Australian Wagyu Forum

Genetic Diversity

Issues of Genetic Diversity

Genetic diversity (or the increasing lack of it) is an issue for all Japanese Black populations. A directly related issue is the selection of appropriate technological tools/breeding plans for improvement programs whilst also maintaining diversity. For more information, see Key Black Wagyu Bloodlines, and Predicting Wagyu Performance/Japanese Predictive Systems.

In brief: the status of genetic diversity and/or inbreeding at population level is measured by the (mathematically complex) discipline of population genetics, which can calculate a numerical value for ‘genetic scale’ of a specified population, the value being identified as effective population size.

For example, in dairy cattle breeding Western researchers have suggested a minimum value of 40 for a breed; with other methods suggesting minimums of 30 to 250 (in Nomura, Honda & Mukai , 2001). In the case of the Japanese Black, the authors used pedigree analysis methodology to identify that by 1997 the domestic Japanese herd had an effective size population of just 17.2, with rapid contraction since the 1960s accelerated by (over) use of a few prominent AI sires from 1991 – almost immediately after these sires were identified by BLUP-generated EBVs. (See Predicting Wagyu Performance.)

In 2014, a study describing similar conclusion was published by US researchers (including several closely associated with the US Wagyu Association) applying molecular tools to the United States fullblood population (see Scraggs, Zanella et al, Jnl Anim Breed Genet 2014). Scraggs et al suggest that in the US, ‘consideration should be given be given to outcrossing to other breeds to manage inbreeding and enhance genetic diversity’.

However, there is a significant difference in the foundation scale of the US and Australian fullblood herds, given that the largest single female group (Westholme 1998) was at import (and, for the most part, subsequently) unavailable to US Wagyu breeders, as a result of decisions made by Westholme’s founding owner, Mr Chris Walker.

Still, the export contingent that founded the subsequently closed Australian fullblood herd from the 1990s remains a tiny subset of the Japanese national herd of some 500-600,000 breeders, with a strong bias to two bloodlines (Hyogo/Tajima and Itozakura/Fujiyoshi). So even with much less prevalent AB, effective population size may also be much less than that in Japan, though hopefully not as low as that of the closed Hyogo herd, which had an effective population size of just 8 in 1988, prior to BLUP application (Takayanagi et al, 1996)

Recent analysis of Japanese selection processes (in the chapter: ‘Japanese beef production’, in Beef Cattle: Production & Trade, Cottle & Kahn, eds, 2014) indicates that clearly defined methods for ensuring diversity are now mandated in official Japanese sire selection, which requires: ‘a higher retention rate of genes of any one of the founders for five specific trait lines’. These are identified as prefectural lines from the Chugoku ‘cradle of the Black’, including Hyogo, Tottori, Shimane and Hiroshima. The source of the information is 2012 official Japanese government literature.

Given that inbreeding co-efficient data are currently available for individual registered Australian fullbloods, and this is pre-requisite foundation data for calculating effective population size, it would appear the basis is available for producing a current ‘effective population size’ for the small, closed Australian herd – but the number is not published.

Further, a singular local emphasis on BREEDPLAN EBVs suggests that currently preferred genetic improvement methodology is the use of new but unrestricted GEBVs (genomic EBVs) generated by BLUP, newly informed by carcass data. But if an equal requirement is to maintain/increase diversity, and the GEBV initiative does not specifically address inbreeding, this method may require adjustment, as it will likely further compromise already limited diversity.

Detailed pedigree/strain profiling of the Australian herd registry to identify pockets of diversity – identical to the Japanese animal science research projects summarized on this site in Key Japanese Bloodlines – would be relatively simple. Again, the Australian inbreeding co-efficients already available indicate pedigree analysis, but the related strain analysis of pedigrees has either not been undertaken and/or publicised. The analytical focus instead appears to have been on individuals, via BREEDPLAN EBVs.

So key questions that Australian FB breeders might ask of the Registry are: What is the current state of genetic diversity in the Australian fullblood herd, /how is it being maintained/are selection strategies beyond EBVs required ?