing differentiation of wild populations, landraces, and reference cultivars. Our studies provide new insights on the origin of Portuguese landraces. [ABSTRACT FROM AUTHOR]