Incorporating body measurement traits to increase genetic gain of feed efficiency and carcass traits in Japanese Black steers.

The objective of the present study was to comprehensively evaluate whether body measurement traits, including body weight and body size, could be used as indicators of genetic selection for feed efficiency and carcass traits in Japanese Black steers. First, we estimated the genetic parameters for body measurements, feed efficiency, and carcass traits. Second, we estimated the correlated responses in feed efficiency and carcass traits when selection was applied to one or multiple-body measurement traits. In total, 4,578 Japanese Black steers with phenotypic values of residual feed intake (RFI) and residual body weight gain (RG) as feed efficiency traits and carcass weight (CWT) and beef marbling standard (BMS) as carcass traits were used. Eleven body measurement traits were measured at the start and finish of the fattening periods (BMT1 and BMT2, respectively), and their growth during the fattening period (BMT3) was used for genetic analyses. The results of genetic parameters showed that the heritability estimates were low to moderate (0.10 to 0.66), and the genetic correlations among body measurement traits were also estimated to be positively moderate to high in each measuring point (0.23 to 0.99). The genetic correlations of body measurement traits with RFI and BMS were estimated to be low (-0.14 to 0.30 and -0.17 to 0.35, respectively), but those with CWT were positively low to high (0.12 to 0.97). The genetic correlation estimates between BMT3 and RG were moderate to high (0.38 to 0.78). Second, correlated responses were estimated under positive selection for body measurement traits. Positive selection for BMT2 and BMT3 increased CWT and RG; however, positive selection for body measurement traits resulted in no change in RFI and BMS. Favorable directions of genetic gains, which were positive for RG, CWT, and BMS and negative for RFI, were obtained by selection indices, including multiple traits in BMT1. Our results suggest that using only one-body measurement trait as an indicator of genetic selection for RFI is difficult. However, body measurement traits can be indirect indicators of improved RG. Our results also suggest that genetic improvement of both RFI and RG without reducing CWT and BMS could be achieved using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Improving feed efficiency is a key objective in the beef cattle industry. Still, high costs and logistical efforts make measuring daily feed intake per animal in many cattle difficult. Here, we focused on body measurement traits, including body weight and body size, as indirect indicators of feed efficiency in Japanese Black cattle, as measuring these traits is easy and inexpensive. When selection was applied to one- or multiple-body measurement traits, we estimated the correlated responses in feed efficiency and carcass traits. We also estimated the genetic relationships of body measurement traits with feed efficiency and carcass traits. Our results showed body measurement traits were heritable and had weak genetic relationships with residual feed intake. Regarding the possibility of genetic selection for residual feed intake using body measurement traits as indirect indicators, our results suggest that using a single body measurement trait as an indicator is difficult. However, our results also suggest that the genetic improvement of residual feed intake could be possible using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Plateau-linear reaction norm model analysis of number born alive in purebred Landrace pigs using meteorological data in Japan.

We performed a plateau-linear reaction norm model (RNM) analysis of number born alive (NBA) in purebred Landrace pigs, where breeding value changes according to maximum temperature at mating day, using public meteorological observation data in Japan. We analysed 52,668 NBA records obtained from 10,320 Landrace sows. Pedigree data contained 99,201 animals. Off-farm daily temperature data at the nearest weather station from each of the farms were downloaded from the Japan Meteorological Agency website. A plateau-linear RNM analysis based on daily maximum temperature on mating day (threshold temperature of 16.6°C) was performed. The percentage of the records with daily maximum temperatures at mating days of ≤16.6, ≥25.0, ≥30.0 and ≥35.0°C were 34.3%, 33.6%, 14.0% and 0.8%, respectively. The value of Akaike's information criterion for the plateau-linear RNM was lower than that for a simple repeatability model (RM). With the plateau-linear RNM, estimated value of heritability ranged from 0.14 to 0.15, while that from the RM analysis was 0.15. Additive genetic correlation between intercept and slope terms was estimated to be -0.52 from the plateau-linear RNM analysis. Estimated additive genetic correlations were >0.9 between NBA at different temperatures ranging from 16.6 to 37.6°C. For the 10,320 sows, average values of prediction reliability of the intercept and slope terms for breeding values in the plateau-linear RNM were 0.47 and 0.16, respectively. Increasing weight for slope term in linear selection index could bring positive genetic gain in the slope part, but prediction accuracy would decrease. Our results imply that genetically improving heat tolerance in sows reared in Japan focusing on NBA using RNM is possible, while RNM is more complex to implement and interpret. Therefore, further study should be encouraged to make genetic improvement for heat tolerance in sows more efficient.

