Kerry cattle originate from the southwest of Ireland and have been recognised as a distinct breed since 1839 (Curran 1990). They are thought to represent a relic population of indigenous Irish cattle that traces its roots back to the origin of cattle husbandry in Ireland. This unique Irish genetic resource is currently classified as endangered (Scherf 2000) as a result of a population bottleneck in the mid-1980’s when the number of breeding females reached a record low of 110 animals. Since then, conservation programmes implemented in 1984 have led to an improvement in numbers with current estimates of ~1,000 breeding females. Levels of inbreeding have been estimated using data from the Kerry herd book and the figure for the breed was 15% in 1985 (O’hUigín & Cunningham 1990).
In 1996, a molecular genetic survey based on a panel of 20 pan-genomic microsatellite markers genotyped in 80 individuals (collected in 1991) revealed low levels of genetic variation in the Kerry breed which were attributable to the recent population bottleneck (MacHugh et al. 1997; MacHugh et al. 1998). This finding was further corroborated by analysis of matrilineal mitochondrial DNA sequences (Troy et al. 2001).
Individual animal clustering using microsatellite genetic marker data (modified from MacHugh et al. 1998)
For the current project, we will build and expand on this previous research by analysing genome variation in the Kerry breed using the Illumina bovine SNP50 BeadChip assay—a high-density genotyping platform that assays 54,000 SNPs distributed across the bovine genome (Matukumalli et al. 2009). In particular, we will analyse genetic variation in representative animals (n = 40) from the 1991 population and supplement these data with animals born in 2001 (n = 40) and animals born in 2010 (n = 40). Analyses of these genetic data in conjunction with SNP genotypic data generated as part of the bovine HapMap project (Gibbs et al. 2009) will allow: (1) an assessment of present-day levels of genomic diversity in Kerry cattle compared with other European and world breeds; (2) the investigation of how the purported levels of inbreeding and recent genetic bottleneck has affected genome diversity in the Kerry breed; (3) the identification of genetic features unique to the Kerry breed particularly those genomic regions that have been subjected to artificial and natural selection since the breed formation ~170 years ago; and (4) an understanding of how the genomic diversity of Kerry cattle has been modified over the past ~20 years and how breeding and management programmes established in the 1980s have contributed to these patterns of variation. This information will be essential for the future conservation and management of the Kerry cattle genome and population during the coming decades.