Abstract for presentation at 11th International Congress of Human Genetics

Ruminant genomics is often hampered by a lack of available informative markers close to genes of interest. The July 2005 release of the bovine genome assembly by Baylor HGSC has greatly assisted marker development in cattle and potentially in other closely-related ruminant species such as sheep and deer. GBrowse is a generic genome browser that has been configured inhouse at AgResearch. This configuration incorporates the July 2005 Bovine Assembly using BCM scaffolds as a backbone. Bovine and human refseqs, inhouse EST libraries, TIGR contigs and SNPs are aligned using GMAP. Dinucleotide simple sequence repeats (SSRs) (>18bp) identified in a separate analysis of the assembly extracted from GBrowse were tested in cattle, sheep and deer. Eighty-nine percent of SSRs amplified in cattle and 70% of these were found to be polymorphic using standard PCR conditions. Corresponding figures for sheep (64% amplified and 38% polymorphic) and red deer (42% amplified and 22% polymorphic), although lower, still reveal high levels of cross species polymorphism. Consequently GBrowse is now used as a major tool for extracting informative dinucleotide SSR markers from genetic regions of interest, such as those involved in production or disease traits. This further reinforces the value of the recent 6.3-fold coverage assembly of the bovine genome and of developing a useful bioinformatics tool to ruminant genomics.