Reaction-norm animal model analysis of average daily gain heat tolerance in purebred Duroc pigs.

The present study aimed to genetically improve growth performance under high-heat environments by specifically designing a reaction-norm animal model (RNAM) for purebred Duroc pigs in Japan. A total of 54,750 records of average daily gain (ADG) measured for pigs reared at four farms in different prefectures were analyzed. Estimated maximum daily temperatures at the respective farm locations were used to calculate the average cumulative thermal load (TL). The TL values served as an indicator of high-heat environments for pigs. The plausible cumulative period length and threshold temperature for calculating TL were determined to be 8 weeks until just before shipping and 25°C, respectively. Variance components were estimated via RNAM analysis using TL as a linear covariate. The estimated additive genetic variances under both responsive and non-responsive to TL were found to be significant. Moreover, the estimated heritability of ADG ranged from 0.38 to 0.73 for TL values of 0-8. These results suggest that the RNAM developed holds the potential for improving the genetic ability of growth under high-heat environments in pigs.

A method of calculating weighted values of objective traits for BLUP of breeding values to achieve relative desired changes.

A method of calculating weighted values for objective traits from the phenotypic records of all animals in a population was devised as an alternative to the conventional method of calculating weighted values from a family selection index. The genetic improvement of this method was verified by Monte Carlo computer simulation. A base population consisting of 10 males and 50 females, and five separate generations, other than the base population that had been randomly selected, was bred for two traits with different heritabilities. The breeding values of animals in generation five were estimated using the bivariate BLUP method. The three different weighted values obtained from this method and two conventional methods for estimated breeding values of the objective traits were used to estimate aggregate breeding values for selection. The results showed that selection using weighted values calculated from all animals in a population resulted in a greater response to selection, especially when the genetic correlation between the two traits was positive, than selection using other conventional methods. The use of the method devised in this study was expected to result in a greater genetic improvement than the conventional family selection index method for pig breeding programs applied in closed herds in Japan.

Prediction of response to truncated selection based on BLUP of breeding values and its prediction accuracy.

Three methods of predicting the response to truncated selection based on BLUP of breeding values (BVs) were compared under conditions in which the phenotypic values for the progenies of selected animals were not available. The following methods were used to predict the response to selection: (1) based on the mean of estimated breeding values (EBV) in the candidate population for selection ( ∆ g 1 $$ \Delta {\mathrm{g}}_1 $$ ), (2) based on the variance of EBV in the candidate population for selection ( ∆ g 2 $$ \Delta {\mathrm{g}}_2 $$ ), and (3) based on diagonal elements of the inverse matrix on the left-hand side of the mixed model equation ( ∆ g 3 $$ \Delta {\mathrm{g}}_3 $$ ). The deviation of the average BV of the selected animals from the average BV of the candidate population for selection was taken as the true response to selection. The pedigree information and phenotypic values used for comparison were generated by Monte Carlo computer simulation. The results showed that ∆ g 1 $$ \Delta {\mathrm{g}}_1 $$ had the smallest absolute mean error and ∆ g 2 $$ \Delta {\mathrm{g}}_2 $$ had the smallest root-mean-square error. We concluded that it is desirable to use ∆ g 1 $$ \Delta {\mathrm{g}}_1 $$ or ∆ g 2 $$ \Delta {\mathrm{g}}_2 $$ to predict the response to truncated selection based on BLUP of BVs. However, in the population where selection is ongoing, the prediction accuracy of selection response is likely to be affected by the distortion of the distribution and the Bulmer effect for ∆ g 2 $$ \Delta {\mathrm{g}}_2 $$ .

Characteristics of restricted selection indices and geometrical interpretation of restricted breeding values.

