Background: The present study was undertaken towards the development of SSR markers and assessing genetic relationships among 32 date palm (Phoenix dactylifera L.) representing common cultivars grown in different geographical regions in Saudi Arabia.

Results: Nintythree novel simple sequence repeat markers were developed and screened for their ability to detect polymorphism in date palm. Around 71% of genomic SSRs were dinucleotide, 25% tri, 3% tetra and 1% penta nucleotide motives. Twenty-two primers generated a total of 91 alleles with a mean of 4.14 alleles per locus and 100% polymorphism percentage. A 0.595 average polymorphic information content and 0.662 primer discrimination power values were recorded. The expected and observed heterozygosities were 0.676 and 0.763 respectively. Pair-wise similarity values ranged from 0.06 to 0.89 and the overall cultivars averaged of 0.41. The UPGMA cluster analysis recovered by principal coordinate analysis illustrated that cultivars trend to group according to their class of maturity, region of cultivation, and fruit color. Analysis of molecular variations (AMOVA) revealed that genetic variation among and within cultivars were 27% and 73%, respectively according to geographical distribution of cultivars.

Conclusions: The developed microsatellite markers are additional values to date palm characterization tools can be used by researchers in population genetics, cultivars identification as well as genetic resources exploration and management. The tested cultivars exhibited a significant amount of genetic diversity and could be suitable for successful breeding program. Genomic sequences generated from this study are available at National Center for Biotechnology Information (NCBI), Sequence Read Archive (Accession numbers. LIBGSS_039019).