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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #194655


item Snelling, Warren

Submitted to: International Conference on Animal Genetics
Publication Type: Abstract Only
Publication Acceptance Date: 5/3/2006
Publication Date: 8/10/2006
Citation: International Bovine Mapping Team. 2006. A comprehensive genetic and physical map of the bovine genome. Proc., 30th International Conference on Animal Genetics (ISAG). Abstract B269, pg 52.

Interpretive Summary:

Technical Abstract: A composite map of the 29 bovine autosomes and X chromosome was constructed. Two linkage and four radiation hybrid (RH) data sets were utilized. Pedigree and marker genotypes from the Shirakawa-USDA linkage data and an eight-breed reference population (MU) were merged with RH vectors from the third-generation Illinois/Texas, SUNbRH, and BovGen maps. The fourth RH data set (UA) represents SNP from the bovine genome sequencing project, which were scored on the BovGen panel. Markers in the MU data set are a subset of the UA SNP. The individual data sets represent a total of 26,076 markers. Twopoint analysis to assign markers to chromosomes resulted in removal of 494 markers not meeting LOD score and distance criteria. The combined data include 17,254 distinct markers, 6,716 of these are shared by two or more data sets. Sequences for 10,329 mapped markers were aligned with sequence from 25,712 BAC clones on the International Bovine BAC Consortium fingerprint map; 14,382 markers were matched to 12,160 whole-genome shotgun contig sequences from the second bovine assembly. Consensus marker orders for each chromosome were computed using maximum likelihood procedures in CarthaGene. Marker positions were projected onto common cM and kbp scales using LDB. Overall agreement between consensus marker order, fingerprint map clone order, and arrangement of contig sequence on whole-chromosome scaffolds is high, although discrepancies exist. The composite map, with markers connected to the BAC fingerprint map and bovine sequence, provides a comprehensive resource, supporting investigations into relationships between genomic and phenotypic variation in cattle.