Targeted sequencing of Panicum miliaceum
Broomcorn millet (Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor grain crop with low yields but a renewed interest for high water use efficiency and gluten-free endosperm. To reverse the downward trend in broomcorn millet cultivation, the crop needs genetic improvement and creation of novel genetic variation to increase productivity. In order to facilitate genomics-assisted breeding, we designed a reduced representation genome-sequencing assay that investigates 1.5% of the nuclear DNA in a targeted and reproducible way, with a genomic sampling that is proportional to gene density and, therefore, adjusted to intrachromosomal variation in recombination rate. We used this tool and set up bioinformatics analyses tailored to the polyploid genome of P. miliaceum for maternity and paternity testing, quantification and genomic distribution of homozygous regions and estimation of parental genome contribution for individual seedlings in advanced inbred lines from a breeding program and compared their genomic composition with registered varieties.