Genomic predictions in Angus cattle: comparisons of sample size, response variables, and clustering methods for cross-validation.

Advances in genomics, molecular biology, and statistical genetics have created a paradigm shift in the way livestock producers pursue genetic improvement in their herds. The nexus of these technologies has resulted in combining genotypic and phenotypic information to compute genomically enhanced measures of genetic merit of individual animals. However, large numbers of genotyped and phenotyped animals are required to produce robust estimates of the effects of SNP that are summed together to generate direct genomic breeding values (DGV). Data on 11,756 Angus animals genotyped with the Illumina BovineSNP50 Beadchip were used to develop genomic predictions for 17 traits reported by the American Angus Association through Angus Genetics Inc. in their National Cattle Evaluation program. Marker effects were computed using a 5-fold cross-validation approach and a Bayesian model averaging algorithm. The accuracies were examined with EBV and deregressed EBV (DEBV) response variables and with K-means and identical by state (IBS)-based cross-validation methodologies. The cross-validation accuracies obtained using EBV response variables were consistently greater than those obtained using DEBV (average correlations were 0.64 vs. 0.57). The accuracies obtained using K-means cross-validation were consistently smaller than accuracies obtained with the IBS-based cross-validation approach (average correlations were 0.58 vs. 0.64 with EBV used as a response variable). Comparing the results from the current study with the results from a similar study consisting of only 2,253 records indicated that larger training population size resulted in higher accuracies in validation animals and explained on average 18% (69% improvement) additional genetic variance across all traits.

Genome-wide association analysis for feed efficiency in Angus cattle.

Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41,028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.

A prototype national cattle evaluation for feed intake and efficiency of Angus cattle.

Recent improvement in technologies for measuring individual feed intake has made possible the collection of data suitable for breed-wide genetic evaluation. The goals of this research were to estimate genetic parameters for components of feed efficiency and develop a prototype system for conducting a genetic evaluation of Angus cattle for feed intake. Weaning weight (WWT), postweaning BW gain (PGN), subcutaneous fat depth (SQF), and feed intake data were accumulated by the American Angus Association from a variety of cooperators and augmented with data collected for routine genetic evaluation of Angus cattle. The feed intake data were standardized (SFI, mean 0 and variance 1) within contemporary groups. Numbers of animals with observed phenotypes were 18,169, 7,107, 4,976, and 4,215 for WWT, PGN, SQF, and SFI, respectively. The 4-generation pedigree for animals with records contained 45,120 individuals. (Co)variance components were estimated with ASREML, fitting a 4-trait animal model with fixed contemporary groups for WWT, PGN, SQF, and SFI. Heritability estimates were 0.33 ± 0.03, 0.31 ± 0.04, 0.26 ± 0.04, and 0.42 ± 0.05 for direct genetic effects on WWT, PGN, SQF, and SFI, respectively. Genetic correlations of WWT and PGN with SFI were 0.40 ± 0.07 and 0.55 ± 0.10, respectively, and indicate their value as indicator traits in predicting EPD for feed intake. The genetic correlation of SQF and SFI was not different from 0. For all animals with a recorded feed intake phenotype, accuracy of their EPD for feed intake ranged from 0.16 to 0.64 with a mean of 0.26. However, 9,075 animals had an accuracy that was equal to or exceeded 0.2 for their feed intake EPD. Postanalysis calculation of measures of efficiency EPD was pursued. This work demonstrates the feasibility of conducting a national cattle evaluation for feed intake using indicator traits to reduce opportunity for selection bias, increase accuracy of the evaluation for a substantial number of animals, and ultimately facilitate calculation of selection indexes including feed intake.

A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle.

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.

Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators.

The objectives were to estimate genetic parameters needed to elucidate the relationships of a molecular breeding value (MBV) for marbling, intramuscular fat (IMF) of yearling bulls measured with ultrasound, and marbling score (MRB) of slaughtered steers, and to assess the utility of MBV and IMF in predicting the breeding value for MRB. Records for MRB (n = 38,296) and IMF (n = 6,594) were from the American Angus Association database used for national cattle evaluation. A total of 1,006 records of MBV were used in this study. (Co)variance components were estimated with ASREML, fitting an animal model with fixed contemporary groups for MRB and IMF similar to those used in the Angus national genetic evaluation. The overall mean was the only fixed effect included in the model for MBV. Heritability estimates for carcass measures were 0.48 +/- 0.03, 0.31 +/- 0.03, and 0.98 +/- 0.05 for MRB, IMF, and MBV, respectively. Genetic correlations of IMF and MBV with MRB were 0.56 +/- 0.09 and 0.38 +/- 0.10, respectively. The genetic correlation between IMF and MBV was 0.80 +/- 0.22. These results indicate the MBV evaluated may yield a greater genetic advance of approximately 20% when used as an indicator trait for genetic prediction of MRB compared with IMF. However, neither of these indicators alone provides sufficient information to produce highly accurate prediction of breeding value for the economically relevant trait MRB. Given that the goal is a highly accurate prediction of true breeding value for MRB, results of this work point to the need to 1) continue progeny testing, and 2) continue increasing the genetic correlation between the MBV and MRB.

