Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels.

Almond is appreciated for its nutraceutical value and for the aromatic profile of the kernels. In this work, an almond collection composed of 96 Sicilian accessions complemented with 10 widely cultivated cultivars was phenotyped for the production of volatile organic compounds using a proton-transfer time-of-flight mass spectrometer and genotyped using the Illumina Infinium®18 K Peach SNP array. The profiling of the aroma was carried out on fresh and roasted kernels enabling the detection of 150 mass peaks. Sixty eight, for the most related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while the concentration of fifty-four mass peaks, for the most belonging to alcohols and terpenes, significantly decreased. Four hundred and seventy-one robust SNPs were selected and employed for population genetic studies. Structure analysis detected three subpopulations with the Sicilian accessions characterized by a different genetic stratification compared to those collected in Apulia (South Italy) and the International cultivars. The linkage-disequilibrium (LD) decay across the genome was equal to r2 = 0.083. Furthermore, a high level of collinearity (r2 = 0.96) between almond and peach was registered confirming the high synteny between the two genomes. A preliminary application of a genome-wide association analysis allowed the detection of significant marker-trait associations for 31 fresh and 33 roasted almond mass peaks respectively. An accurate genetic and phenotypic characterization of novel germplasm can represent a valuable tool for the set-up of marker-assisted selection of novel cultivars with an enhanced aromatic profile.

An improved protocol for the production of AFLP markers in complex genomes by means of capillary electrophoresis.

The amplified fragment-length polymorphism (AFLP) technology is a recently introduced method to investigate genomes of different complexity, from microbial to higher organisms. It is applied to purposes as diverse as identification of species, strain and varieties, investigation of genetic diversity within and between populations, simple and complex trait mapping, and construction of linkage and physical maps. This technology has been designed on the use of primers labelled with radioactivity and on AFLP fragment separation on sequencing gel. We show that the original EcoRI/TaqI AFLP protocol does not perform appropriately when transferred to fluorescent labelling and capillary electrophoresis (CE), and propose an improved protocol for the production of high-quality AFLP markers in fish, rodents and artiodactyles by means of the Beckman-Coulter CEQ2000 automatic DNA sequencer. In addition, we describe the procedure routinely used in our laboratory to obtain binary matrices from AFLP profiles with the aid of Genographer free-share software (vers. 1.6.0, J.J. Benham, Montana State University), able to elaborate original fragment data and convert them to standard graphical formats for phylogenetic analyses. Comparison with radioactive AFLPs in goats confirmed the reliability of the protocol developed for CE. In fact, 107 fragments generated by two primer combinations and identified by both techniques were attributed the same scoring. Compared with traditional methods, the use of capillary systems and automated analysis increases data throughput and scoring reliability, decreasing the overall experimental error.

A RAPD, AFLP and SSR linkage map, and QTL analysis in European beech (Fagus sylvatica L.).

The genetic linkage map of European beech ( Fagus sylvatica L.) that we report here is the first to our knowledge. Based on a total of 312 markers (28 RAPDs, 274 AFLPs, 10 SSRs) scored in 143 individuals from a F(1) full-sib family. Two maps (one for each parent) were constructed according to a "two-way pseudo-testcross" mapping strategy. In the male map 119 markers could be clustered in 11 major groups (971 cM), while in the female map 132 markers were distributed in 12 major linkage groups (844 cM). In addition, four and one minor linkage groups (doublets and triplets) were obtained for the male and female map respectively. The two maps cover about 82% and 78% of the genome. Based on the position of 15 AFLP and 2 SSR loci segregating in both parents, seven homologous linkage groups could be identified. In the same pedigree we investigated the association with genetic markers of several quantitative traits: leaf area, leaf number and shape in 2 different years, specific leaf area, leaf carbon-isotope discrimination and tree height. A composite interval-mapping approach was used to estimate the number of QTLs, the amount of variation explained by each of them, and their position on the genetic linkage maps. Eight QTLs associated with leaf traits were found that explained between 15% and 35% of the trait variation, five on the female map and three on the male map.