A Reference Genome and HapMap for Pearl Millet (Pennisetum glaucum)

With an objective to develop much-required genomic resources in pearl millet, Tift23D₂B₁P₅, the global reference genotype was chosen for generating the draft genome. A total of 1.49 TB raw data was generated from 9 insert libraries as well as from BAC-pools using whole-genome shotgun sequencing approach. By using a range of approaches including high-density genetic map, a genome assembly of 1.79 Gb with 25,241 scaffolds (N50 = 884.94 Kb) and >92% scaffolds of assembly were anchored onto 7 linkage groups. Of 38,579 genes identified, 76.06% of genes had functional annotation. Comprehensive repeat annotation of the assembly showed that 73.69% of the genome comprised of transposable elements. In addition to draft genome, this study also reports a hapmap of pearl millet that is based on re-sequencing of 963 pearl millet germplasm lines including 580 B and R-lines, 345 pearl millet inbred genotypes association panel (PMiGAP) and 38 parental lines of mapping populations (PMP). Comparison of whole genome re-sequencing data from PMiGAP and PMP lines with the reference genome provided 29.54 million SNPs, 3.84 million indels and 12.18 million SNPs, 1.11 million indels respectively. Similarly, RAD-sequencing of B- and R-lines provided 2.86 million SNPs and 693,731 indels. Genome-wide association study based on re-sequencing data and phenotyping data have provided several significant marker-trait associations (MTAs). The reference genome together with the hapmap and MTAs is expected to serve a strong foundation for accelerating molecular breeding in pearl millet across the world.