SSR-Based Genetic Diversity and Marker–Trait Associations in Sudanese Date Palm (Phoenix dactylifera L.) Germplasm from River Nile State
Barakat Ali Abdelfarag Mohammed
Department of Horticulture, Faculty of Agriculture, University of Khartoum, P.O. Box 321, Shambat, Sudan and Hudeiba Research Station, Horticultural Crops Research Center, Agricultural Research Corporation, P. O. Box 31, Edammer, Sudan.
Mayada M. Beshir *
Biotechnology and Biosafety Research Corporation, Agricultural Research Corporation, P.O. Box: 30, Shambat, Sudan.
Elfatih M. Mahdi
Department of Horticulture, Faculty of Agriculture, University of Khartoum, P.O. Box 321, Shambat, Sudan.
Ahmed B.O. Abdelmajid
Biotechnology and Biosafety Research Corporation, Agricultural Research Corporation, P.O. Box: 30, Shambat, Sudan and Makerere University Regional Center for Crop Improvement (MaRCCI), Makerere University, P.O. Box 7062, Kampala, Uganda.
*Author to whom correspondence should be addressed.
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.
Keywords: Date palm (Phoenix dactylifera L.), genetic diversity, marker–trait association, polymorphic information content, Simple sequence repeats (SSR)