A whole genome scan for differences in recombination rates among three Bostaurus breeds

Twenty paternal half-sib families of a granddaughter design were genotyped for 265 genetic markers, most of them microsatellites. These were 16 Holste in families, 3 Simmental families, and 1 Brown Swiss family. The number of sires per breed was 872, 170, and 32, respectively. Two-point recombination rates were estimated both jointly for all breeds and each single breed sep arately. Of 1168 marker intervals, 865 provided estimates for at least two breeds. Differences between breeds were tested by likelihood ratio tests. F our marker intervals, representing three genomic regions on BTA19, BTA24, a nd BTA27, show a significant impact of the breed at a false discovery rate of 0.23 and indicate a genetic component of observed heterogeneity of recom bination. The variability of recombination rates between cattle breeds migh t not be a common feature of the whole genome, but rather might be restrict ed to certain chromosomal segments. Thus, attention should be paid to heter ogeneities when pooling data of such regions from different breeds.