High-Density Genotyping for Pearl Millet Linkage Map Improvement with Next-Generation Sequencing Data

Pearl millet [Pennisetum glaucum (L.) R. Br; also Cenchrus americanus (L.) Morrone] is a hardy, drought tolerant and climate-smart crop that performs well even in extreme temperatures. Until recently it was considered an orphan crop with poor genomic resources, but recent next-generation sequencing (NGS) technologies have moved it into the modern genomics era. There are several maps in pearl millet containing different types of markers. We used our own published genetic map developed from 16,650 Genotyping by Sequencing (GBS) markers and compared it with other published maps. The map was used to confirm the collinearity of markers against a consensus map. We report that this map contained the highest density of markers per cM compared to other maps. The order of markers and orientation of chromosomes remained the same for the majority of regions. The recombinant inbred line (RIL) population used for linkage map construction was also evaluated for several agronomic and physiological traits. Quantitative trait locus (QTL) analysis revealed that high-density genotyping increases the resolution of genetic map confidence intervals identified for the traits. In summary, these results reveal that NGS studies play a prominent role in improving linkage map saturation and its utility in breeding programs. The information gained from this study can further enhance breeding programs through marker-assisted selection and genomic selection.