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.     

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 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.     

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.     

Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.     

非常规饲料原料日粮对肉牛生长性能、胴体性状、肉品质及经济效益的影响

文章旨在评估不同非常规饲料原料替代浓缩料对肉牛生长性能、胴体性状及肉品质的影响。试验选择初始体重为（291.69±5.7）kg的肉牛80头,随机分为4组,每组20头,每头牛为1个重复。对照组肉牛在8周试验期每天自由采食水稻秸秆粗饲料并补充基础浓缩料,处理组肉牛自由采食水稻秸秆粗饲料并分别补充用8%米糠、亚麻籽和葵花粕替代基础浓缩料混合物。结果：与米糠组相比,对照组和亚麻籽组肉牛的平均日增重分别显著提高10.74%和12.40%（P＜0.05）,同时米糠组肉牛的料重比较对照组和亚麻籽组分别显著提高11.69%和15.52%（P＜0.05）。亚麻籽组肉牛的背膘厚度较对照组和米糠组分别显著提高7.84%和8.65%（P＜0.05）。对照组肉牛眼肌C14：0脂肪酸含量显著低于处理组（P＜0.05）,而米糠组肉牛眼肌饱和脂肪酸含量较对照组显著提高16.55%（P＜0.05）,单不饱和脂肪酸含量显著降低11.95%（P＜0.05）。亚麻籽和葵花粕组眼肌中蛋氨酸含量较对照组和米糠组分别显著提高168%、179.17%和154%、164.58%（P＜0.05）。结论：在本研究条件下,用8%亚麻籽替代浓缩料饲喂肉牛可以提高肌肉蛋氨酸含量,对肉牛生长表现及肌肉脂肪酸组成无负面影响。 [关键词]非常规原料|肉牛|生长性能|胴体性状|肉品质     

Genomic and single-step evaluations of carcass traits of young bulls in dual-purpose cattle

Genetic evaluations for carcass traits of young bulls in Normande and Montbeliarde breeds are currently being developed in France. In order to determine a suitable genomic evaluation for three carcass traits of young bulls, genomic breeding values were estimated for young candidates to selection using different approaches. Records of 111,789 Normande and 118,183 Montbeliarde were used. Average progeny pre-adjusted performances (DYD) were calculated for sires. Evaluation approaches were compared based on an assessment of their accuracy (correlation between DYD and estimated breeding values [EBVs]) and bias (regression coefficient of DYD on EBVs) on the 20% youngest AI sires. All genomic approaches were generally more accurate than BLUP (+.045 to +.116 correlation points), except for age at slaughter where single-step GBLUP (SSGBLUP) was the only genomic method leading to a greater accuracy (+.038 to +.126 points). The best setting of the SSGBLUP relationship matrix was characterized by a weight of 30% for pedigree information in the genomic relationship matrix. SSGBLUP was the most valuable evaluation approach for the evaluation of carcass traits of Normande and Montbeliarde young bulls.     

QTL detection for milk production traits in goats using a longitudinal model.

Eight paternal half-sib families were used to identify chromosomal regions associated with variation in the lactation curves of dairy goats. DNA samples from 162 animals were amplified by PCR for 37 microsatellite markers, from Capra hircus autosomes CHI3, CHI6, CHI14 and CHI20. Milk samples were collected during 6 years, and there were 897 records for milk yield (MY) and 814 for fat (FP) and protein percentage (PP). The analysis was conducted in two stages. First, a random regression model with several fixed effects was fitted to describe the lactation function, using a scale (alpha) plus four shape parameters: beta and gamma, both associated with a decrease in the slope of the curve, and delta and phi that are related to the increase in slope. Predictions of alpha, beta, gamma, delta and phi were regressed using an interval mapping model, and F-tests were used to test for quantitative trait loci (QTL) effects. Significant (p < 0.05) QTLs were found for: (i) MY: CHI6 at 70-80 cM for all parameters; CHI14 at 14 cM for delta and phi; (ii) FP: CHI14, at 63 cM was associated with beta; CHI20, at 72 cM, showed association with alpha; (iii) PP: chromosomal regions associated with beta were found at 59 cM in CHI3 and at 55 cM in CHI20 with alpha and gamma. Analyses using more families and more animals will be useful to confirm or to reject these findings.     

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.     

