The use of link provider data to improve national genetic evaluation across weakly connected subpopulations.

Data from 3 prefectures and a nationwide farming corporation were used to assess the usefulness of the "link provider data" in providing indirect genetic links for the national genetic evaluation for carcass weight across weakly connected subpopulations of the Japanese Black cattle. The data from the farming corporation provided genetic links to those of all prefectures and was therefore used as the link provider data. Two national genetic evaluation strategies under an animal model were compared, based on the generalized coefficient of determination (CD) of contrasts between mean EBV of sires or maternal grandsires (MGS) from different prefectures: strategy PA-1 was a pooled analysis of the data sets of the 3 prefectures, and strategy PA-2 was a pooled analysis of the data sets of the 3 prefectures and the farming corporation. The CD of the contrasts were greater for PA-2 than for PA-1. Under PA-2, the CD of the contrasts between mean EBV of sires or MGS ranged from 0.67 to 0.78 or from 0.61 to 0.70, respectively. Pooling the data from the 3 prefectures and the farming corporation increased the degree of connectedness through the link provider data rather than the amount of information by adding more data, thus improving the accuracy of prediction. The differences between mean EBV of sires or MGS from different prefectures were smaller for PA-1 than for PA-2. This finding suggests that genetic differences in carcass weight among prefectures are present, but that they would be confused with the environmental differences under PA-1 because of the lack of genetic connectedness among the prefectures. On the other hand, the genetic differences among the prefectures would be predicted precisely under PA-2 because the genetic connectedness among the prefectures was improved by using the link provider data. The results demonstrate that the link provider data could be used to unify within-prefecture evaluation to form a Japanese national genetic evaluation across weakly connected subpopulations.

Effectiveness of adjusting for heterogeneity of variance in genetic evaluation of Japanese Black cattle.

Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. The objectives of this study were to quantify the heterogeneity of variance in carcass weight in Japanese Black cattle, to develop an adjustment method to account for the heterogeneity, and to evaluate the effectiveness of the method. A total of 96,950 records were collected from steers and heifers slaughtered from 1997 to 2005. These records were grouped into 2,767 farm-market-year-sex subclasses. Fourteen log-linear models for the variances were set up to estimate the heterogeneous phenotypic variances within subclasses. Schwarz's Bayesian information criterion was used for model selection. The preadjustment of records to a baseline variance was based on maximum likelihood estimates obtained from the selected model. As a result of adjustment, the SD, the CV, and the Gini coefficient for the phenotypic variance decreased by 68.6, 69.8, and 70.1%, respectively. When the top 5% of sires and top 1% of dams were selected, Spearman's rank correlation coefficients between the adjusted and unadjusted data were 0.95 for the selected sires and 0.78 for the selected dams. The effectiveness of the adjustment was evaluated in terms of the ability to predict breeding values, using the results of the successive genetic evaluations. Mean squared error between the parent averages and actual predicted values of the genetic merit for the sires whose progeny had a carcass record only from 2003 to 2005 was significantly reduced by the adjustment (P < 0.05). The results suggest that the genetic evaluation becomes more accurate by adjusting the data using the procedure developed in this study.

Comparison of genetic gains per year for carcass traits among breeding programs in the Japanese Brown and the Japanese Black cattle.

The breeding program for beef cattle in Japan has changed dramatically over 4 decades. Visual judging was done initially, but progeny testing in test stations began in 1968. In the 1980s, the genetic evaluation program using field records, so-called on-farm progeny testing, was first adopted in Oita, Hyogo, and Kumamoto prefectures. In this study, genetic trends for carcass traits in these 3 Wagyu populations were estimated, and genetic gains per year were compared among the 3 different beef cattle breeding programs. The field carcass records used were collected between 1988 and 2003. The traits analyzed were carcass weight, LM area, rib thickness, s.c. fat thickness, and beef marbling standard number. The average breeding values of reproducing dams born the same year were used to estimate the genetic trends for the carcass traits. For comparison of the 3 breeding programs, birth years of the dams were divided into 3 periods reflecting each program. Positive genetic trends for beef marbling standard number were clearly shown in all populations. The genetic gains per year for all carcass traits were significantly enhanced by adopting the on-farm progeny testing program. These results indicate that the on-farm progeny testing program with BLUP is a very powerful approach for genetic improvement of carcass traits in Japanese Wagyu beef cattle.

