Additional File 1 - IBS and IBD matrices

This file contains all genotype scores of the identity-by-state (IBS) and identity-by-descent (IBD) genotype matrices.

Polymorphic SNP alleles originating from Barke or the wild barley donors of the NAM population HEB-25 are easily distinguishable by state. Based on the Barke reference genotype, the wild barley allele can be specified in each segregating family. To setup the IBS matrix the state of the homozygous Barke allele was coded as 0, while HEB lines that showed a homozygous wild barley genotype were assigned a value of 2. Consequently, heterozygous HEB lines were assigned a value of 1. If a SNP was monomorphic in one HEB family but polymorphic in a second family, lines of the first HEB family were assigned a genotype value of 0, since their state is not different from the Barke allele. Gaps resulting from missing genotypes (0.6% of all data points) were filled with the mean of polymorphic flanking markers, based on the map of Maurer et al. (2015). This way a complete genotype data set (IBS) was retained, which is required to carry out the following multiple regression GWAS.

To convert the IBS matrix into an IBD matrix we first replaced each marker value that was monomorphic in a HEB family by an empty value. Then, the resulting gaps (44.9% of all data points) were filled with the mean of the next polymorphic flanking markers of this gap. This way we can distinguish whether the allele is inherited from the recurrent parent Barke or a wild donor across the whole NAM population. The newly assigned IBD value reflects the marker’s probability of being inherited from the wild barley donor.