Genetic parameters for gestation length and the relationship with birth weight and carcass traits in Japanese Black cattle

The objectives of this study were to estimate genetic parameters for gestation length (GL), including estimation of maternal effects, and to investigate the genetic relationships of GL with birth weight and carcass traits in a Japanese Black cattle population. The original data comprised 34 775 records of animals born from October 1999 to August 2003. Two different models were used to analyze the data for GL. The first model (M1) included direct genetic effect of the calf and maternal genetic effect as random effects. The second model (M2) treated GL as a trait of the dam and included direct genetic effects only. M1 was used in bi-variate analysis. The direct and maternal heritabilities for GL estimated from M1 were 0.53 and 0.14, respectively. This result shows that GL is moderately inherited and can be controlled genetically. The direct × maternal genetic correlation for GL was −0.73. Direct genetic correlations of GL with carcass traits were close to zero. However, genetic correlation of maternal GL with carcass weight was moderate (0.25).     

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.     

Multivariate analyses of carcass traits for Angus cattle fitting reduced rank and factor analytic models

Summary Multivariate analyses of carcass traits for Angus cattle, consisting of six traits recorded on the carcass and eight auxiliary traits measured by ultrasound scanning of live animals, are reported. Analyses were carried out by restricted maximum likelihood, fitting a number of reduced rank and factor analytic models for the genetic covariance matrix. Estimates of eigenvalues and eigenvectors for different orders of fit are contrasted and implications for the estimates of genetic variances and correlations are examined. Results indicate that at most eight principal components (PCs) are required to model the genetic covariance structure among the 14 traits. Selection index calculations suggest that the first seven of these PCs are sufficient to obtain estimates of breeding values for the carcass traits without loss in the expected accuracy of evaluation. This implied that the number of effects fitted in genetic evaluation for carcass traits can be halved by estimating breeding values for the leading PCs directly.     

Mapping QTL for porcine muscle fibre traits in a White Duroc × Erhualian F2 resource population

Muscle fibre traits are related with meat quality in meat animals. In this study, a whole‐genome scan with 183 microsatellite markers covering the pig genome was performed to identify quantitative trait loci (QTL) for cross‐sectional area, numerical percentage and relative area of type I, IIA and IIB myofibres, fibre number per square centimetre and total fibre number in the longissimus muscle by using 120 F₂ animals in a White Duroc × Erhualian intercross. In total, 20 QTL were mapped on pig chromosomes (SSC) 1, 2, 7, 8, 9, 11, 15, 16 and X, of which eight reached genome‐wide significance levels and explained large proportions (6.53–34.63%) of phenotypic variance. Five QTL detected in this study confirmed the previous QTL reports and the others were detected for the first time. Chinese Erhualian alleles are generally associated with muscle fibre traits favourable for meat quality.     

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.     

Interval mapping of growth quantitative trait loci in Japanese Black beef cattle using microsatellite DNA markers and half-sib regression analysis

A confirmatory scan for the regions of bovine chromosome 1 segregating the quantitative trait loci (QTL) influencing birthweight, weaning weight, yearling weight, and preweaning and postweaning average daily gains was performed by genotyping half‐sib progeny of four Japanese Black sires using microsatellite DNA markers. Data were analyzed by generating an F‐statistic every 1 cM on a linkage map by the regression of phenotype on the probabilities of inheriting an allele from the sire after adjusting for the fixed effects of sire, sex, parity and season of birth as well as age as a covariate. Permutation tests at chromosome‐wide significance thresholds were carried out over 10 000 iterations. A significant QTL for birthweight at 114 cM was detected in the sire 2 family. This identification of a birthweight QTL in Japanese Black cattle may be useful for the implementation of marker‐assisted selection.     

Tag-SNP selection using Bayesian genomewide association study for growth traits in Hereford and Braford cattle

The aim of this study was to perform a Bayesian genomewide association study (GWAS) to identify genomic regions associated with growth traits in Hereford and Braford cattle, and to select Tag-SNPs to represent these regions in low-density panels useful for genomic predictions. In addition, we propose candidate genes through functional enrichment analysis associated with growth traits using Medical Subject Headings (MeSH). Phenotypic data from 126,290 animals and genotypes for 131 sires and 3,545 animals were used. The Tag-SNPs were selected with BayesB (π = 0.995) method to compose low-density panels. The number of Tag-single nucleotide polymorphism (SNP) ranged between 79 and 103 SNP for the growth traits at weaning and between 78 and 100 SNP for the yearling growth traits. The average proportion of variance explained by Tag-SNP with BayesA was 0.29, 0.23, 0.32 and 0.19 for birthweight (BW), weaning weight (WW205), yearling weight (YW550) and postweaning gain (PWG345), respectively. For Tag-SNP with BayesA method accuracy values ranged from 0.13 to 0.30 for k-means and from 0.30 to 0.65 for random clustering of animals to compose reference and validation groups. Although genomic prediction accuracies were higher with the full marker panel, predictions with low-density panels retained on average 76% of the accuracy obtained with BayesB with full markers for growth traits. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene products related to the growth traits. The proposed Tag-SNP panels may be useful for future fine mapping studies and for lower-cost commercial genomic prediction applications.     

