A physical map of the bovine genome

Abstract

Background: Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.

Results: A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.

Conclusion: Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.

Figure 1

Comparison of the bovine BAC fingerprint map, composite marker map and Bt3.1 sequence assembly. For each chromosome, top and bottom lines are the composite map, the second line from the top is the assembly, and the third is the BAC map. The upper (blue) region depicts connections between the composite map to the assembly, the middle (green) connects the assembly and BAC map, and the lower (maroon) connects the BAC and composite maps.

Figure 2

Phylogenic tree depicting relationships between whole-genome order of markers on bovine maps and sequence. Pairwise distances between maps are the 1 - τ, where τ is Kendall's rank correlation coefficient. Whole-genome τ values were computed by summing the number of inversions necessary to reconcile orders of each chromosome over all chromosomes. Maps included in the comparison are the Btau3.1 sequence assembly (Btau3.1), the BAC fingerprint map (BAC), the composite marker map, the third generation Illinois/Texas (ILTX-2005) radiation hybrid (RH) map [29], the Shirikawa (SIAG) RH map [30], and the SIAG-USDA linkage map [28]. BovGen RH and Alberta/Missouri (UAMU) linkage data also contribute to the composite map, but are not included here because an independent map of all markers scored on the BovGen panel is not available, and a lack of markers shared by UAMU and data sets other than BovGen precludes meaningful comparison.

Figure 3

Data flow diagram of the composite map construction process.