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.     

Genetic relationship of body measurement traits at early age with carcass traits in Japanese black cattle

Estimates of genetic parameters were obtained for body measurement traits of 648 animals at 4 months of age, of 545 at 8 months and carcass traits of 14 972 animals with the use of an animal model by the restricted maximum likelihood procedure. The estimated heritabilities for carcass traits were high (0.41 to 0.54). At 4 months the estimated direct heritabilities for body measurement traits were moderate to high (0.28 to 0.64), except for chest width (0.19); at 8 months they were also moderate to high (0.23 to 0.49), except for chest depth and chest width (0.18 and 0.06, respectively). Maternal heritabilities for all body measurement traits were low at both ages. The results indicate that because of their moderate direct genetic correlations with body measurement traits, carcass weight, rib thickness and subcutaneous fat thickness can be improved; however, rib eye area and beef marbling standard show little such possibility considering their correlation with body measurement traits.     

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.     

Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle

The objective of this study was to estimate variance components related to imprinting for carcass traits and physiochemical characteristics in Japanese Black cattle. The carcass records obtained from 4,220 Japanese Black feedlot cattle included carcass weight (CW), rib eye area (REA), rib thickness, subcutaneous fat thickness, and beef marbling score (BMS), and the physiochemical characteristics were fat, moisture, glycogen per proportion of moisture content, oleic acid, and monounsaturated fatty acids (MUFA). To detect gametic effects, an imprinting model was fitted. High additive heritabilities were estimated for all traits (from 0.516 for glycogen to 0.853 for fat) and were reduced in Mendelian heritability. The range of the differences was from 0.002 (CW) to 0.331 (fat and moisture), and the reductions were due to their imprinting variances. The ratio of the imprinting variance to the total additive genetic variance for REA (0.374), BMS (0.291), fat (0.387), moisture (0.388), and MUFA (0.337) were large (p < 0.05). These imprinting variances were due to the maternal contribution and suggested the existence of maternally expressed genomic imprinting effects on the traits in Japanese Black cattle. Therefore, maternal gametic effects should be considered in breeding programs for Japanese Black cattle.     

Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data

Genomic selection using high‐density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy‐three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.     

Estimation of genetic parameters for growth and feed utilization traits in Japanese Black cattle

Performance test results of 3250 sire candidates were used to estimate the genetic parameters of growth and feed utilization traits in Japanese Black cattle. Growth traits analyzed were six body measurements at the end of the performance test and daily gain (DG) during the test. Feed utilization traits were intakes and conversions of concentrate, roughage, digestible crude protein and total digestible nutrient (TDN). Genetic (co)variance components were estimated by the restricted maximum likelihood procedure using an expectation maximization algorithm under the two‐trait animal model. Heritabilities for growth traits ranged from 0.40 to 0.70 and for feed utilization traits from 0.21 to 0.74. Genetic correlations of DG were positive with feed intake (0.15–0.77) and negative with feed conversions (?0.63 to ?0.30). These relationships indicate that the selection based on DG improves feed efficiency but it simultaneously increases feed intake. Feed conversions showed genetic correlations ranging from ?0.09 to 0.03 with total available energy consumption, TDN intake. Thus the results suggested that feed conversions were not efficient selection criteria to decrease TDN intake and to improve comprehensive feed utilization ability.     

Genetic parameters of postnatal mortality and birth weight in Japanese Black calves

Postnatal mortality (PM) of calves is an economically important trait, because a high mortality rate of calves decreases farm income and significantly increases production costs. In spite of the economic importance of PM, genetic studies on PM have been scarce for Japanese Black cattle. The objectives of this study were to estimate the direct and maternal heritability for PM using a Bayesian threshold model with Gibbs sampling in Japanese Black cattle. The original data consisted of 43 723 records of animals born from January 2005 to June 2006. Four binary traits of mortality were considered: D1‐14, D15‐60, D61‐180 and D1‐180 with numbers indicating the period of risk in days after birth. Direct heritabilities for PM ranged from 0.12 to 0.31 and maternal heritabilities for PM were lower than the direct heritabilities and ranged from 0.02 to 0.16. Direct genetic correlations between D1‐14 and D15‐60, between D15‐60 and D61‐180, and between D1‐14 and D61‐180 were 0.501, 0.689 and 0.062, respectively. Direct genetic correlations of birth weight with D1‐14, D15‐60, D61‐180 and D1‐180 were 0.089, 0.482, 0.434 and 0.394, respectively. These results indicated that different genes were responsible for early and late PM and early PM (D1‐14) can be genetically reduced without influencing birth weight.     

