Application of single-step single nucleotide polymorphism best linear unbiased predictor model with unknown-parent groups for type traits in Japanese Holsteins.

The objectives of this study were to investigate the computational performance and the predictive ability and bias of a single-step SNP BLUP model (ssSNPBLUP) in genotyped young animals with unknown-parent groups (UPG) for type traits, using national genetic evaluation data from the Japanese Holstein population. The phenotype, genotype, and pedigree data were the same as those used in a national genetic evaluation of linear type traits classified between April 1984 and December 2020. In the current study, 2 data sets were prepared: the full data set containing all entries up to December 2020 and a truncated data set ending with December 2016. Genotyped animals were classified into 3 types: sires with classified daughters (S), cows with records (C), and young animals (Y). The computing performance and prediction accuracy of ssSNPBLUP were compared for the following 3 groups of genotyped animals: sires with classified daughters and young animals (SY); cows with records and young animals (CY); and sires with classified daughters, cows with records, and young animals (SCY). In addition, we tested 3 parameters of residual polygenic variance in ssSNPBLUP (0.1, 0.2, or 0.3). Daughter yield deviations (DYD) for the validation bulls and phenotypes adjusted for all fixed effects and random effects other than animal and residual (Yadj) for the validation cows were obtained using the full data set from the pedigree-based BLUP model. The regression coefficients of DYD for bulls (or Yadj for cows) on the genomic estimated breeding value (GEBV) using the truncated data set were used to measure the inflation of the predictions of young animals. The coefficient of determination of DYD on GEBV was used to measure the predictive ability of the predictions for the validation bulls. The reliability of the predictions for the validation cows was calculated as the square of the correlation between Yadj and GEBV divided by heritability. The predictive ability was highest in the SCY group and lowest in the CY group. However, minimal difference was found in predictive abilities with or without UPG models using different parameters of residual polygenic variance. The regression coefficients approached 1.0 as the parameter of residual polygenic variance increased, but regression coefficients were mostly similar regardless of the use of UPG across the groups of genotyped animals. The ssSNPBLUP model, including UPG, was demonstrated as feasible for implementation in the national evaluation of type traits in Japanese Holsteins.

Selection on milk production and conformation traits during the last two decades in Japan.

OBJECTIVE: The purpose of this study was to compare intended and actual yearly genetic gains for milk production and conformation traits and to investigate the simple selection criterion practiced among milk production and conformation traits during the last two decades in Japan. Learning how to utilize the information on intended and actual genetic gains during the last two decades into the genomic era is vital. METHODS: Genetic superiority for each trait for four paths of selection (sires to breed bulls [SB], sires to breed cows [SC], dams to breed bulls [DB], and dams to breed cows [DC]) was estimated. Actual practiced simple selection criteria were investigated among milk production and conformation traits and relative emphasis on milk production and conformation traits was compared. RESULTS: Selection differentials in milk production traits were greater than those of conformation traits in all four paths of selection. Realized yearly genetic gain was less than that intended for milk production traits. Actual annual genetic gain for conformation traits was equivalent to or greater than intended. Retrospective selection weights of milk production and conformation traits were 0.73:0.27 and 0.56:0.44 for intended and realized genetic gains, respectively. CONCLUSION: Selection was aimed more toward increasing genetic gain in milk production than toward conformation traits over the past two decades in Japan. In contrast, actual annual genetic gain for conformation traits was equivalent to or greater than intended. Balanced selection between milk production and conformation traits tended to be favored during actual selection. Each of four paths of selection (SB, SC, DB, and DC) has played an individual and important role. With shortening generation interval in the genomic era, a young sire arises before the completion of sire's daughters' milk production records. How to integrate these four paths of selection in the genomic era is vital.

Optimal value for the exponential term of Wilmink's function according to current Holstein lactation curves in Japan.

We compared values of Wilmink's exponential term to describe the lactation curves of Holstein cows in Japan. Data were a total of 100,971,798 test-day records from the first through fifth parities during 1991 through 2018. The lactation curve model used fourth-order Legendre polynomials and Wilmink's exponential term. In total, 810 analyses were executed to compare six values (-0.02, -0.03, …, -0.07) for the exponential term to select the one that yielded the smallest root mean square error. For all parities, daily milk yield and lactation persistency increased consistently and peak lactation days occurred later from year to year. For the years evaluated, the optimal exponential term was -0.05 for first and second parities, -0.04 for third parity, and -0.03 for fourth and fifth parities. The change in the exponential parameter with increasing year was related to delays in peak lactation.

