Whole genome sequence data on diverse pearl millet accessions across the African continent

Pearl millet (Pennisetum glaucum (L.) R. Br.) is a major staple cereal in Asia and West Africa but remains underrepresented in genomic research compared with other major cereals. This dataset presents whole-genome sequencing (WGS) variant data for a diverse panel of 231 pearl millet accessions collected across Africa. A total of 7.1 Tb of sequencing data were generated resulting in high-coverage (20x per sample) paired-end sequencing reads. The data were aligned to two reference genomes, '843B' and the updated 'Tift 23D₂B₁-P1-P5' assembly, and processed variant files were generated for each reference. These variant datasets provide a foundational genomic resource and will be utilized for a targeted DArTag marker panel, with marker coordinates defined relative to both reference genomes. The panel was also phenotyped for flowering time, downy mildew response, and panicle length across four field locations in Senegal, enabling downstream association analyses. All genomic and phenotypic datasets are publicly available to support genetic research, marker development, and breeding efforts aimed at improving pearl millet adaptation and productivity.