VCF files from the study of low recombining genomic regions in pearl millet

We conducted a comprehensive investigation of large low-recombining regions in cultivated populations of pearl millet, an outcrossing diploid African cereal. We adopted a population genomic approach based on the analysis of single nucleotide polymorphisms. The repository contains the VCF files generated for three datasets: a Senegalese (126 accessions, exome sequencing, 76,018 SNPs), an African (125 wild and cultivated accessions from Western, Central and Eastern Africa, whole genome sequencing, 25,969,513 SNPs) and a temporal dataset (377 accessions from 1976 and 2016, exome sequencing, 39,672 SNPs). We studied seven large regions ranging from 5 to 88 Mb. These regions exhibit an excess of heterozygotes, a distinctive hallmark of overdominance. They displayed a tendency towards a higher diversity and ratio of non-synonymous and deleterious variants. A total of 17% of the cultivated pearl millet genome exhibits a local population structure suggestive of overdominance or possibly pseudo-overdominance. Our empirical results contribute to the accumulation of knowledge that will enhance our understanding of the potential role of overdominance or pseudo-overdominance in maintaining genetic diversity, particularly in low recombining regions.