Abstract
There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits) and PRLR (reproductive performance traits) also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the lentivirus.
Highlights
The genetics and conservation of locally adapted livestock breeds is attracting considerable interest currently [1,2,3]
Analysis of retrotypes Recent studies have shown that endogenous retroviruses, related to the Jaagsiekte sheep retrovirus are useful genetic markers to study the historical origins of domestic sheep breeds across the world [17]
Whilst most endogenous Jaagsiekte sheep retrovirus (enJSRV) loci were found to be fixed in domestic sheep, others were insertionally polymorphic [31]
Summary
The genetics and conservation of locally adapted livestock breeds is attracting considerable interest currently [1,2,3]. Of importance to the global and national conservation strategies of these breeds is their genetic characterization, confirmation that they are genetically distinctive and an assessment of the biodiversity each breed may contribute to future trait selection [4,5,6] In this context, the UK has a substantial number of native sheep breeds [7]. Many of these are numerically scarce and largely maintained in small numbers by breeders committed to conservation of rare, endangered livestock There is another category of native sheep breeds that are not rare, are commercially farmed and continue to exist in tens of thousands [7]. These are recognized to be at risk, but for the reason that they are highly concentrated in specific geographical regions to which they are adapted [8]
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