Quantitative Genotyping from GBS Data in Autopolyploids

Despite of the importance of polyploid crop species in agriculture, their genetic studies have been limited by the exclusive usage of single dosage markers (SDMs). However, SDMs may not allow full exploitation of all available, polymorphic markers. In this work, we extend upon the results of Li et al. [G3: Genes, Genomes, Genetics, 4(10), 1971-1979 (2014)] to also look for multiple dosage markers (MDMs) into genotyping-by-sequencing (GBS) data from 384 full-sibs of Medicago sativa, an autotetraploid alfalfa (2n = 4x = 32). Actual allele read depth from GBS was used to perform quantitative genotype calling in SuperMASSA software. We were able to find 7,596 SDMs and 77 MDMs. Here, we calculated pairwise recombination fractions between SDMs using the R Onemap package and heatmap plot revealed 8 marker clusters. The previous study has shown a map composed by 3,591 markers distributed over 64 linkage groups (32 for each parent). Although that previous map has driven important insights on Medicago genome evolution, an integrated map is still preferable due to its statistical and genetic properties when looking for quantitative trait loci. In conclusion, using count data for genotyping calling ends up with the detection of both SDMs and MDMs for more in-depth genetic studies in autopolyploid species.