The almond, ['Prunus dulcis' (Mill) D.A. Webb syn. 'P. amygdalus' Batsch] is an important nut crop belonging to the family Rosaceae. Almond consumption has shown steady growth during the last decades due to the increased awareness of its excellent flavour, nutritional value and health benefits. The Australian climate provides great potential for growing almonds and the Australian almond breeding program was initiated in 1997 to develop cultivars better suited to growing conditions and to meet market demands. The construction of a genetic linkage map for one of the breeding populations (Nonpareil x Lauranne) was a part of this breeding program. This population comprised 181 individuals, of which 93 were used for map construction and quantitative trait loci (QTL) analysis in this study. Important traits that were investigated included flowering time, flower structures in relation to fruit set and autogamy and shell and kernel traits.

Background: Despite a high genetic similarity to peach, almonds ('Prunus dulcis') have a fleshless fruit and edible kernel, produced as a crop for human consumption. While the release of peach genome v1.0 provides an excellent opportunity for almond genetic and genomic studies, well-assessed segregating populations and the respective saturated genetic linkage maps lay the foundation for such studies to be completed in almond. Results: Using an almond intraspecific cross between 'Nonpareil' and 'Lauranne' (N × L), we constructed a moderately saturated map with SSRs, SNPs, ISSRs and RAPDs. The N × L map covered 591.4 cM of the genome with 157 loci. The average marker distance of the map was 4.0 cM. The map displayed high synteny and colinearity with the 'Prunus' T × E reference map in all eight linkage groups (G1-G8). The positions of 14 mapped gene-anchored SNPs corresponded approximately with the positions of homologous sequences in the peach genome v1.0. Analysis of Mendelian segregation ratios showed that 17.9% of markers had significantly skewed genotype ratios at the level of P < 0.05. Due to the large number of skewed markers in the linkage group 7, the potential existence of deleterious gene(s) was assessed in the group. Integrated maps produced by two different mapping methods using JoinMap® 3 were compared, and their high degree of similarity was evident despite the positional inconsistency of a few markers. Conclusions: We presented a moderately saturated Australian almond map, which is highly syntenic and collinear with the 'Prunus' reference map and peach genome V1.0. Therefore, the well-assessed almond population reported here can be used to investigate the traits of interest under Australian growing conditions, and provides more information on the almond genome for the international community.