Identification, development, and application of 12 polymorphic EST-SSR markers for an endemic Chinese walnut (Juglans cathayensis L.) using next-generation sequencing technology

The Chinese walnut (Juglans cathayensis L.), valued for both its nut and wood, is an ecologically important tree species endemic temperate southern China. Investigation of the genetic diversity of Chinese walnut has been limited to natural population genetics and genetic germplasm resources. Here, we describe the development of 12 polymorphic microsatellite markers using next-generation sequencing to screen 96 Chinese walnut individuals collected from 11 natural populations. The number of alleles per locus ranged from 5 to 12. The observed heterozygosity (0.288-0.748) overlapped well with the expected heterozygosity (0.337-0.751). This species has high genetic diversity and gene flow among different populations (FST = 0.075, Nm = 3.088). These markers will be useful for future studies on population genetic structure, evolutionary ecology, and genetic breeding of this walnut tree or other Juglans species.