Identification of the core rumen bacterial taxa and their population dynamics during the fattening period in Japanese Black cattle

The rumen microbiota comprises a vast range of bacterial taxa, which may affect the production of high-quality meat in Japanese Black cattle. The aim of this study was to identify core rumen microbiota in rumen fluid samples collected from 74 Japanese Black cattle raised under different dietary conditions using 16S rRNA gene amplicon sequencing. In the rumen of fattening Japanese Black cattle, 10 bacterial taxa, showing >1% average relative abundance and >95% prevalence, irrespective of the dietary conditions and the fattening periods, were identified as the core rumen bacterial taxa, which accounted for approximately 80% of the rumen microbiota in Japanese Black cattle. Additionally, population dynamics of the core rumen bacterial taxa revealed two distinct patterns: Prevotella spp. and unclassified Bacteroidales decreased in the mid-fattening period, whereas unclassified Clostridiales, unclassified Ruminococcaceae, Ruminococcus spp., and unclassified Christensenellaceae increased during the same period. Therefore, the present study reports the wide distribution of the core rumen bacterial taxa in Japanese Black cattle, and the complementary nature of the population dynamics of these core taxa, which may ensure stable rumen fermentation during the fattening period.     

Genetic relationships between temperament of calves at auction and carcass traits in Japanese Black cattle

Correlations of calves’ temperament with carcass traits were estimated to clarify the genetic relationships between them in Japanese Black cattle. The temperament records for 3128 calves during auction at a calf market were scored on a scale of 1 (calm) to 5 (nervous) as temperament score (TS ), and the TS were divided into two groups (TSG ): TS 1 and 2 comprised TSG 1, and 3 to 5 constituted TSG 2. Carcass data were obtained from 33 552 fattened cattle. A threshold animal model was used for analyzing the underlying liability for TSG , whereas a linear one was used for TS and carcass traits. The heritability estimates for TS and TSG were 0.12 and 0.11, respectively. On the other hand, moderate to high heritability estimates were obtained for carcass traits (0.40 to 0.68). The temperament scores were negatively correlated with carcass weight, rib thickness and subcutaneous fat thickness (?0.13 to ?0.59). In contrast, weak to moderate positive correlations were found between the temperament scores and rib eye area or yield estimate (0.16 to 0.45). The temperament scores and beef marbling score had no correlation. These results showed that it is possible to improve temperament and carcass traits simultaneously.     

Effects of parent‐of‐origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Genomic imprinting should be considered in animal breeding systems to avoid lead in bias in genetic parameter estimation. The objective of this study was to clarify the effects of pedigree information on imprinting variances for carcass traits and fatty acid composition in Japanese Black cattle. Carcass records [carcass weight, rib eye area, rib thickness (RT), subcutaneous fat thickness and beef marbling score (BMS)] and fatty acid composition were obtained for 11,855 Japanese Black feedlot cattle. To estimate and compare the imprinting variances for the traits, two imprinting models with different pedigree information [the sire–dam gametic relationship matrix (Model 1) and the sire–maternal grandsire (MGS) numerator relationship matrix (Model 2)] were fitted. The ratio of the imprinting variance to the total additive genetic variance for RT (6.33%) and BMS (19.00%) was significant in Model 1, but only that for BMS (21.09%) was significant in Model 2. This study revealed that fitting the sire–MGS model could be useful in estimating imprinting variance under certain conditions, such as when restricted pedigree information is available. Furthermore, the present result suggested that the maternal gametic effects on BMS should be included in breeding programmes for Japanese Black cattle to avoid selection bias caused by imprinting effects.     

Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole‐genome resequencing in Japanese Black cattle

In our previous study, we performed genome‐wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10–30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole‐genome resequencing data. Based on whole‐genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p‐value (p = .0009) than the most significant SNP in GWAS (p = .0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR.     

