Highly polymorphic novel simple sequence repeat markers from Class I repeats in walnut (Juglans regia L.)

Abstract

Walnut (Juglans regia L.) is the most important species in the genus Juglans due to the high commercial value of its nutsand timber. Simple sequence repeats (SSRs) are considered as the markers of choice owing to their codominant nature. Since very fewSSRs have been developed in walnut, this study aimed to develop numerous polymorphic SSRs from Class I repeats by using DNAsequences of the Chandler cultivar. In all, 800 SSRs were designed and tested in 8 Turkish, 3 French, and 5 US walnut cultivars, ofwhich 88 (11%) did not produce bands, 161 (20.1%) were monomorphic, and 551 (68.9%) were polymorphic. In all, 2696 alleles wereproduced by the 551 polymorphic SSR loci in the 16 walnut cultivars, ranging from 2 to 14 alleles per locus with an average numberof 4.9. Polymorphism information content ranged from 0.21 to 0.89 with an average of 0.62. Cluster analysis produced a very robustdendrogram. The walnut cultivars were separated into two main groups: all Turkish cultivars were included in one group, whereas theUS and French cultivars were included in the other group. A set of 20 SSRs was selected for their high genetic diversity values to be usedin further genetic studies in walnut. The novel SSR markers developed in this study could be used in future studies for constructing agenetic linkage map, analyzing population genetics, identifying parents, and conducting marker-assisted breeding, fingerprinting, andgermplasm characterization in walnut.