Suitable indicator of heat stress for genetic evaluation of heat tolerance in Holstein cows in Japan.

Only a few, principal, weather stations in Japanese prefectures have the daily humidity records required to calculate the temperature-humidity index (THI) as a dairy cow heat-stress indicator. We compared three heat-stress indices: (1) THI calculated from daily average temperature and daily relative humidity at a principal weather station (PTHI); (2) daily average temperature at each herd's closest local weather station (TEMP); and (3) THI calculated from daily average temperature at each herd's closest local weather station and daily relative humidity at the principal weather station (HTHI). We used daily records from 532 provincial weather stations and test-day records of milk production from Days 6 to 305 post-first-calving in Holsteins to compare the indices as indicators of heat-stress effects on milk yield and somatic cell score (SCS). The models used the BLUPF90 package to analyze the effects of herd-year, calving age, days in milk, and PTHI, TEMP, or HTHI. We estimated each model's mean square error (MSE) and compared suitabilities among indices for each trait. TEMP heat-stress thresholds were ~18°C (milk yield) and 15-20°C (SCS). The MSE of the HTHI model was the smallest, but no significant differences were found among the indices for milk yield.

Genetic evaluation of heat tolerance in Holstein cows in Japan.

We used test-day records and daily records from provincial weather stations in Japan to evaluate heat tolerance (HT) in Holstein cows according to a random regression test-day model. Data were a total of 1,641,952 test-day records for heritability estimates and 17,245,694 test-day records for genetic evaluation of HT by using milk yield and somatic cell score (SCS) in Holstein cows that had calved for the first time in 2000 through 2015. Temperature-humidity index (THI) values were estimated by using average daily temperature and average daily relative humidity records from 60 provincial Japanese weather stations. The model contained herd-test-day, with lactation curves on days in milk within month-age group as a fixed effect. General additive genetic effect and HT of additive genetic effect were included as random effects. The threshold value of THI was set to 60. For milk yield, estimated mean heritabilities were lower during heat stress (THI = 78; 0.20 and 0.28) than when below the heat stress threshold (THI ≤ 60; 0.26 and 0.31). For SCS, heritability estimates (range 0.08-0.10) were similar under all heat stress conditions. Genetic trends of HT indicated that EBVs of HT are changing in an undesirable direction.

Length of lags in responses of milk yield and somatic cell score on test day to heat stress in Holsteins.

We used daily records from provincial Japanese weather stations and monthly test-day records of milk production to investigate the length of the lags in the responses of cows' milk yield and somatic cell score (SCS) to heat stress (HS). We also investigated the HS thresholds in milk yield and SCS. Data were a total of 17,245,709 test-day records for milk and SCS in Holstein cows that had calved for the first time between 2000 and 2015, along with weather records from 60 weather stations. Temperature-humidity index (THI) values were estimated by using average daily temperature and average daily relative humidity. Adjusted THI values were calculated by using temperature, relative humidity, wind speed, and solar radiation. The model contained herd, calving year, month of test day, age group, days in milk, and THI as a fixed effect. THIs for each day from 14 days before the test day until the test day were used to represent the HS effects. The HS occurring 3 days, and between 8 and 10 days, before the test day had the greatest effect on the milk yield and SCS, respectively. The threshold THI values for the HS effect were about 60-65 for both traits.

Effects of heat stress on production, somatic cell score and conception rate in Holsteins.

We examined the effects of heat stress (HS) on production traits, somatic cell score (SCS) and conception rate at first insemination (CR) in Holsteins in Japan. We used a total of 228 242 records of milk, fat and protein yields, and SCS for the first three lactations, as well as of CR in heifers and in first- and second-lactation cows that had calved for the first time between 2000 and 2012. Records from 47 prefectural weather stations throughout Japan were used to calculate the temperature-humidity index (THI); areas were categorized into three regional groups: no HS (THI < 72), mild HS (72 ≤ THI < 79), and moderate HS (THI ≥ 79). Trait records from the three HS-region groups were treated as three different traits and trivariate animal models were used. The genetic correlations between milk yields from different HS groups were very high (0.91 to 0.99). Summer calving caused the greatest increase in SCS, and in the first and second lactations this increase became greater as THI increased. In cows, CR was affected by the interaction between HS group and insemination month: with summer and early autumn insemination, there was a reduction in CR, and it was much larger in the mild- and moderate-HS groups than in the no-HS group.