Estimates of genetic parameters for chemical traits of meat quality in Japanese black cattle

Genetic parameters for 54 carcass and chemical traits, such as general composition (moisture, crude fat and crude protein), fatty acid composition and water‐soluble compounds (free amino acids, peptides, nucleotides and sugars) of 587 commercial Japanese Black cattle were assessed. Heritability estimates for carcass traits and general composition ranged between 0.19–0.28, whereas those for fatty acid composition ranged between 0.11–0.85. Most heritability estimates for water‐soluble compounds were lower than 0.30; these traits were affected by aging period. Moderate heritability was observed for glutamine, alanine, taurine, anserine, inosine 5′‐monophosphate (IMP), inosine and myo‐inositol. In particular, heritability estimates were the highest (0.66) for taurine. Traits with moderate heritability were unaffected by aging period, with the exception of IMP, which was affected by aging period but exhibited moderate heritability (0.47). Although phenotypic correlations of water‐soluble compounds with carcass weight (CW), beef marbling standard (BMS) and monounsaturated fatty acid were generally low, genetic correlations between these traits were low to high. At the genetic level, most of the water‐soluble compounds were positively correlated with monounsaturated fatty acid but negatively correlated with CW and BMS. Thus, our results indicate that genetic variance and correlations could exist and be captured for some of the water‐soluble compounds.     

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.     

Genetic analysis of residual feed intakes and other performance test traits of Japanese Black cattle from revised protocol

The performance test protocol for Japanese Black cattle was revised in April 2002. This resulted in restriction of access to concentrate (based on body weight) and modification of the concentrate's ingredients. Genetic parameters of growth and feed utilization traits of the performance test were estimated using 1304 records using the revised protocol. Residual feed intakes (RFIs) as alternative indicators for feed utilization efficiency were included. (Co)variance components were estimated by EM-REML. Heritabilities for growth traits were between 0.26 and 0.47. Heritabilities for feed intakes and conversions ranged from 0.25 to 0.37 and from 0.03 to 0.29, respectively. Genetic variances and heritabilities were lower for the revised protocol. Highly positive genetic correlations of daily gain (DG) with feed intakes indicated selection on DG is expected to increase feed intake. Selection on feed conversion may lead to higher DG. The heritability estimates for RFIs ranged from 0.10 to 0.33 and were generally higher than corresponding estimates for feed conversion ratios. RFI of TDN showed positive genetic correlations with all feed intakes. The reduction of feed intakes could be expected through selection on the RFI without changing body size. RFIs were considered to be alternative indicators to improve feed utilization efficiency under the new performance test.     

Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle

Marker‐assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.     

Genetic parameters for dry matter, energy and protein intake, and their relationships with performance and carcass traits in Japanese Black cattle

Genetic parameters for feed intake and performance traits of 514 bulls and carcass traits of 22 099 of their progeny, and the relationships of measures of feed intake with performance and carcass traits were estimated. Feed intake traits were dry matter intake (DMI), concentrate intake (CONI), roughage intake, ratio of roughage intake to DMI, metabolizable energy intake (MEI) and digestible crude protein intake (DCPI). Performance traits included daily gain, metabolic weight, live weight at the end of test, dry matter conversion ratio and residual feed intake. Progeny carcass traits were carcass weight, percentage of meat yield, rib eye area (REA), subcutaneous fat, marbling score, meat colour (MCS), fat colour (FCS) and meat quality grade. All the feed intake and performance traits were moderately heritable. The heritabilities for REA and MCS were moderate, and that for FCS was low, while those for the other carcass traits were high. Selection against DMI, CONI and DCPI would reduce excessive intake of feed, but would have undesirable effects on growth and most of the carcass traits. Selection against MEI would lead to improvements in feed efficiency and growth traits. Selection against DCPI would also improve feed efficiency; however, responses in growth traits would decrease. Results indicate that selection against MEI might be better than any other measures of feed intake to improve feed efficiency with simultaneous improvement in growth and most of the carcass traits.     