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.     

肉牛生长性状和肉质性状全基因组关联分析的研究进展

全基因组关联分析(genome-wide association studies,GWAS)是研究家畜复杂经济性状和疾病遗传变异的有效方法,GWAS的核心是挖掘遗传变异与目标表型性状间的关系.随着牛全基因组测序工作完成,海量单核苷酸多态性(single nucleotide polymorphism,SNP)位点被标记...     

Evaluation of estimated genetic merit for carcass weight in beef cattle: Blood metabolites, carcass measurements, carcass composition and selected non-carcass components

In Ireland, a new beef genetic index has been developed. Growth rate is expressed as expected progeny difference for carcass weight (EPD_CWT) and is estimated on an across-breed basis. Cross-breeding of dairy cows with both Aberdeen Angus and Belgian Blue beef sires is widely practised. The objective of this study was to compare blood metabolites, slaughter traits and carcass composition of progeny from Holstein–Friesian dairy cows and Aberdeen Angus (AA), Belgian Blue (BB), Friesian (FR) and Holstein (HO) sires. The AA and BB sires were selected, within breed, to be of either high (H) or low (L) estimated genetic merit for carcass weight. A total of 170 male progeny from spring-calving cows and 42 sires (10 AA, 13 BB, 7 FR and 12 HO) were artificially reared indoors and managed together until the end of their second grazing season when they were assigned to either a Light (560 kg) or Heavy (620 kg) slaughter weight. Blood metabolite concentrations were measured six times throughout life and feed intake was recorded during the first and second winter. Carcass measurements and selected non-carcass components were recorded after slaughter and the right side of each carcass was dissected into lean, fat and bone. Differences in blood metabolite concentrations amongst genetic groups were negligible although there were some effects of the prevailing level of nutrition. M. longissimus area scaled for carcass weight was 0.220, 0.221, 0.260, 0.255, 0.212 and 0.208 (SE 0.004) cm²/kg for AAH, AAL, BBH, BBL, FR and HO, respectively. Carcass measurements scaled for carcass weight were greater for L, AA, HO and the dairy strains than for H, BB, FR and the beef breeds, respectively. There was no effect of estimated genetic merit for carcass weight on carcass composition. Statistically significant interactions between genetic merit and beef breed existed for some traits with the genetic merit effect largely evident for AA only. BB and the beef breeds had more lean, less fat and more high value lean in the carcass than AA and the dairy strains, respectively. It is concluded that genetic group had little effect on blood metabolite concentrations but there were some feeding level effects. Estimated genetic merit for carcass weight affected carcass weight, m. longissimus area and carcass measurements scaled for carcass weight but the effects were confined to AA. There were large effects of beef breed and dairy strain on carcass composition.     

Adjusting for heterogeneity of variance for carcass traits affects single and multiple trait selections in genetic evaluation of Japanese Black cattle

Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. Degrees of the heterogeneity of variance among farm‐market‐year‐sex (FMYS) subclasses for carcass weight, beef marbling standard number, rib‐eye area, rib thickness and subcutaneous fat thickness were investigated in Japanese Black cattle. Consequences of adjusting for the heterogeneity on the predicted breeding values (PBVs) or on the genetic indexes derived from the PBVs of the five carcass traits were assessed. A total of 57 461 records were collected between 1997 and 2002 from steers and heifers fattened at farms across Japan. These records were grouped into 1591 FMYS subclasses. Bartlett's test showed that the degree of the heterogeneity of variance among the FMYS subclasses was sizeable in all traits (P < 0.0001). By applying a two‐step adjustment procedure it was possible to reduce the standard deviation, the coefficient of variation and the Gini coefficient of the phenotypic variances by 67.5% to 75.0% in the different traits. The applied adjustment caused a substantial re‐ranking of elite dams in the PBV for each trait as well as in the genetic index. This study provided evidence that the applied adjustment reduces the bias in the PBVs due to heterogeneous variances and increases the accuracy of bull‐dam selection.