Data from: Estimating parent-specific QTL effects through cumulating linked identity-by-state SNP effects in multi-parental populations

The emergence of multi-parental mapping populations enabled plant geneticists to gain deeper insights into the genetic architecture of major agronomic traits and to map quantitative trait loci (QTL) controlling the expression of those traits. Although the investigated mapping populations are similar, one open question is whether genotype data should be modelled as identical-by-state (IBS) or identical-by-descent (IBD). While IBS simply makes use of raw genotype scores to distinguish alleles, IBD data are derived from parental offspring information. We report on comparing IBS and IBD by applying two multiple regression models on four traits studied in the barley nested association mapping (NAM) population HEB-25.
We observed that modelling parent-specific IBD genotypes produced a lower number of significant QTL with increased prediction abilities compared to modelling IBS genotypes. However, at lower trait heritabilities the IBS model produced higher prediction abilities. We developed a method to estimate multi-allelic QTL effects in multi-parental populations from simple bi-allelic IBS data. This method is based on cumulating IBS-derived SNP effect estimates in a defined genetic region surrounding a QTL. Comparing the resulting parent-specific QTL effects with those obtained from IBD approaches revealed high accordance that could be confirmed through simulations. The method turned out to be also applicable to a barley multi-parent advanced generation inter-cross (MAGIC) population. The ‘cumulation method’ represents a universal approach to differentiate parent-specific QTL effects in multi-parental populations, even if no IBD information is available. In future, the method could further benefit from the availability of much denser SNP maps.