Restricted selection is used to control genetic changes in one or more characters. Three main selection indices are adopted for this purpose. First, Kempthorne's index is used to maximize aggregate breeding value (BV) with changes in some traits restricted to zero; second, Harville's index is used to maximize aggregate BV with proportional changes for some traits; and third, Yamada's index is mathematically used to achieve the relative desired changes for all traits. Kempthorne's index is equivalent to Harville's index. However, the relationship between Kempthorne's and Yamada's indices has not been clarified. In addition, the characteristics of restricted selection indices and the relationship between BV and restricted BV (RBV) are also unknown. The aim of this study was to clarify the characteristics of restricted selection indices and describe the relationship between BV and RBV by using linear algebra and geometric techniques, respectively. First, I proved that Yamada's index is part of Kempthorne's index. Second, I investigated the relationship between BVs that were estimated using an ordinary selection index (EBVs) and RBVs estimated using a restricted selection index (ERBVs) and proved that the ERBVs of the restricted traits are proportional to the relative desired changes. Third, I proved that RBV is represented by a linear function of BV and geometrically represented the relationship between BV and RBV. In this study, new findings on restricted selection indices and RBV were obtained. This useful clarification of the relationship between BV and RBV will make it possible to evaluate the response to selection using not only a restricted selection index, but also a restricted BLUP in computer simulation studies.

Estimation of off-farm temperatures and temperature-humidity index from meteorological observation records.

The objective of this study was to devise an optimal method for estimating air temperatures outside pig farms to be able to evaluate the genetic performance of pigs. Using daily temperature data from Japan Meteorological Agency meteorological stations, we investigated the optimal number of observation weather stations (number of records), and methods of estimating outside temperature when temperature records are missing. We also considered the possibility of using relative humidity data. Our results showed that it is possible to use records from the three nearest weather stations to estimate off-farm ambient temperatures. We also concluded that estimates of outside temperatures when records are missing can be made by using data from at least one weather station that holds a full set of data. The correlation coefficients between the true THI (temperature-humidity index) and the estimated THI and the average daily temperature were almost the same, indicating that the daily average temperature can be used instead of estimated THI.

Randomized controlled trial of new hemostatic material "sodium calcium alginate" in a preclinical model.

BACKGROUND: The demand for nonbiological hemostatic materials has increased in surgical practice; however, few have sufficient hemostatic efficacy. This study investigated whether optimizing the composition of sodium calcium alginate, which forms a stable gel, improves hemostatic efficacy. METHODS: The sodium calcium alginate was changed for each composition, including powder size, calcium substitution rate, molecular weight, and mannuronic/guluronic acid ratio. The hemostasis in liver punch-out injury and bleeding was evaluated using swine. For the study, sodium calcium alginate with different compositions was randomly applied to bleeding sites. Previous hemostatic materials, including cellulose and sodium alginate, were used as a control. We investigated hemostasis at 2 and 5 minutes after application. RESULTS: Each powder size (53-150 µm, 150-250 µm, 53-250 µm) had a similar hemostatic effect. However, the hemostatic rate was significantly higher in sodium calcium alginate than in previous hemostatic materials (P value < .01). A 74.1% calcium substitution rate had the highest hemostasis at 2 and 5 minutes after application (2 minutes: 100%, 5 minutes: 95.2%). Regarding molecular weight, the hemostatic rate was significantly higher in 333,000 than in 50,000 (2 minutes: 95% vs 70%, 5 minutes: 95% vs 70%, P = .038). Moreover, a 1.9 mannuronic/guluronic acid ratio had the highest hemostasis compared with the 0.4 mannuronic/guluronic acid ratio (2 minutes: 58.8% vs 11.8%, 5 minutes: 58.8% vs 0%, P = .033) CONCLUSION: The composition of sodium calcium alginate with a high hemostatic effect was optimized. This new hemostatic material demonstrated potential usefulness for bleeding during surgery.

Genetic parameter estimation for pork production and litter performance traits of Landrace, Large White, and Duroc pigs in Japan.

