SNP-based assessment of genetic diversity in MPOB's Tanzania, Angola and Ghana oil palm germplasm

A subset of 349 palms, initially selected from 1,025 palms based on phenotypic diversity across six agronomic and physiological traits, was genotyped using a high-density 92 K SNP array, yielding 67,180 informative markers after quality filtering. SNPs were unevenly distributed across chromosomes, with the highest density observed on Chromosome 4 (12.6%) and the lowest on Chromosome 14 (0.02%). Transition SNPs were more frequent than transversions (61.5% vs. 38.5%). Genetic diversity analyses revealed moderate variation overall, with higher heterozygosity and polymorphism in the Tanzania and Angola populations compared to Ghana, which formed a distinct genetic cluster indicative of a narrow gene pool. Analysis of molecular variance (AMOVA) showed that 82% of genetic variation resided within populations, while pairwise Fst indicated low differentiation between Tanzania and Angola but higher differentiation with Ghana. Population structure analyses, including PCA, phylogenetic trees, and fastSTRUCTURE, consistently identified nine genetic groups. Angola and Tanzania accessions exhibited high levels of admixture, whereas Ghana accessions displayed genetic uniformity. A unique subcluster (TZA13) was detected in Tanzania, highlighting its potential value for conservation and breeding. These high-resolution SNP data provide critical insights into the genetic diversity and structure of MPOB germplasm, supporting the development of representative core collections and enabling marker-assisted selection, genome-wide association studies (GWAS), and genomic selection (GS) in Elaeis guineensis breeding programs.

The online version contains supplementary material available at 10.1007/s13205-025-04613-x.