Accurate calling of homeoallelic genotypes of iSelect markers using inbred structured populations

Abstract Motivation Genetic map construction is a foundational step in the analysis of structured experimental populations. For markers that hybridize to several genetically similar locations, or where several alleles are present (such as in multiparental populations), current methods often discard the marker or incorrectly call the genotypes. These errors result in information loss, or incorrect genotypes that can corrupt map construction. Results We present a new approach for simultaneously performing genetic map construction and marker calling. Our new approach allows the calling of a larger number of markers, a larger number of unique alleles per marker and the correct use of markers which hybridize to multiple genetically similar locations. We demonstrate our new approach using simulations, a biparental wheat population and an eight-parent population of spring bread wheat. Applying our method to the eight-parent population increased the number of mapped markers by 71%. We show that the new genetic map allows the investigation of synteny in ways that were not previously possible in that dataset. Availability and implementation The method described in this article has been incorporated into R package mpMap2. It is available from CRAN and also from https://github.com/rohan-shah/mpMap2. Supplementary information Supplementary data are available at Bioinformatics online.