We estimated genetic parameters for two pork production and six litter performance traits of Landrace, Large White, and Duroc pigs reared in Japan. Pork production traits were average daily gain from birth to end of performance testing and backfat thickness at end of testing (46,042 records for Landrace, 40,467 records for Large White, and 42,920 records for Duroc). Litter performance traits were number born alive, litter size at weaning (LSW), number of piglets dead during suckling (ND), survival rate of piglets during suckling (SV), total piglet weight at weaning (TWW), and average piglet weight at weaning (AWW) (27,410, 26,716, and 12,430 records for Landrace, Large White, and Duroc, respectively). ND was calculated as the difference between LSW and litter size at start of suckling (LSS). SV was calculated as LSW/LSS. AWW was calculated as TWW/LSW. Pedigree data for Landrace, Large White, and Duroc breeds contained 50,193, 44,077, and 45,336 pigs, respectively. Trait heritability was estimated via single-trait analysis and genetic correlation between two traits was estimated via two-trait analysis. When considering the linear covariate of LSS in the statistical model for LSW and TWW, for all breeds, the heritability was estimated to be 0.4-0.5 for pork production traits and below 0.2 for litter performance traits. Estimated genetic correlation between average daily gain and backfat thickness was small, ranging from 0.057 to 0.112, and those between pork production traits and litter performance traits were negligible to moderate, ranging from -0.493 to 0.487. A wide range of genetic correlation values among the litter performance traits was estimated, while that between LSW and ND could not be obtained. The results of genetic parameter estimation were affected by whether the linear covariate of LSS was included in the statistical model for LSW and TWW or not. This finding implies the necessity of carefully interpreting the results according to the choice of statistical model. Our results could give fundamental information on simultaneously improving productivity and female reproductivity for pigs.

Genome-wide detection of changes in allelic frequency in Landrace pigs selected for resistance to mycoplasma pneumonia of swine.

Closed-pig line breeding could change the genetic structure at a genome-wide scale because of the selection in a pig breeding population. We investigated the changes in population structure among generations at a genome-wide scale and the selected loci across the genome by comparing the observed and expected allele frequency changes in mycoplasma pneumonia of swine (MPS)-selected pigs. Eight hundred and seventy-four Landrace pigs, selected for MPS resistance without reducing average daily gain over five generations, had 37,299 single nucleotide polymorphisms (SNPs) and were used for genomic analyses. Regarding population structure, individuals in the first generation were the most widely distributed and then converged into a specific group, as they were selected over five generations. For allele frequency changes, 96 and 14 SNPs had higher allele frequency changes than the 99.9% and 99.99% thresholds of the expected changes, respectively. These SNPs were evenly spread across the genome, and a few of these selected regions overlapped with previously detected quantitative trait loci for MPS and immune-related traits. Our results indicated that the considerable changes in allele frequency were identified in many regions across the genome by closed-pig line breeding based on estimated breeding value.

Effect of ambient temperature on average daily gain of pigs evaluated using public weather data and a plateau-linear regression model.

We performed a plateau-linear regression model analysis of the average daily gain (ADG) of pigs on daily average temperature at the end of performance testing (T). Records for performance testing between 30 kg and 105 kg of 2268 purebred Duroc pigs raised at the National Livestock Breeding Center Miyazaki Station were used. Off-farm ambient temperatures were measured at the nearest Automated Meteorological Data Acquisition System station at Kobayashi, Miyazaki (Kobayashi station). A plateau-linear regression equation was obtained in which ADG decreased by 12.6 g for every 1°C when T > 21.1°C. We calculated the expected age in day at the end of testing (D105) using the regression equation obtained and T observed at the Kobayashi station in 2020. The number of days that D105 was prolonged due to higher T was 125 days, corresponding to approximately one third of the year. These results could contribute to planning and management of stable pork production in response to heat in Japan.

Genomic dissection of repeatability considering additive and nonadditive genetic effects for semen production traits in beef and dairy bulls.

The low heritability and moderate repeatability of semen production traits in beef and dairy bulls suggest that nonadditive genetic effects, such as dominance and epistatic effects, play an important role in semen production and should therefore be considered in genetic improvement programs. In this study, the repeatability of semen production traits in Japanese Black bulls (JB) as beef bulls and Holstein bulls (HOL) as dairy bulls was evaluated by considering additive and nonadditive genetic effects using the Illumina BovineSNP50 BeadChip. We also evaluated the advantage of using more complete models that include nonadditive genetic effects by comparing the rank of genotyped animals and the phenotype prediction ability of each model. In total, 65,463 records for 615 genotyped JB and 48,653 records for 845 genotyped HOL were used to estimate additive and nonadditive (dominance and epistatic) variance components for semen volume (VOL), sperm concentration (CON), sperm motility (MOT), MOT after freeze-thawing (aMOT), and sperm number (NUM). In the model including both additive and nonadditive genetic effects, the broad-sense heritability (0.17 to 0.43) was more than twice as high as the narrow-sense heritability (0.04 to 0.11) for all traits and breeds, and the differences between the broad-sense heritability and repeatability were very small for VOL, NUM, and CON in both breeds. A large proportion of permanent environmental variance was explained by epistatic variance. The epistatic variance as a proportion of total phenotypic variance was 0.07 to 0.33 for all traits and breeds. In addition, heterozygosity showed significant positive relationships with NUM, MOT, and aMOT in JB and NUM in HOL, when the heterozygosity rate was included as a covariate. In a comparison of models, the inclusion of nonadditive genetic effects resulted in a re-ranking of the top genotyped bulls for the additive effects. Adjusting for nonadditive genetic effects could be expected to produce a more accurate breeding value, even if the models have similar fitting. However, including nonadditive genetic effects did not improve the ability of any model to predict phenotypic values for any trait or breed compared with the predictive ability of a model that includes only additive effects. Consequently, although nonadditive genetic effects, especially epistatic effects, play an important role in semen production traits, they do not improve prediction accuracy in beef and dairy bulls.

