Homogeneity of recombination rate within a conserved region on BTA3 that contains QTL

The D3S20-D3S34-D3S3 region on BTA3 contains quantitative trait loci (QTL) controlling milk production traits. This region also displays extensive conservation of synteny among several species including cattle, humans, mice and sheep. In this study, we evaluated the adjacent intervals D3S20-D3S34 and D3S34-D3S3 for differences in recombination rate (θ) among bulls in order to assess the suitability of population-based estimates of θ for marker assisted selection and to explore the relationship between variation in θ and chromosome breakpoints associated with mammalian evolution. Using sperm typing, θ_D3S20-D3S34 and θ_D3S34-D3S3 were estimated for six triply heterozygous bulls. Recombination frequency ranged from 6.2 to 12.5% and from 9.7 to 19.2% for the D3S20-D3S34 and D3S34-D3S3 intervals, respectively. However, significant variation in θ was not detected between bulls for either interval (D3S20-D3S34 χ₅² d.f. = 2.59, P < 0.90; D3S34-D3S3 χ₅² d.f. = 3.72, P < 0.75). The observed differences in θ were most readily attributed to differences in allele-specific amplification efficiencies among bulls. Our results suggest that the positions of QTL in this region can be reliably determined from population data and therefore accurate marker-assisted selection can be performed for desirable alleles without concern for variation in θ. Furthermore, when considered with results of earlier studies, these findings support a correlation between the existence of evolutionary breakpoints or chromosome rearrangements and variation in θ.