Development and screening of large-scale simple sequence repeat (SSR) markers for genetic diversity analysis in date palm (Phoenix dactylifra L.)

Abstract

Simple sequence repeat (SSR) markers remain highly useful for cultivar identification, germplasm characterization and genetic diversity analysis in date palm (Phoenix dactylifera L.). The primary objective of this study was to develop a validated panel of informative SSR markers from a larger candidate pool for routine germplasm characterization, diversity analysis and molecular fingerprinting of date palm cultivars. A large SSR marker panel derived mainly from the genomic resource developed by Hamwieh et al. (Acta Hort 882: 269–277, 2011), together with previously published mPdCIR and PDCAT loci, was screened across 17 date palm accessions representing Oman, Kuwait, Bahrain and the Kingdom of Saudi Arabia. A total of 868 primer pairs were screened, including 580 evaluated in Oman and 288 evaluated in Qatar. The Oman-screened markers were assessed by fragment analysis, whereas the Qatar-screened markers were evaluated using polyacrylamide gel electrophoresis only. Of the Oman-screened primers, 367 amplified successfully, while 213 failed to amplify; among the amplified loci, 274 were polymorphic and 93 were monomorphic. In the Qatar-screened set, 196 primers amplified successfully, of which 67 were polymorphic and 129 were monomorphic. The final allele-based dataset used for diversity analysis comprised 367 SSR loci. Marker informativeness analysis showed a mean polymorphic information content (PIC) of 0.412, with 172 loci exceeding 0.50, and the most informative loci included DPALM295, DPALM413, DPALM986, DPALM483 and DPALM341. Population-level analysis revealed that Oman possessed the highest genetic diversity and the greatest number of private alleles. The analysis of molecular variance (AMOVA) showed that 80% of the total variation occurred within populations and 20% among populations, indicating moderate genetic differentiation. Pairwise Fst, Nei’s genetic distance, principal coordinate analysis (PCoA), and cluster analysis consistently supported genetic structuring among the four Gulf groups. These findings confirm the usefulness of large-scale SSR screening for identifying robust and informative loci and provide a valuable basis for developing a reduced core SSR set for date palm fingerprinting, germplasm management and future breeding applications.