Genotype x environment interaction effects on carcass traits in Japanese Black cattle.

The importance of genotype x environment (region or management system) interactions for carcass traits in Japanese Black cattle was investigated using both univariate and multivariate animal models. The univariate approach was used mainly to test the significance of interaction effects. The multivariate approach was used to estimate genetic correlations, which indicated the magnitude of genotype x environment (GE) interactions. The more a genetic correlation deviates from 1, the larger the interaction. From the univariate approach, the addition of genotype x environment (region or management system) interaction (co)variance components resulted in an improved fit of the model for all traits in both cases (P < 0.001). However, estimates of genetic correlation between regions obtained from the multivariate approach for hot carcass weight, LM area, rib thickness, s.c. fat thickness, and marbling score were 0.97, 0.95, 0.93, 0.97, and 0.93, respectively. The corresponding estimates between management systems were 0.84, 0.92, 0.84, 0.90, and 0.97, respectively. These results indicate that GE interaction effects on carcass traits of Japanese Black cattle may be biologically unimportant. Therefore, breeding values obtained using the multivariate method would rank sires similarly in all environments. Consequently, carcass traits measured in these two different regions or management systems can be treated as the same traits.

Production of calves by transfer of nuclei from cultured somatic cells obtained from Japanese black bulls.

We investigated the possibility of producing calves from transferable bovine embryos obtained by nuclear transfer using somatic cell-derived cell lines. Muscle cells obtained from 2 Japanese Black bulls were dispersed in Hank's solution supplemented with collagenase Type-I. The separated muscle cells were cultured in Dulbecco's Modified Eagle's medium (D-MEM) supplemented with 10% fetal bovine serum (FBS) at 39 degrees C in an atmosphere of 5% CO2 in air. Cells were passaged at least 4 times, and for 5 d prior to nuclear transfer they (donor cells: karyoplasts) were cultured in D-MEM supplemented with 0.5% FBS (to induce quiescence) or 10% FBS. Recipient oocytes were produced by in vitro culture of bovine oocytes that were obtained at a slaughterhouse and then enucleated in modified phosphate buffered saline supplemented with cytochalasin B. Embryos were reconstructed by 3 protocols using karyoplasts cultured in the medium with 0.5% FBS. 1) Group A: recipient oocytes (cytoplasts; n = 157) were treated with Ca ionophore A 23187, ethanol and cycloheximide, and then a karyoplast was fused to an activated cytoplast. 2) Group B: karyoplasts were transferred to cytoplasts (n = 117), and the couplets were treated with electric stimulation and then Ca ionophore A 23187 and cycloheximide. 3) Group C: cytoplasts (n = 104) were cultured for a further 12 h before fusion, and then the couplets were treated with electric stimulation and cycloheximide. 4) Group D: in addition to the above 3 groups, karyoplasts cultured in the medium with 10% FBS were transferred to recipient cytoplasts (n = 137) and treated as in Protocol 2. Reconstructed embryos were cultured in modified CR1aa for 8 d, and the development of embryos was assessed. In total 73 blastocysts were obtained, and the frequency of development to the blastocyst stage in Group A (2.5%) was lower than that of Groups B, C and D (20.5, 18.3 and 19.0%, respectively; P < 0.01). Of these the sex of 21 blastocysts was determined by rapid Y-chromosome detection assay, and all were male, suggesting that nuclear replacement had been achieved successfully. When 26 blastocysts were transferred to 20 recipient cows, 8 of them became pregnant; 4 cows subsequently aborted about 60 d after embryo transfer while the remaining 4 cows calved. These results indicate that reconstructed embryos obtained by nuclear transfer of muscle cell-derived cell lines can develop to the blastocyst stage, and some are sufficiently competent to develop to term. Particularly important was the finding that special culture protocols for somatic cells prior to nuclear transfer were not necessary in our system.