Masahiro Satoh

Including Dominance Effects in the Genomic BLUP Method for Genomic Evaluation

We evaluated the performance of GBLUP including dominance genetic effect (GBLUP-D) by estimating variances and predicting genetic merits in a computer simulation and 2 actual traits (T4 and T5) in pigs. In simulation data, GBLUP-D explained more than 50% of dominance genetic variance. Moreover, GBLUP-D yielded estimated total genetic effects over 1.2% more accurate than those yielded by GBLUP. In particular, when the dominance genetic variance was large, the accuracy could be substantially improved by increasing the number of markers. The dominance genetic variances in T4 and T5 accounted for 9.6% and 6.3% of the phenotypic variances, respectively. Estimates of such small dominance genetic variances contributed little to the improvement of the accuracies of estimated total genetic effects. In both simulation and pig data, there were nearly no differences in the estimates of additive genetic effects or their variance between GBLUP-D and GBLUP. Therefore, we conclude GBLUP-D is a feasible approach to improve genetic performance in crossbred populations with large dominance genetic variation and identify mating systems with good combining ability.

Genetic evaluation of the longevity of the Holstein population in Japan using a Weibull proportional hazard model.

The objective of this study was to confirm the stability of the genetic estimation of longevity of the Holstein population in Japan. Data on the first 10 lactation periods were obtained from the Livestock Improvement Association of Japan. Longevity was defined as the number of days from first calving until culling or censoring. DATA1 and DATA2 included the survival records for the periods 1991-2003 and 1991-2005, respectively. The proportional hazard model included the effects of the region-parity-lactation stage-milk yield class, age at first calving, the herd-year-season, and sire. The heritabilities on an original scale of DATA1 and DATA2 were 0.119 and 0.123, respectively. The estimated transmitting abilities (ETAs) of young sires in DATA1 may have been underestimated, but coefficient δ, which indicated the bias of genetic trend between DATA1 and DATA2, was not significant. The regression coefficient of ETAs between DATA1 and DATA2 was very close to 1. The proportional hazard model could steadily estimate the ETA for longevity of the sires in Japan.

Economic effects of using sexed semen in Japanese dairy herds.

Dairy farm agricultural income should increase when sexed semen is used instead of unsexed semen. This study simulated three scenarios: using unsexed semen (N), using X sperm of Holstein and unsexed semen of Japanese Black (H), and using X sperm of Holstein and Y sperm of Japanese Black (HJ). Two management scenarios were considered: conventional management (CONV); and the use of Japanese Black semen with surplus cows to produce F(1) s where sufficient replacement female Holstein calves were obtained for maintenance (MAINT). In CONV, the agricultural incomes of H and HJ were 610,000-2,400,000 yen higher than that of N. The agricultural income increased when the difference in the prices between Holstein males and average F(1) male/female calves was 34,000-50,000 yen, that between Holstein male and female calves was 80,000-110,000 yen, and that between F(1) male and female calves was 50,000-90,000 yen. Therefore, the agricultural income can be increased by using sexed semen to select calves of a more valued breed and sex.

CONSERVATION AND UTILIZATION OF BEEF CATTLE GENETIC RESOURCES IN JAPAN

There are four cattle beef breeds in Japan: Japanese Black, Japanese Brawn, Japanese Poll and Japanese Shorthorn. These breeds were crossed with European breeds in the early 1900s. As a result of introducing European blood, Japanese beef cattle have an expanded and more diverse gene pool. Furthermore, both the breed used for crossing and the selection criteria employed varied significantly from prefecture to prefecture Consequently, a number of distinct strains have been established. At present, however, the genetic diversity is becoming increasingly concentrated around a limited number of strains noted for their superior meat quality. From the genetic conservation view point, it is necessary to stock minor strains by frozen semen and embryos for future domands of genetic resources. This paper discusses the conservation and current utilization of beef cattle genetic resources in Japan.

Correlated responses of respiratory disease and immune capacity traits of Landrace pigs selected for Mycoplasmal pneumonia of swine (MPS) lesion.

Five generations of Landrace pigs selected for average daily gain, backfat thickness, Mycoplasmal pneumonia of swine (MPS) lesion score, and plasma cortisol levels, was executed to decrease the MPS lesion score. Genetic parameters and correlated genetic responses for respiratory disease and peripheral blood immune traits were estimated in 1395 Landrace pigs. We estimated the negative genetic correlation of MPS lesion score with phagocytic activity (PA) at 7 weeks of age (-0.67). The breeding values of PA at 7 weeks of age and 105 kg body weight and the correlated selection response of the ratio of granular leukocytes to lymphocytes at 105 kg body weight were significantly increased, and sheep red blood cell-specific antibody production (AP) was significantly decreased in a selection-dependent manner. Increasing of natural immunological indicators (e.g. PA) and decreasing of humoral immunological indicator (e.g. AP) were observed due to genetically decreasing MPS lesion score.