Estimation of direct and maternal genetic parameters for growth and carcass traits in a herd of Japanese Black cattle in Miyagi prefecture, using a multitrait animal model

Data from 1170 records of fattening calves were collected on growth and carcass traits from a Japanese Black cattle herd located in Miyagi prefecture, Japan. The objective was to determine direct and maternal heritabilities, direct and maternal genetic correlations and phenotypic correlations between bodyweight at the beginning of the fattening period (BWS), bodyweight at the end of the fattening period (BWF), carcass weight (CW), average daily gain during the fattening period (ADG), rib eye area (REA), rib thickness, subcutaneous backfat thickness (SFT), yield estimate (YE) and beef marbling score (BMS). Direct heritability estimates of 0.16 (SFT) and 0.07 (BMS) were low, whereas estimates of the other traits were medium to high and ranged between 0.44 (REA) and 0.78 (CW). Direct genetic correlations were all positive, except those that were between BWS and SFT, and between BWS and YE (?0.49 and ?0.14, respectively). The lowest positive genetic correlation was between BWS and BMS (0.04) and the highest was between BWF and CW (0.99). The phenotypic correlation coefficients ranged between ?0.41 (between SFT and YE) and 0.96 (between BWF and CW). Maternal heritability estimates were generally low and ranged between 0.00 for BMS and 0.08 for BWS, CW and ADG. Selection programs comprising information on growth and carcass traits of calves and maternal traits of dams were suggested.     

Estimation of variance and genomic prediction using genotypes imputed from low‐density marker subsets for carcass traits in Japanese black cattle

The influence of genotype imputation using low‐density single nucleotide polymorphism (SNP) marker subsets on the genomic relationship matrix (G matrix), genetic variance explained, and genomic prediction (GP) was investigated for carcass weight and marbling score in Japanese Black fattened steers, using genotype data of approximately 40,000 SNPs. Genotypes were imputed using equally spaced SNP subsets of different densities. Two different linear models were used. The first (model 1) incorporated one G matrix, while the second (model 2) used two different G matrices constructed using the selected and remaining SNPs. When using model 1, the estimated additive genetic variance was always larger when using all SNPs obtained via genotype imputation than when using only equally spaced SNP subsets. The correlations between the genomic estimated breeding values obtained using genotype imputation with at least 3,000 SNPs and those using all available SNPs without imputation were higher than 0.99 for both traits. While additive genetic variance was likely to be partitioned with model 2, it did not enhance the accuracy of GP compared with model 1. These results indicate that genotype imputation using an equally spaced low‐density panel of an appropriate size can be used to produce a cost‐effective, valid GP.     

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.     

Genetic relationship of feed efficiency traits of bulls with growth and carcass traits of their progeny for Japanese Black (Wagyu) cattle

Genetic parameters for feed efficiency traits of 740 Wagyu bulls and growth and carcass traits of 591 of their progeny, and the genetic relationship between the traits of bulls and their progeny were estimated with the residual maximum likelihood procedure. The estimations were made for the test periods of 140 days (77 bulls), 112 days (663 bulls) and 364 days (591 steer progeny). Feed efficiency traits of bulls included feed conversion ratio (FCR), phenotypic residual feed intake (RFI_phe) and genetic residual feed intake (RFI_gen). Progeny traits were bodyweight at the start of the test (BWS), bodyweight at finish (BWF), average daily gain (ADG), rib eye area (REA), marbling score (MSR), dressing percentage (DRS) and subcutaneous fat thickness (SFT). The estimated heritability for MSR (0.52) was high and for BWS (0.35), BWF (0.40) and ADG (0.30) were moderate, whereas REA, DRS and SFT were low. Positive genetic correlations among BWS, BWF, ADG and SFT and negative genetic correlations between MSR and DRS and between REA and SFT were found. The genetic correlations between residual feed intake (RFI_phe and RFI_gen) of bulls and bodyweights (BWS and BWF) of their progeny ranged from ?0.27 to ?0.61. Residual feed intake was positively correlated with REA and DRS and negatively correlated with MSR and SFT. No responses in ADG and weakly correlated responses in REA and DRS of progeny were found to select against feed efficiency traits of bulls. The present experiment provides evidence that selection against lower RFI (higher feed efficiency) would be better than selection against lower FCR for getting better correlated responses in bodyweights.     