IARS mutation causes prenatal death in Japanese Black cattle

Isoleucyl‐tRNA synthetase (IARS) c.235G > C (p.V79L) is a causative mutation for a recessive disease called IARS disorder in Japanese black cattle. The disease is involved in weak calf syndrome and is characterized by low birth weight, weakness and poor suckling. The gestation period is often slightly extended, implying that intrauterine growth is retarded. In a previous analysis of 2597 artificial insemination (AI) procedures, we suggested that the IARS mutation might contribute toward an increase in the incidence of prenatal death. In this study, we extended this analysis to better clarify the association between the IARS mutation and prenatal death. The IARS genotypes of 92 animals resulting from crosses between carrier (G/C) × G/C were 27 normal (G/G), 55 G/C and 10 affected animals (C/C) (expected numbers: 23, 46 and 23, respectively). Compared to the expected numbers, there were significantly fewer affected animals in this population (P < 0.05), suggesting that more than half of the affected embryos died prenatally. When the number of AI procedures examined was increased to 11 580, the frequency of re‐insemination after G/C × G/C insemination was significantly higher at 61‐140 days (P < 0.001). The findings suggested that the homozygous IARS mutation not only causes calf death, but also embryonic or fetal death.     

Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture

The polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality-related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.     

Genome‐wide association study for fatty acid composition in Japanese Black cattle

Fatty acid composition is one of the important traits in beef. The aim of this study was to identify candidate genomic regions for fatty acid composition by genome‐wide association study with 50 K single nucleotide polymorphism (SNP) array in Japanese Black cattle. A total of 461 individuals and 40 657 SNPs were used in this study. We applied genome‐wide rapid association using mixed model and regression (GRAMMAR) and genomic control approaches to estimate the associations between genotypes and fatty acid composition. In addition, two SNPs in fatty acid synthase (FASN) (T1952A) and stearoyl‐CoA desaturase (SCD) (V293A) genes were also genotyped. Association analysis revealed that 30 significant SNPs for several fatty acids (C14:0, C14:1, C16:1 and C18:1) were located in the BTA19 FASN gene located within this region but the FASN mutation had no significant effect on any traits. We also detected one significant SNP for C18:1 on BTA23 and two SNPs for C16:0 on BTA25. The region around 17 Mb on BTA26 harbored two significant SNPs for C14:1 and SNP in SCD in this region showed the strongest association with C14:1. This study demonstrated novel candidate regions in BTA19, 23 and 25 for fatty acid composition.     

Economic losses related to internal diseases in Japanese black cattle

The objective of this study was to estimate the direct economic losses due to the condemnation of the liver and large intestine because of internal diseases (multifocal necrosis in the liver (MNL) and inflammation of the large intestine (ILI)), and the indirect losses because of reductions in carcass performance from MNL, bovine abdominal fat necrosis (BFN) and ILI using data from 5383 Japanese Black cattle. Direct losses were estimated by multiplying the price of the condemned part by the frequency of its occurrence owing to the disease. Similarly, indirect losses were estimated as the product of unit carcass price and reduction in carcass weight (CW) due to the disease. The direct impact on the beef cattle industry from MNL and ILI was estimated at around $1.29 million (US$1 = ¥120) per year. A least‐squares analysis showed that MNL had no influence on any carcass trait, whereas BFN and ILI significantly reduced CW, rib eye area and darkened the beef. ILI also reduced rib thickness. The indirect losses from BFN and ILI were estimated as a maximum of $131.7 and $256.4 per animal and around $6.26 million and $4.03 million for the industry, respectively, mostly because of the reduction in CW.     

Effects of feeding different levels of concentrate on growth and carcass characteristics in younger Japanese Black cattle

The effects of a higher concentrate feed during the raising period on the growth and carcass of Japanese Black cattle being fattened at a younger age were investigated using three pairs of artificially bred identical twins and three pairs of full‐sibs. The animals were fed the concentrate at 2.4%/day (2.4% group) and 1.2%/day (1.2% group) comparative bodyweight (BW) during the raising period. The BW and subcutaneous fat thickness were measured every month using ultrasonic equipment. The animals were slaughtered at the age of 24 months. The BW of the 2.4% group from the age of 6–10 months appeared to be higher than that of the 1.2% group (P < 0.1). The subcutaneous fat of the 2.4% group from the age of 7–11 months was thicker than that of the 1.2% group (P < 0.1). After those ages, the BW and subcutaneous fat of the two groups did not differ and there was no difference in the carcass characteristics between the two groups. Using a higher concentrate feed during the raising period for younger fattening of Japanese Black cattle influenced growth from the late half of the raising period to the early part of the fattening period.     

