SSR-Based Genetic Diversity and Marker–Trait Associations in Sudanese Date Palm (Phoenix dactylifera L.) Germplasm from River Nile State

Abstract

Date palm (Phoenix dactylifera L., 2n = 36) is a major fruit crop of North Africa and the Middle East, and Sudan holds diverse farmer-selected seedling germplasm that has not been characterised molecularly. This study assessed the genetic diversity of 17 date palm genotypes from River Nile State (seven Hudeiba gene-bank accessions, eight farmer-selected seedling genotypes and the commercial cultivars Barakawi and Wad Lagai) using 18 simple sequence repeat (SSR) markers, and tested for preliminary associations between SSR markers and five morphological traits (fruit length, leaf base width, leaf length, bunch weight and seed length) and six chemical traits (ash, acidity, fibre, moisture, monosaccharides and tannin concentration). Nine of the 18 SSR markers (50%) were polymorphic, with two or three alleles per locus. Major allele frequency ranged from 0.64 to 0.94 (mean 0.74), gene diversity from 0.12 to 0.48 (mean 0.37), observed heterozygosity from 0.13 to 0.71 (mean 0.51) and polymorphic information content (PIC) from 0.11 to 0.40 (mean 0.31), indicating moderate genetic diversity; SSR070 and SSR048 were the most informative loci. Single-marker analysis detected nominally significant associations of SSR085 with leaf length (R² = 0.30), bunch weight (R² = 0.51), acidity (R² = 0.32) and fibre (R² = 0.42); SSR048 with leaf base width (R² = 0.42), moisture (R² = 0.31) and monosaccharides (R² = 0.33); SSR020 with ash (R² = 0.30), fibre (R² = 0.42) and tannin concentration (R² = 0.48); SSR070 with fruit length (R² = 0.39); and SSR035 with fruit length (R² = 0.31) and seed length (R² = 0.36). Because the panel was small and no correction for multiple testing was applied, these associations are preliminary and require validation in larger, independent populations with higher-resolution genotyping before use in marker-assisted selection.