Figure 1.

General principles of the proposed IBD fine-mapping method for QTL. In dairy cattle, QTL typically are mapped by using the granddaughter design, i.e., a series of paternal half-brother-ships with phenotypic values corresponding to the sons’ breeding values estimated from the milking performances of their daughters. The proposed approach consists of (i) identifying heterozygous Qq sires (highlighted in red) based on marker-assisted segregation analysis in their respective sons, (ii) genotyping these sires for a high-density marker map in the region of interest and establishing the linkage phase, (iii) sorting the sire chromosomes into two pools according to the associated effect on phenotype, and (iv) identifying a shared haplotype flanking the IBD QTL allele with large substitution effect present in one of the two pools.