Bos indicus type of growth hormone receptor gene is retained in Japanese Black cattle

The growth hormone receptor (GHR) gene is responsible for growth and carcass traits, and polymorphisms associated with the variation of meat production are thought to occur in the liver‐specific promoter of the GHR gene in cattle. The aim of this study was to analyse the structure of the liver‐specific promoter of GHR in Japanese Black cattle, as the relationship between GHR polymorphism and meat production is poorly understood in this breed. Typically in European cattle, the LINE‐1 element, a family of retrotransposons, is inserted in the liver‐specific promoter. However, a short GHR promoter without the LINE‐1 sequence was found in the Japanese Black breed as in Bos indicus cattle. The frequency of the short allele was approximately 60%. In addition, 24 of 29 Holstein/Japanese Black crosses carried the short allele from their sire. The present result suggests that the short allele for GHR may be a candidate marker for improving meat production of Japanese Black cattle.     

Age-related changes in leukocytes and T cell subsets in peripheral blood of Japanese Black cattle

It is well known that the immune system changes with age during development and maturation in Holstein cattle. But age-related changes in leukocytes and T cell subsets in peripheral blood of Japanese Black cattle still remain unclear. The aim of the present study was to investigate comparative changes of leukocytes (granulocytes, monocytes, B cells and T cells) and T cell subsets (CD4⁺, CD8⁺, γδ, CD8⁺γδ and WC1⁺γδ T cells) in Japanese Black cattle aged 0.5, 1, 2, 6, 18 and 36–41 (adult) months on flow cytometry using specific monoclonal antibodies for the cell surface markers. T cell proportion was approximately 40% in 2-month-old cattle and decreased to 20.6% in adults. In contrast, B cell proportion significantly increased from 7.4% to 28.2% with age. In T cell subsets the percentage of CD4⁺ T cells significantly increased from 40.5% to 60%, but that of WC1⁺γδ T cell subset significantly decreased with age. The percentages of CD8⁺ and CD8⁺γδ T cells did not change. The present study details the proportional changes in leukocyte and T cell subsets with age in the peripheral blood of Japanese Black cattle and these findings are similar to those described for Holstein cattle.     

Identification of leptin gene polymorphisms associated with carcass traits and fatty acid composition in Japanese Black cattle

Previous studies have indicated that some leptin gene polymorphisms were associated with economically important traits in cattle breeds. However, polymorphisms in the leptin gene have not been reported thus far in Japanese Black cattle. Here, we aimed to identify the leptin gene polymorphisms which are associated with carcass traits and fatty acid composition in Japanese Black cattle. We sequenced the full‐length coding sequence of leptin gene for eight Japanese Black cattle. Sequence comparison revealed eight single nucleotide polymorphisms (SNPs). Three of these were predicted to cause amino acid substitutions: Y7F, R25C and A80V. Then, we genotyped these SNPs in two populations (JB1 with 560 animals and JB2 with 450 animals) and investigated the effects on the traits. Y7F in JB1 and A80V in JB2 were excluded from statistical analysis because the minor allele frequencies were low (< 0.1). Association analysis revealed that Y7F had a significant effect on the dressed carcass weight in JB2; R25C had a significant effect on C18:0 and C14:1 in JB1 and JB2, respectively; and A80V had a significant effect on C16:0, C16:1, C18:1, monounsaturated fatty acid and saturated fatty acid in JB1. The results suggested that these SNPs could be used as an effective marker for the improvement of Japanese Black cattle.     

Mapping the quantitative trait loci (QTL) for body shape and conformation measurements on BTA1 in Japanese Black cattle

The detection and mapping of segregating quantitative trait loci (QTL) that influence withers height, hip height, hip width, body length, chest width, chest depth, shoulder width, lumbar width, thurl width, pin bone width, rump length, cannon circumference, chest girth, abdominal width and abdominal girth at weaning was conducted on chromosomal regions of bovine chromosome one. The QTL analysis was performed by genotyping half‐sib progeny of five Japanese Black sires using microsatellite DNA markers. Probability coefficients of inheriting allele 1 or 2 from the sire at specific chromosomal locations were computed. The phenotypic data of progeny were regressed on these probability coefficients in a within‐common‐parent regression analysis using a linear model that included fixed effects of sex, parity and season of birth, as well as age as a covariate. F‐statistics were calculated every 1 cM on a linkage map. Permutation tests of 10 000 iterations were conducted to obtain chromosome‐wide significance thresholds. A significant QTL for chest width was detected at 91 cM in family 3. The detection of this QTL boosts the prospects of implementing marker‐assisted selection for body conformation traits in Japanese Black beef cattle.     

