First simple sequence repeat-based genetic linkage map reveals a major QTL for leafing time in walnut (Juglans regia L.)

Walnut (Juglans regia L.) is one of the most important nut tree species. Simple sequence repeat (SSR)-based genetic linkage maps are valuable and effective tools for studies on integrative and comparative mapping. The data available in literature on walnut is inadequate for linkage mapping. Therefore, in the present study, we aimed to construct the first SSR-based genetic linkage map using the ‘Chandler’ × ‘Kaplan-86’ F1 population and to identify QTL (Quantitative Trait Loci) for leafing time in walnut. A total of 386 SSRs were mapped to 16 linkage groups (LGs) after screening 1437 SSR primer pairs. Among the mapped markers, 166 SSRs (43.0%) were heterozygous in both the parents, whereas 113 (29.3%) and 107 (27.7%) markers were from one of the parents that were integrated into the female and male maps, respectively. The total length of the consensus map was 1568.2 cM, with an average length of 98.0 cM. It included an average of 24.1 markers per LG, and the mean distance between SSR markers was 4.3 cM. The Chandler maternal linkage map included 279 SSR markers of total map length 1285.8 cM, whereas the Kaplan-86 male genetic map contained 273 SSRs of total map length 1574.4 cM. The SSR-based linkage maps presented in this study are moderately dense and can be considered as a fundamental genetic linkage map for further genetic and molecular studies in walnut, as well as in other Juglans species. A major QTL was identified for leafing time on LG4 explaining 52.0–68.8% of the phenotypic variation at similar positions in parental and consensus maps. The identified QTL region with associate markers can be potential for marker-assisted selection in the future for walnut breeding programs.