Improving reproductive efficiency is a key objective in the beef and dairy cattle industries, and bull fertility is an important determinant of the reproductive performance of cows. The heritability of semen production traits is generally low; however, their repeatability is moderate. This difference between repeatability and heritability suggests that nonadditive genetic effects, such as dominance and epistatic genetic effects, could have an important role in semen production traits in bulls. Here, we estimated repeatability for semen production traits in beef and dairy bulls by considering additive and nonadditive genetic effects. Our results suggest that the contribution of nonadditive genetic effects to differences between repeatability and heritability was very high. Nonadditive genetic effects, especially epistatic effects, played important roles in semen production traits in beef and dairy bulls. However, we found that the inclusion of nonadditive genetic effects in a predictive model does not improve phenotypic prediction accuracy; further studies are needed to improve the predictive ability when using nonadditive genetic effects.

Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-ß-IGFBP7 axis.

Tissue fibrosis and organ dysfunction are hallmarks of age-related diseases including heart failure, but it remains elusive whether there is a common pathway to induce both events. Through single-cell RNA-seq, spatial transcriptomics, and genetic perturbation, we elucidate that high-temperature requirement A serine peptidase 3 (Htra3) is a critical regulator of cardiac fibrosis and heart failure by maintaining the identity of quiescent cardiac fibroblasts through degrading transforming growth factor-ß (TGF-ß). Pressure overload downregulates expression of Htra3 in cardiac fibroblasts and activated TGF-ß signaling, which induces not only cardiac fibrosis but also heart failure through DNA damage accumulation and secretory phenotype induction in failing cardiomyocytes. Overexpression of Htra3 in the heart inhibits TGF-ß signaling and ameliorates cardiac dysfunction after pressure overload. Htra3-regulated induction of spatio-temporal cardiac fibrosis and cardiomyocyte secretory phenotype are observed specifically in infarct regions after myocardial infarction. Integrative analyses of single-cardiomyocyte transcriptome and plasma proteome in human reveal that IGFBP7, which is a cytokine downstream of TGF-ß and secreted from failing cardiomyocytes, is the most predictable marker of advanced heart failure. These findings highlight the roles of cardiac fibroblasts in regulating cardiomyocyte homeostasis and cardiac fibrosis through the Htra3-TGF-ß-IGFBP7 pathway, which would be a therapeutic target for heart failure.

Genetic relationship between superovulatory response traits and carcass traits in Japanese Black cattle.

We estimated the genetic correlations between superovulatory response traits and carcass traits in Japanese Black cattle. As regards the superovulatory response traits in cows, we analyzed the phenotypic records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donors between 2008 and 2018. As regards the carcass traits in fattened animals, we analyzed the phenotypic records for cold carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, estimated yield percent, and marbling score for 1448 progenies derived from 596 donors and slaughtered between 2004 and 2020. Variance components were estimated using single-trait and two-trait animal models and the restricted maximum likelihood approach. The estimated genetic correlations with the carcass traits ranged from -0.05 to 0.04 for TNE and from -0.14 to 0.04 for NGE, and their standard errors ranged from 0.10 to 0.14. These results imply that the genetic relationship between the superovulatory response traits in Japanese Black donor cows and the carcass traits in their fattened progenies was weak to negligible. Therefore, we concluded that selecting donors with superior genetic ability for superovulatory responses would not have antagonistic effects on carcass performance in their fattened progenies.

Genetic relationships of feed efficiency and growth traits with carcass traits in Japanese Shorthorn cattle.

