Whole-Genome Sequencing variants (VCF) and phenotypic data for diverse pearl millet accessions across the African continent

This repository contains whole-genome sequencing (WGS) variant data, along with associated metadata and phenotypic measurements, for a diverse panel of pearl millet (Pennisetum glaucum) accessions collected from 22 countries across Africa. These include landraces, breeding materials, and improved cultivars, which have been categorized into four germplasm groups: Senegalese core collection, Senegalese germplasm, West African material, and PMiGAP. The VCF files were generated from high-coverage paired-end sequencing reads of 231 accessions aligned independently to two pearl millet reference genomes: 843B and the updated Tift 23D2B1-P1-P5 assembly (Ramu et al., 2023). Variants were filtered to retain high-quality biallelic SNPs by removing indels, very low and excessively high-depth sites (5 and 95% threshold), loci with minor allele frequency (MAF) < 5%, and variants or individuals with >20% missing data. The accompanying phenotype dataset includes field-measured traits such as flowering time, downy mildew incidence, and panicle length for 288 accessions evaluated across four experimental locations in Senegal. These datasets are intended for targeted marker panel development, genetic mapping, and genomic-assisted breeding efforts for pearl millet improvement.