Genetic analysis of fat‐to‐protein ratio, milk yield and somatic cell score of Holstein cows in Japan in the first three lactations by using a random regression model

We estimated the genetic parameters of fat-to-protein ratio (FPR) and the genetic correlations between FPR and milk yield or somatic cell score in the first three lactations in dairy cows. Data included 3,079,517 test-day records of 201,138 Holstein cows in Japan from 2006 to 2011. Genetic parameters were estimated with a multiple-trait random regression model in which the records within and between parities were treated as separate traits. The phenotypic values of FPR increased soon after parturition and peaked at 10 to 20 days in milk, then decreased slowly in mid- and late lactation. Heritability estimates for FPR yielded moderate values. Genetic correlations of FPR among parities were low in early lactation. Genetic correlations between FPR and milk yield were positive and low in early lactation, but only in the first lactation. Genetic correlations between FPR and somatic cell score were positive in early lactation and decreased to become negative in mid- to late lactation. By using these results for genetic evaluation it should be possible to improve energy balance in dairy cows.

Parameters affecting genome simulation for evaluating genomic selection method

The present study investigated the parameter settings for obtaining a simulated genome at steady state of allele frequency (mutation-drift equilibrium) and linkage disequilibrium (LD), and evaluated the impact of whether or not the simulated genome reached steady state of allele frequency and LD on the accuracy of genomic estimated breeding values (GEBVs). After 500 to 50,000 historical generations, the base population and subsequent seven generations were generated as recent populations. The allele frequency distribution of the last generations of the historical population and LD in the base population were calculated when varying the values of five parameters: initial minor allele frequency, mutation rate, effective population size, number of markers and chromosome length. The accuracies of GEBVs in the last generation of the recent population were calculated by genomic best linear unbiased prediction. The number of historical generations required to reach mutation-drift equilibrium depended on the initial allele frequency and mutation rate. Regardless of the parameters, LD reached a steady state before allele frequency distribution reached mutation-drift equilibrium. The accuracies of GEBVs largely reflect the extent of linkage disequilibrium with the exception of varying chromosome length, although there were no associations between the accuracies of GEBVs and allele frequency distribution.

Impacts of genotyping strategies on long-term genetic response in genomic selection

The present study investigated the effects of the choices of animals of reference populations on long-term responses to genomic selection. Simulated populations comprised 300 individuals and 10 generations of selection practiced for a trait with heritability of 0.1, 0.3 or 0.5. Thirty individuals were randomly selected in the first five generations and selected by estimated breeding values from best linear unbiased prediction (BLUP) and genomic BLUP in the subsequent five generations. The reference populations comprise all animals for all generations (scenario 1), all animals for 6-10 generations (scenario 2) and 2-6 generations (scenario 3), and half of the animals for all generations (scenario 4). For all heritability levels, the genetic gains in generation 10 were similar in scenarios 1 and 2. Among scenarios 2 to 4, the highest genetic gains were obtained in scenario 2, with heritabilities of 0.1 and 0.3 as well as scenario 4 with heritability of 0.5. The inbreeding coefficients in scenarios 1, 2 and 4 were lower than those in BLUP, especially within cases with low heritability. These results indicate an appropriate choice of reference population can improve genetic gain and restrict inbreeding even when the reference population size is limited.

Selection for testis size and correlated responses of female reproductive traits in golden hamsters

Golden hamsters were selected for large (high selection direction: H) and small (low selection direction: L) testis size, as measured in live males at age 13 weeks over six generations. The selection response and correlated responses in female reproductive traits were evaluated in terms of the divergence between H and L lines for testis size. In males, the differences in testis size at 13 weeks, testis weight at 19 weeks, and body weight at 13 and 19 weeks were significant at the 1% level from generation 1 onward. The realized heritability of testis size, as estimated from regression of the selection responses on effective selection differentials, was 0.29. This was similar to the heritability estimated by using the multiple-trait animal model restricted maximum likelihood (0.30). In females, significant differences in ovulation rate at the 5% level were detected in generations 5 and 6. Litter size 1 day after birth also diverged between the H and L lines, but the difference was not consistently significant. The realized genetic correlation between testis size and ovulation rate was 0.67.

Comparison of production systems for efficient use of indigenous pig breeds in developing countries.

Conserving pig genetic resources and improving their productivity is important to increase returns over investment in developing countries. The purebred, first-cross, rotational cross and backcross matings representing production systems based on pig breeds indigenous to the country and exotic pig breeds were investigated. The number of pigs in the nucleus and commercial herds necessary to produce a defined quantity of pork was considered. The amount of heterosis between the indigenous and exotic breeds, superiority in meat production, and degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed were investigated. The number of breeding pigs in the whole system was in the following order: pure breeding (PB) > first-cross (F1) > rotational cross (RC) > backcross (BC) systems. The number of breeding pigs in the nucleus herds of the RC and BC systems was smaller than that in the nucleus herds of the PB and F1 systems. The degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed affected the efficiency of the production system.