Abstract

Local breeds of livestock are of conservation significance as components of global
biodiversity and as reservoirs of genetic variation relevant to the future sustainability of
agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a
350-year history of isolation and inbreeding yet shows no diminution of viability or fertility.
The Chillingham cattle have not been subjected to selective breeding. It has been suggested
previously that the herd has minimal genetic variation. In this study, high-density SNP
genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic
in the herd, compared with 62–90% seen in commercial cattle breeds. Instead of being
homogeneously distributed along the genome, these loci are clustered at specific
chromosomal locations. A high proportion of the Chillingham individuals examined were
heterozygous at many of these polymorphic loci, suggesting that some loci are under
balancing selection. Some of these frequently heterozygous loci have been implicated as sites
of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was
found to span up to 1350 kb, and LD was above r2 = 0.25 up to more than 5000 kb. This
strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous
regions in the Chillingham cattle may be the locations of genes relevant to fitness or
survival, which may help elucidate the biology of local adaptation in traditional breeds and
facilitate selection for such traits in commercial cattle.