Forty one simple sequence repeats were isolated from two microsatellite enriched libraries of date palm (Phoenix dactylifera L.). After screening, 17 selected microsatellite loci were characterized and evaluated on a set of 31 cultivars and clones from Algerian and Californian germplasm. All primer pairs produced an amplification product of the expected size and detected high polymorphism among the analysed samples. These nuclear simple sequence repeat (SSR) markers are expected to be a very effective tool for evaluating genetic diversity in date palm germplasm. Acrosstaxa amplification showed the usefulness of most SSR markers in 14 other species across the genus Phoenix.Additional key words: across-taxa transferability, date palm, simple sequence repeats.

The European hazelnut (Corylus avellana L.) is one of the most important nut crops. In this work we characterize functional microsatellite or simple sequence repeat (SSR) markers for genetic analysis and molecular breeding in this species. A total of 38,454 Betulaceae EST sequences from NCBI resulted in 1,282 non-redundant EST-SSRs. Dinucleotide repeats were the most abundant (63.9%), followed by trinucleotides (33.8%). The putative functions of the non-redundant EST-SSRs were classified according to gene ontology (GO) categories (biological process, molecular function, and cellular component). A total of 921 sequences showed significant hits with the non-redundant protein database, and GO categories were assigned to 696 (75.5%) of them. Flanking primer pairs were designed for 78 di-and trinucleotide EST-SSRs from Alnus glutinosa L. ( 29), Betula pendula Roth (26), and Betula platyphylla Suckaczev (23).Further, 41 dinucleotide repeats selected from hazelnut transcriptome sequences were added. Thirty-six out 119 primer pairs generated amplification products in six hazelnut accessions and in the samples of the species from which they were isolated. Among them, 20 were polymorphic when tested on 18 hazelnut cultivars. Fifteen loci are suitable for mapping in a F1 population of 'Tonda Gentile delle Langhe' x 'Merveille de Bollwiller' and 11 of them were functionally annotated. The cross-species transferability of 36 EST-SSR loci within nine Corylus species was also performed. The success rate of markers transferability (including C. avellana) ranged from 11% to 100%, with an average of 55%. The EST-SSRs developed increase the number of markers currently available for hazelnut.

The European hazelnut (Corylus avellana L.) is the most economically important nut species in the Betulaceae family. Despite the need for new improved hazelnut cultivars, few breeding programs are carried out because of the large plant size, the long life cycle of the plant, and the expense and time required. To date, there are no reports of maps with Quantitative Trait Loci (QTL) in hazelnut. Our objective in the present study was to identify QTL associated with vegetative traits to allow marker-assisted selection (MAS). A F1 progeny (275 plants) of 'Tonda Gentile delle Langhe' X 'Merveille de Bollwiller' obtained in 2009 was used to develop a QTL linkage map for vigour, sucker habit and time of bud burst, after three years of observations. A set of 163 plants were analysed with 152 microsatellite markers. A map of 11 linkage groups was obtained, covering 663.1 cM and 15 QTLs were identified and mapped for the examined traits. Among them, 10 were 'major' QTL, including a stably expressed region on LG_02 for leaf budburst. At least one major QTL for each year underlays the variation in each trait and a clustering of QTL for tc and s/tc ratio with a high inter-trait correlations was observed on LG_05, suggesting a single pleiotropic locus. 3 This research represents an initial step for the future identification of chromosomal regions carrying genes of interest, important for breeding programs and MAS.

The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.

Castanea sativa Mill. is an important multipurpose tree species for north-western Italy, and specially for Piedmont Region. The preservation of its germplasm from the genetic erosion due to the changes in socio-economic structure of rural areas and specific pathogen attacks is critical. The principal aims of this work were to characterize the chestnut germplasm grown in Piedmont and investigate its genetic structure. Sixty-eight grafted chestnut trees were evaluated using 10 SSRs (simple sequence repeats) loci and 20 morphological descriptors.Thirty-six different genotypes were identified; the analysis of the genetic structure of this germplasm revealed that four gene pools contributed to the formation of the population sampled . In general, cultivars tended to group into a main gene pool on the basis of their prevalent use and growing area. These results are substantially in agreement with those of the cluster analysis that was carried out to estimate the genetic relationships among the cultivars.Morphological analyses showed large variation of traits among the individuals, related with the market destination of the nuts and useful for cultivar and clonal selection. Discriminant analysis was applied to find a correlation between genetic and morphological data: nut and leaf shape, nut hairness and male flower type resulted to be the most discriminant traits associated with the genetic structure.In the end, this work clarified the genetic structure of the cultivated germplasm in Piedmont describing the main cultivars of the Region, giving useful information for conservation and breeding purposes.

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Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. Only few DMV genomes are publicly available. Here, we report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. RNA from 15 tissue samples of cetaceans stranded along the Italian and French coasts (2008–2017) was purified and processed using custom probes (by bait hybridization) for target enrichment and sequenced on Illumina MiSeq. Data were mapped against the reference genome, and the novel sequences were aligned to the available genome sequences. The alignment was then used for phylogenetic and phylogeographic analysis using MrBayes and BEAST. We herein report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples. By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. The phylogenetic tree well discriminated the Mediterranean and the NE-Atlantic strains, circulating in the Mediterranean Sea and causing two different epidemics (2008–2015 and 2014–2017, respectively), with a limited time overlap of the two strains, sharing a common ancestor approximately in 1998.

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