Background: Assessments of genetic diversity are essential for germplasm characterization and exploitation. Molecular markers are valuable tools for exploring genetic variation and identifying germplasm. They have key roles in a Xanthoceras sorbifolia breeding program.

Results: We analyzed the genetic diversity of populations of this species using 23 simple sequence repeat (SSR) loci and data on kernel oil content. The 11 populations included in the study were distributed across a large geographic range in China. The kernel oil content differed significantly among populations. SSR marker analysis detected high genetic diversity among the populations. All SSRs were polymorphic, and we identified 80 alleles across the populations. The number of alleles at each locus ranged from two to six, averaging 3.48 per primer pair. The polymorphic information content (PIC) values ranged from 0.35 to 0.70, averaging 0.51. Expected heterozygosity (He), observed heterozygosity (Ho), and Shannon's information index (I) calculations detected large genetic variations among populations of different provenance. The high average number of alleles per locus and the allelic diversity observed in the set of genotypes analyzed indicated that the genetic base of this species was relatively wide. The statistically significant positive correlation between genetic and geographic distances suggested adaptations to local conditions.

Conclusions: Microsatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.