The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

Three cases of idiopathic eosinophilic enteritis with chronic obstinate diarrhea in Japanese Black fattening cattle

Eosinophilic enteritis (EOE) is a type of inflammatory bowel disease and is characterized clinically by chronic obstinate diarrhea. Three Japanese Black (JB) fattening cattle (2 males and 1 female) on different cattle farms presented with chronic episodic diarrhea without fever or dehydration. Soft reddish spherical carneous tissues (1−3 cm) were occasionally excreted within the diarrheic feces. Administration of antibiotics, antidiarrheal drugs and vermicides had no therapeutic effect, but dexamethasone improved the fecal characteristics. The symptoms persisted until the animals were slaughtered at 27–30 months of age. Histopathological examination of the intestines revealed marked eosinophilic infiltration in the lamina propria and submucosa. From these findings, we diagnosed these cattle as the first cases of EOE in JB cattle.     

Economic efficiency of Japanese Black cattle selection schemes utilizing crossbreeding with the Holstein breed

The economic efficiency of Japanese Black (JB) cattle selection schemes utilizing crossbreeding with the Holstein (H) breed was evaluated in the context of maximizing profitability. Selection schemes were defined that differed in the records available for use as selection criteria. The selection schemes were assessed based on profitability per cow in the JB cattle population. Within each selection scheme, two terminal crossbreeding systems were considered: two‐way crossbreeding without backcrossing (F₁ system) and two‐way crossbreeding with backcrossing (F₁ cross system). The impact on profitability of varying number of sires selected per year and the proportion of H cows that were inseminated by JB semen and of F₁ females that are retained for replacement was examined for all selection schemes. Utilizing crossbreeding with the H breed was less profitable than purebreeding of the JB. Profitability was higher in the F₁ system than in the F₁ cross system in all selection schemes. Profitability was influenced more by changes in the number of sires selected per year than by the proportion H cows that were inseminated by JB semen and of F₁ females that were retained for replacement. Implications of these results for the JB breeding program are discussed.     

Estimation of genetic parameters for carcass defects of Japanese Black cattle in Kagoshima

Cattle exhibit a range of carcass defects, including blood splash (BLS), intramuscular edema (INE), muscle steatosis (MUS), bruising (BR), trim loss (TRL) and others (OTH). These defects lower the carcass value and can result in significant economic loss to producers. We estimated the incidence, relationship with inbreeding coefficients and genetic parameters of carcass defects in Japanese Black cattle using 561 619 carcass records from Kagoshima, Japan during April 1988 through March 2011. The defect incidence ranged from 0.22% for TRL to 5.73% for BR. The incidence of MUS and BR increased from 1.21% to 6.57% and from 1.06% to 9.31%, respectively. The incidence of INE peaked at 7.44% in 1999 and decreased thereafter. We observed a positive linear relationship between the defect incidence and the inbreeding coefficients in MUS, BR and TRL (P < 0.01). The heritabilities estimated by univariate animal model with Gibbs sampling for BLS, INE, MUS, BR and TRL were 0.24, 0.06, 0.18, 0.05 and 0.02, respectively. The contribution of farm variance to phenotypic variance was negligible (0.01 to 0.04). Significant genetic correlations of TRL were estimated with MUS (0.63) and BR (0.63). Our results suggest that genetic factors contribute to the incidence of BLS and MUS.     

