Abstract Almond is one of the most important nut crops in Turkey. Simple sequence repeat (SSR)‐based linkage maps are very reliable in constructing linkage maps due to the co‐dominant and highly reproducible nature of the SSR markers. The objective of this study was to construct well‐saturated, SSR‐based genetic linkage maps using ‘Gulcan‐2 × Lauranne’ and ‘Guara × Nurlu’ F1 populations and to identify QTLs related to the flower colour, stigma–anther position and full blooming date in almond. A total of 275 SSR primer pairs selected from the previous studies of various Prunus species were tested in both populations. A total of 175 SSR loci segregated in ‘Gulcan‐2 × Lauranne’ population and 162 SSR loci were mapped into eight linkage groups. The total map length was 514.6 cM, with an average marker density of 3.2 cM. In ‘Guara × Nurlu’ population, 159 markers segregated, and 153 SSR loci were mapped. The total map length was 493.9 cM with an average marker distance of 3.2 cM. Five and four major QTLs were detected in ‘Gulcan‐2 × Lauranne’ and ‘Guara × Nurlu’ populations, respectively. The linkage maps constructed in this study can be used in QTL analysis of important phenotypic traits in almond, whereas identified QTL regions and closely related markers can be used for marker assisted selection in future almond breeding programmes.
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