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The distribution of haplotypic diversity of 38 European chestnut (Castanea sativa Mill.) populations was investigated by PCR/RFLP analysis of regions of the chloroplast and mitochondrial genomes in order to shed light on the history of this heavily managed species. The rapid expansion of chestnut starting from 3000 years ago is strongly related to human activities such as agricultural practice. This demonstrates the importance of human impact, which lasted some thousands of years, on the present-day distribution of the species. No polymorphism was detected for the single mitochondrial analysed region, while a total of 11 different chloroplast (cp) haplotypes were scored. The distribution of the cpDNA haplotypes revealed low geographical structure of the genetic diversity. The value of population subdivision, as measured by GSTc, is strikingly lower than in the other species of the family Fagaceae investigated. The actual distribution of haplotypic diversity may be explained by the strong human impact on this species, particularly during the Roman civilization of the continent, and to the long period of cultivation experienced during the last thousand years.

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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 ESTSSRs. Furthermore, the EST-SSR transferability among related Castanea and Quercus species was stated. Our results confirm that combining genomic SSRs and ESTSSRs is a useful tool to give complementary information to explain the genetic and adaptive diversity in chestnut.

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The distribution of haplotypic diversity of 17 Tilia cordata Mill. populations was investigated by PCR–RFLP markers of the chloroplast genomes. A high number of haplotypes (14) and high total genetic diversity (hT = 0.881) were detected. The distribution of the chloroplast DNA haplotypes revealed low geographic structure of the genetic diversity; the coefficient of differentiation between populations, Gst = 0.552, was lower than the mean value reported for maternally inherited markers in Angiosperm tree species. The value of population subdivision for ordered alleles, as measured by Nst, was significantly higher than the value of population subdivision for unordered alleles (Nst = 0.662, Gst = 0.552), thus indicating the presence of a phylogeographic structure. The relatively low genetic differentiation among T. cordata populations may be explained mainly as a consequence of human impact on this species.

European chestnut (Castanea sativa) is an important multipurpose tree that has been cultivated for wood and fruit in the Mediterranean basin since ancient times. Cultivation of traditional chestnut varieties has a long tradition in Italy, where cultivars have been selected over centuries as a function of the best nut traits. In this study, 94 grafted chestnuts corresponding to 26 representative cultivars from Italy were evaluated by seven simple sequence repeat (SSR) markers to establish whether they corresponded to varieties in the narrow sense. The results allowed 20 genotypes to be identified that corresponded to the same number of clones. In total, 52 alleles were identified, eight of which were exclusive. Cases of homonymies and synonymies were detected. Moreover, our results highlighted a considerable genetic uniformity among ‘Marrone‐type’ cultivars and, on the contrary, a high genetic diversity among the evaluated cultivars demonstrating that this is a valuable germplasm and an important genetic resource to be preserved.