Generation of bovine multisite haplotypes using random cosmid clones.

One hundred ten random cosmids were used to probe Southern blots of DNA from nine unrelated cattle digested with 12 restriction enzymes. Although only one-third of the expected fragments were explored, 85% of the cosmids revealed at least one polymorphism. The mean heterozygosity of the generated haplotypes was estimated at 51.9%. A surprisingly high proportion of polymorphisms (approximately 25%) was attributed to insertion-deletion events, compensating for the lower level of nucleotide diversity observed in cattle (pi approximately 0.0007) compared to that in human. The mutation rate at cytosines in the CpG dinucleotide was estimated approximately 10 times higher than that at other nucleotides. When used in linkage studies, the generated markers should cover approximately 50% of the bovine genome.