Contemporary prefectural sub-genomes continue to be identified by variation in genetic composition and performance characteristics between descendants of five major Japanese Black sub-populations, which evolve from the once- isolated Japanese prefectural herds of Hyogo, Tottori, Shimane, Okayama, Hiroshima etc – See Key Black Wagyu Bloodlines on this site). In 2012 Japanese government descriptors for breed development, selection from specific subgenomes or strains is officially specified (NLBC 2012).
Nationally available carcass data has most informed Japanese genetic progress since the 1960s. But although relying most heavily on both national market prices for outstanding breeding and in-herd carcass EBV feedback information, Japanese breeding decisions continue to leverage traditional prefectural traits. An important decision in predictive selection for a traditional Japanese breeder lies in specifying an appropriate ‘mix’. Japanese animal science studies since the 1980s have supported the persistence of prefectural genetic differences and reveal that Japanese breeding selection from the five key sub-genomes has varied substantially over the last 50 years, depending on the economic emphasis of the period and maintaining a balance between growth and meat quality.
Government sponsored systems today assist in the selection of new candidate AI sires from ongoing progeny test programs, run at a prefectural level, with accompanying specifications to maintain diversity. In recent decades, carcass EBVs derived from national Japanese Government carcass databases, updated continuously and analysed by BLUP, have provided the single most influential tool. Over 90% of fullblood feeder progeny are subsequently produced by AI, generally from a tiny sub-group of ‘most popular’ carcass EBV sires selected by the above means from an extensive national catalogue.