Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive, non-random SNP heterozygosity.

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 r(2) = 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.

Admixture analysis in relation to pedigree studies of introgression in a minority British cattle breed: the Lincoln Red.

Investigation of historic population processes using molecular data has been facilitated by the use of approximate Bayesian computation (ABC), which enables the consideration of multiple alternative demographic scenarios. The Lincoln Red cattle breed provides a relatively simple example of two well-documented admixture events. Using molecular data for this breed, we found that structure did not resolve very low (<5% levels) of introgression, possibly due to sampling limitations. We evaluated the performance of two ABC approaches (2BAD and DIYABC) against those of two earlier methodologies, ADMIX and LEADMIX, by comparing their interpretations with the conclusions drawn from herdbook analysis. The ABC methods gave credible values for the proportions of the Lincoln Red genotype that are attributable to Aberdeen Angus and Limousin, although estimates of effective population size and event timing were not realistic. We suggest ABC methods are a valuable supplement to pedigree-based studies but that the accuracy of admixture determination is likely to diminish with increasing complexity of the admixture scenario.

Prioritization based on neutral genetic diversity may fail to conserve important characteristics in cattle breeds.

Conservation of the intraspecific genetic diversity of livestock species requires protocols that assess between-breed genetic variability and also take into account differences among individuals within breeds. Here, we focus on variation between breeds. Conservation of neutral genetic variation has been seen as promoting, through linkage processes, the retention of useful and potentially useful variation. Using public information on beef cattle breeds, with a total of 165 data sets each relating to a breed comparison of a performance variable, we have tested this paradigm by calculating the correlations between pairwise breed differences in performance and pairwise genetic distances deduced from biochemical and immunological polymorphisms, microsatellites and single-nucleotide polymorphisms. As already observed in floral and faunal biodiversity, significant positive correlations (n=54) were found, but many correlations were non-significant (n=100) or significantly negative (n=11). This implies that maximizing conserved neutral genetic variation with current techniques may conserve breed-level genetic variation in some traits but not in others and supports the view that genetic distance measurements based on neutral genetic variation are not sufficient as a determinant of conservation priority among breeds.

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data.

Accurate measures of effective population sizes (Ne ) in livestock require good quality data and specialized skills for their computation and analysis. Ne can be estimated by Wright's equation Ne =4MF/(M+ F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes Nc of livestock breeds are collated globally. This paper investigates whether estimates of Ne can be made from Nc ; this would facilitate conservation monitoring. Some Ne methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation, of Ne . Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding Ne (LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding Ne (DF). Considering breeds of cattle, sheep, horses, pigs and goats for which Nc and either Ne (LD) or N e(DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between Nc and these measures of Ne . Ne (LD) was found to increase with Nc , significantly in sheep and horses, less so in cattle, but not at all in pigs. Ne (DF) was correlated with log10(Nc ) in cattle, sheep and horses (53, 56, 43 breeds, respectively). Ne (LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log10 transformation of Ne as calculated by Wright's equation. Further verification and refinement are needed, particularly of census data, but credible predictions of Ne are obtainable by applying the following multipliers to log10(Nc ): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log10(Ne (Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of Ne could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio Ne /Nc varied among species with an overall median value of 0.03, less than a tenth of that typically observed in wild mammals. Characteristics were also investigated of a distinct herdbook-based methodology, namely the development of Wright's equation to take into account variances of progeny numbers to yield what has been termed here Ne (Hill). Comparison of these values with Ne (Wright) could help to identify breeds with breeding structures conducive or inimical to genetic conservation. However, Ne (Hill) requires breed-specific values for these variances, and this restricts its applicability.

Number of females in cattle, sheep, pig, goat and horse breeds predicted from a single year's registration data.

An objective and accountable method is needed for deducing the number of registered animals in a breed from registration data. By following the principle that individual breeders register sufficient young females to be certain of having enough replacements for their current breeding stock, the ratios were calculated of the number of adult females in a breed to the number of female registrations, in a given year. Number of breeds considered were 8 cattle, 16 sheep, 8 pigs, 1 goat and 2 equines, all in the United Kingdom or Ireland. This yielded multipliers (4.4 for cattle, 3.3 for sheep, 3.1 for pigs, with confidence limits; and a point estimate of 5.2 for goats) enabling total adult female population to be predicted from a single year's registration data. There was considerable variation between breeds in values of the multiplier, apparently for reasons of breed history and function. This was particularly evident for equines where the two breeds yielded multipliers of 3.8 and 13.9. Multipliers, using registration data that are already in the public domain, can provide an estimate of breed numerical size, which a breed society can either accept or replace with an audited census.