Developing and genetic mapping of simple sequence repeat (SSR) markers in walnut

There are not adequate number of published SSR (simple sequence repeat) markers, and there is no a SSR-based genetic linkage map for walnut in the literature. Therefore, the first objective of this study was to develop new SSR markers in walnut for further genetic studies. The second objective of this study was to construct a SSR-based genetic linkage map using Chandler x Kaplan-86 F1 population in walnut. A total of 558 bacterial artificial chromosome end sequences (BES-SSR) primer pairs from J. regia were designed and 507 primers (91%) had successfully amplification patterns. A total of 1097 alleles were generated from 307 polymorphic SSR primers, ranging from 2 to 11, with an average of 3.6 per locus. Polymorphism information contents (PIC) varied from 0.11 to 0.88 with an average of 0.46. Walnut consensus map was successfully constructed, and 285 SSR loci were mapped along with 16 linkage groups. The total map length was 1.320,2 cM, with a mean marker density of 4.63 cM. The LG length varied from 40.8 cM (LG16) to 143.6 cM (LG8). The average marker distance varied from 2.63 (LG10) to 8.38 (LG15). The number of markers changed between 6 (LG16) to 27 (LG3). In conclusion, the first SSR genetic linkage map of walnut was constructed with the new SSR markers developed in this study. However, more SSR markers are necessary to extent the short linkage groups and to fill gaps in the current map.