Construction of high density genetic linkage map of walnut by SSR, SNP AND DArT markers

Walnut (Juglans regia L.) is one of the most important nut tree species in the world. It is also an important tree species in Turkey. Cultivar breeding programs in walnut take long time due to its extensive juvenile period. So, it is necessary to use molecular approach to overcome such problem. Therefore, this thesis aimed (1) to construct the first SSR-based genetic linkage map, (2) to construct a high-density genetic linkage map based on SSR, DArT and SNP markers in walnut. Chandler x Kaplan-86 F1 population was used in genetic linkage mapping. A total of 1,438 SSR primer pairs were screened and 505 segregating ones were analyzed in whole F1 population. Chandler genetic map included 279 markers, while Kaplan-86 genetic map consisted 274 SSR markers. The SSR-based consensus map was constructed with 387 SSR markers and 166 of them were common markers. The total length of SSR-based consensus map was 1,569.9 cM with an average length of 98.1 cM. High density genetic linkage maps were constructed by adding DArT and SNP markers to the SSR linkage maps by genotyping by sequencing approach. Chandler genetic map included a total of 3,483 SNP, DArT and SSR markers, while Kaplan-86 map consisted 4,275 markers. The total length of Chandler map was 1,248.9 cM, while Kaplan-86 map was 1,826.5 cM length. There were 3.0 and 2.4 markers per cM in Chandler and in Kaplan-86 genetic maps, respectively. Chandler map had 234.7 markers per LG, while Kaplan-86 map had 267.2 markers per LG. In conclusion, the first SSR based genetic linkage map and high density genetic linkage map of walnut was constructed in this study. The data produced in this thesis will be very useful and framework for QTL analysis, breeding and genetic studies in the future for walnut.