In this study, we examined genetic parameters for feed efficiency, growth, and carcass traits in Japanese Shorthorn cattle, based on 714 performance tests and 15,790 field carcass records. Feed efficiency traits, including residual feed intake (RFI) and residual body weight gain (RG), were calculated. Single-trait and two-trait animal models were used to estimate heritability and genetic correlations. Heritability estimates for feed efficiency traits were found to be low to moderate (ranging from 0.03 to 0.36); notably, heritability was moderate for RG and low for RFI. Estimates for genetic correlations between feed efficiency traits and average daily gain (DG) were favorably moderate to high (absolute values of 0.43-0.85), and those with daily feed intake were low (absolute values of 0.00-0.32). We also estimated a high genetic correlation between RG and DG. The backfat thickness (BF) of bull calves showed favorable or no genetic correlation estimates with feed efficiency and growth traits, whereas RG and BF showed favorable or no genetic correlation estimates with carcass traits. Our findings indicate that genetic improvements in both feed utilization ability and carcass traits could be achieved by utilizing RG and BF in Japanese Shorthorn cattle.

Heritability and genetic correlation estimates of semen production traits with litter traits and pork production traits in purebred Duroc pigs.

We estimated heritabilities of semen production traits and their genetic correlations with litter traits and pork production traits in purebred Duroc pigs. Semen production traits were semen volume, sperm concentration, proportion of morphologically normal sperms, total number of sperm, and total number of morphologically normal sperm. Litter traits at farrowing were total number born, number born alive, number stillborn, total litter weight at birth, mean litter weight at birth, and piglet survival rate at birth. Litter traits at weaning were litter size at weaning, total litter weight at weaning, mean litter weight at weaning, and piglet survival rate from birth to weaning. Pork production traits were average daily gain, backfat thickness, and loin muscle area. We analyzed 45,913 semen collection records of 896 boars, 6,950 farrowing performance records of 1,400 sows, 2,237 weaning performance records of 586 sows, and individual growth performance records of 9,550 animals measured at approximately 5 mo of age. Heritabilities were estimated using a single-trait animal model. Genetic correlations were estimated using a 2-trait animal model. Estimated heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of estimated genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.

Genetic parameters of 5 semen production traits, 10 litter traits, and 3 pork production traits in purebred Duroc pigs was estimated. Heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.

Performance of using opposing homozygotes for paternity testing in Japanese Black cattle.

Genome-wide single nucleotide polymorphism (SNP) markers in Japanese Black cattle enable genomic prediction and verifying parent-offspring relationships. We assessed the performance of opposing homozygotes (OH) for paternity testing in Japanese Black cattle, using SNP genotype information of 50 sires and 3,420 fattened animals, 1,945 of which were fathered by the 50 genotyped sires. The number of OH was counted for each sire-progeny pair in 28,764 SNPs with minor allele frequencies of ≥0.05 in this population. Across all pairs of animals, the number of OH tended to increase as the pedigree-based coefficient of relationship decreased. With a threshold of 288 (1% of SNPs) for paternity testing, most sire-progeny pairs were detected as true relationships. The frequency of Mendelian inconsistencies was 2.4%, reflecting the high accuracy of pedigree information in Japanese Black cattle population. The results indicate the utility of OH for paternity testing in Japanese Black cattle.

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis.

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge ) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.

Estimation of genetic parameters for superovulatory response traits in Japanese Black cows.

The aim of this study was to estimate genetic parameters for superovulatory response traits in order to explore the possibility of genetic improvement in Japanese Black cows. We analyzed 19 155 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) collected from 1532 donor cows between 2008 and 2018. A two-trait repeatability animal model analysis was performed for both. Because records of TNE and NGE did not follow a normal distribution, the records were analyzed following no, logarithmic, or Anscombe transformation. Without transformation, the heritability estimates were 0.26 for TNE and 0.17 for NGE. With logarithmic transformation, they were 0.22 for TNE and 0.18 for NGE. With Anscombe transformation, they were 0.26 for TNE and 0.18 for NGE. All analyses gave similar genetic correlations between TNE and NGE, ranging from 0.60 to 0.71. Spearman's rank correlation coefficient between breeding values of cows with more than 10 records was ≥0.95 with both transformations. Thus, the genetic improvement of TNE and NGE of donor cows could be possible in Japanese Black cattle.