Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.