Genetic relationships between meat quality traits and fatty acid composition in Japanese black cattle

Genetic parameters were estimated to investigate the relationships between meat quality traits and fatty acid composition from 11 855 Japanese Black cattle. The meat quality traits included beef marbling score (BMS), beef color score, firmness of beef (FIR), texture of beef (TEX) and beef fat color score (BFS). The data on fatty acid composition included oleic acid and monounsaturated fatty acids (MUFA) contents, the ratio of MUFA to saturated fatty acids (MUS) and the ratio of elongation. The heritability estimates for meat quality traits ranged from moderate (0.30) to high (0.72). The strong genetic correlations between them were useful for simultaneous genetic improvement. In addition, high heritability estimates of fatty acid composition, ranging from 0.60 to 0.63, indicated that they could also be improved genetically. The genetic correlations of fatty acid composition with BMS, FIR and TEX were weak and negative. In contrast, positive and stronger genetic correlations were found between BFS and fatty acid composition, in particular, related to the level of unsaturation (0.77 and 0.79 for MUFA and MUS, respectively). This implies that improving the level of unsaturation makes fat darker (more yellow) and thus requires balancing with BFS.     

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.     

Effects of GH gene polymorphism and sex on carcass traits and fatty acid compositions in Japanese Black cattle

To investigate the effects of bovine growth hormone (bGH) gene polymorphism on carcass traits and fatty acid compositions in Japanese Black cattle caused by nucleotide substitution of CTG (allele A)/GTG (allele B) at codon 127 and of ACG (allele A and B)/ATG (allele C) at codon 172 of bGH, GH genotypes of 135 cattle were determined using allele specific-multiplex polymerase chain reaction (PCR). Allele A gave greater rib thickness and lower melting point of fat (MP) while allele B gave higher C18:1% ( P  < 0.05). Allele C gave higher C18:1, monounsaturated fatty acid (MUFA), unsaturated fatty acid (USFA) percentages ( P  < 0.05). It also gave lower saturated fatty acid (SFA) percentages, higher MUFA/SFA and USFA/SFA ratios, and lower MP ( P  < 0.05). Interactions of sex and GH alleles were analyzed. In heifers, allele A gave higher carcass weight, daily carcass gain, rib eye area, rib thickness, subcutaneous fat thickness, and BMS while allele B gave greater rib eye area and rib thickness ( P  < 0.05). Allele C gave higher C18:1 ( P  < 0.01), MUFA ( P  < 0.01), USFA percentages ( P  < 0.05) and MUFA/SFA and USFA/SFA ratios ( P  < 0.01), and lower C16:0 and SFA percentages ( P  < 0.05) and MP ( P  < 0.01). GH gene polymorphism affected carcass traits and fatty acid compositions although the effects were more pronounced in heifers.     

Variations in genes involved in fat metabolism and their association with ultrasonic and carcass traits in Japanese Black steers

Polymorphisms in genes involved in lipid metabolism have been reported to be associated with fatty acid composition of adipose tissue. However, the relationship of these polymorphisms with premortem ultrasonic traits is unknown. The objective of this study, therefore, was to assess the association between polymorphisms in fatty acid synthase, stearoyl‐coenzyme A desaturase (SCD), sterol regulatory element‐binding protein 1 (SREBP1), diacylglycerol acyltransferase 1, and nuclear receptor subfamily 1, group H, number 3 genes with ultrasonic and carcass traits in Japanese Black steers (n = 300) under progeny testing at the Livestock Improvement Association of Miyazaki. To have a comprehensive analysis of the association between the aforementioned genetic polymorphisms and ultrasonic traits, longitudinal measurements of ultrasonic traits were taken. Furthermore, the association of these genetic polymorphisms and carcass traits was evaluated. The polymorphisms in the SCD gene and SREBP1 were associated (P < 0.05) with some ultrasonic traits at multiple stages. To add to that, the polymorphisms were associated (P < 0.05) with some carcass traits. These findings suggest that the polymorphisms in SCD and SREBP1 are functional mutations or could be related to mutations that can aid in selection to improve some ultrasonic and carcass traits.