Differences between carcass grades in some morphological, behavioral and physiological measurements at early and middle stages of fattening in crossbred steers

The differential variables for carcass grades were identified from morphological, behavioral and physiological measurements of young steers at a commercial farm. Thirty‐five Japanese Black × Holstein steers aged 6–10 months were randomly assigned to three pens. The steers had free access to ryegrass hay and a restricted amount of concentrate diet for the first 6 months of trial. They were then given oat straw ad libitum and an additional concentrate diet until slaughter. Behavioral observations (15 categories) were carried out once every 2 weeks for 2 h after feeding. Bodyweight was measured, blood sampled (for seven metabolic hormones and five metabolites), ultrasonic scanning conducted and physical measurements taken (10 parts for each animal) in months 1, 3 and 5 (early fattening stage, EFS) and in months 7, 9 and 11 (middle fattening stage, MFS) of the trial. Temperament scores during these procedures, entry order into restraint stalls, social rank and average daily gain were also assessed. A factor analysis and one‐way anova were used to identify clusters of variables which had different factor scores between carcass grades. As for the carcass yields, a cluster of chest girth and depth, bodyweight, withers and hip height, and rump length (P < 0.01), and a cluster of the frequency of scratching the body with facilities (P < 0.05) were identified as differential variables in the EFS. In the MFS, a cluster of concentrations of cortisol and epinephrine, and the frequency of eating straw were identified (P < 0.10). As for the carcass quality grade, a cluster of social rank, triglyceride concentration and the frequencies of stand‐chewing cud and eating hay, and a cluster of the frequency of investigating facilities (both P < 0.10) were identified in the EFS. In the MFS, a cluster of hip height, bodyweight, cannon circumference, chest depth, withers height and chest girth, and a cluster of the frequencies of eating a concentrate diet and stand‐chewing the cud, and social rank (both P < 0.10) were identified. In conclusion, bodyweight, chest girth and depth, withers and hip height were identified as good differential variables for future carcass grades of young steers. Facility enrichment that encourages steers to eat hay in the EFS, and to eat a concentrate diet in and after the MFS would be effective in upgrading carcass grades. High incidence of investigating and scratching the body with facilities and stand‐chewing the cud might lead to lower carcass grades.     

Effect of probiotics on blood fatty acid metabolism during the late middle stage of fattening period in Japanese Black cattle

This study was conducted to investigate the effects of probiotics administration on fatty acid metabolism in Japanese Black cattle as per changes in blood fatty acid concentrations and blood biochemical tests. Eighteen clinically healthy Japanese Black female fattening cattle bred on the same fattening farm were randomly classified into the probiotics administration group (n=9) or the control group (n=9). In the probiotics administration group, 50 g of probiotics were started per animal per day at the age of 18 months, and the administration period was 2 months from the start date of the study. Blood was collected twice before starting the probiotics administration and at 2 months after starting the probiotics administration. In the probiotics administration group, palmitic, linoleic, arachidonic and α-linolenic acid tended to be higher at the end of the administration compared with those before probiotics administration. Additionally, as a result of multiple comparison test, monounsaturated fatty acids at Post was significantly higher, and the ω6 / ω3 ratio was significantly lower than in the control group. Vitamin A, E and albumin were significantly higher at the end of the administration than in the control group. In this study that administering probiotics to Japanese Black cattle in the late middle stage of fattening period did not have a significant effect on fatty acid metabolism during feed digestion and absorption, but suggested that may alter some blood fatty acids concentrations.     

Effects of genetic and environmental factors on muscle glycogen content in Japanese Black cattle

Monosaccharides such as glucose contribute to the development of meat flavor upon heating via the Maillard reaction; therefore, monosaccharide content is related to beef palatability. Here, we analyzed the effects of genetic and environmental factors on the content of glycogen, one of the precursors of monosaccharides, in the muscles of 958 fattened Japanese Black cattle from Yamagata Prefecture. Analysis of variance showed that muscle glycogen content was affected by the farm and postmortem periods, but not by sex, slaughter age, slaughter month or number of days detained at the slaughter yard. Additionally, consumption of digestible brown rice feed elevated muscle glycogen levels. Glycogen heritability was estimated to be 0.34, and genetic correlations between glycogen and carcass weight (CW) or beef marbling standard (BMS) were weak. The predicted breeding values varied among paternal lines. These results demonstrated that genetic factors might improve muscle glycogen content and therefore beef palatability, but do not influence CW or BMS.