National cattle evaluation system for combined analysis of carcass characteristics and indicator traits recorded by using ultrasound in Angus cattle.

The objectives were to 1) evaluate genetic relationships of sex-specific indicators of carcass merit obtained by using ultrasound with carcass traits of steers; 2) estimate genetic parameters needed to implement combined analyses of carcass and indicator traits to produce unified national cattle evaluations for LM area, subcutaneous fat depth (SQF), and marbling (MRB), with the ultimate goal of publishing only EPD for the carcass traits; and 3) compare resulting evaluations with previous ones. Four data sets were extracted from the records of the American Angus Association from 33,857 bulls, 33,737 heifers, and 1,805 steers that had measures of intramuscular fat content (IMF), LM area (uLMA), and SQF derived from interpretation of ultrasonic imagery, and BW recorded at the time of scanning. Also used were 38,296 records from steers with MRB, fat depth at the 12th to 13th rib interface (FD), carcass weight, and carcass LM area (cLMA) recorded on slaughter. (Co)variance components were estimated with ASREML by using the same models as used for national cattle evaluations by the American Angus Association. Heritability estimates for carcass measures were 0.45 +/- 0.03, 0.34 +/- 0.02, 0.40 +/- 0.02, and 0.33 +/- 0.02 for MRB, FD, carcass weight, and cLMA, respectively. Genetic correlations of carcass measures from steers with ultrasonic measures from bulls and heifers indicated sex-specific relationships for IMF (0.66 +/- 0.05 vs. 0.52 +/- 0.06) and uLMA (0.63 +/- 0.06 vs. 0.78 +/- 0.05), but not for BW at scanning (0.46 +/- 0.07 vs. 0.40 +/- 0.07) or SQF (0.53 +/- 0.06 vs. 0.55 +/- 0.06). For each trait, estimates of genetic correlations between bulls and heifers measured by using ultrasound were greater than 0.8. Prototype national cattle evaluations were conducted by using the estimated genetic parameters, resulting in some reranking of sires relative to previous analyses. Rank correlations of high-impact sires were 0.91 and 0.84 for the joint analysis of MRB and IMF with previous separate analyses of MRB and IMF, respectively. Corresponding results for FD and SQF were 0.90 and 0.90, and for cLMA and uLMA were 0.79 and 0.89. The unified national cattle evaluation for carcass traits using measurements from slaughtered animals and ultrasonic imagery of seed stock in a combined analysis appropriately weights information from these sources and provides breeders estimates of genetic merit consistent with traits in their breeding objectives on which to base selection decisions.

National Beef Quality Audit-1995: survey of producer-related defects and carcass quality and quantity attributes.

The National Beef Quality Audit-1995 was conducted to evaluate the progress of the beef industry since the time of the National Beef Quality Audit-1991 in improving quality and consistency of beef. Nine plants were assigned for auditing to Colorado State University, Oklahoma State University, and Texas A&M University. Personnel from each institution visited three of their nine plants twice, once in the spring/summer and once in the fall/winter. Data were collected on 50% of each lot on the slaughter floor and 10% in the cooler during a single day's production (one or two shifts, as appropriate). Of the cattle audited on the slaughter floor, 47.7% had no brands, 3.0% had a shoulder brand, 16.8% had a side brand, 38.7% had a butt brand, and 6.2% had brands in multiple locations. Data revealed that 51.6% of the carcasses had no bruises, 30.9% had one bruise, 12.8% had two bruises, 3.7% had three bruises, .9% had four bruises, and .1% had more than four bruises. In addition, 7.2% of the bruises evaluated were located on the round, 41.1% were on the loin, 20.8% on the rib, and 30.8% on the chuck. Livers, lungs, tripe, heads, tongues, and whole carcasses were condemned at rates of 22.2, 5.0, 11.0, .9, 3.8, and .1%, respectively. Mean USDA yield grade and quality grade traits were as follows: USDA yield grade, 2.8; carcass weight, 338.4 kg; adjusted fat thickness, 1.2 cm; longissimus muscle area, 81.9 cm2; kidney, pelvic, and heart fat, 2.1%; USDA quality grade, High Select; overall maturity, A60; and marbling score, Small-minus.

Estimation of non-additive genetic variances in three synthetic lines of beef cattle using an animal model.

Dominance and additive x additive genetic variances were estimated for birth and weaning traits of calves from three synthetic lines of beef cattle differing in mature size. Data consisted of 3,992 and 2,877 records from lines of small-, medium-, and large-framed calves in each of two research herds located at Rhodes and McNay, IA, respectively. Variance components were estimated separately by herd and line for birth weight (BWT), birth hip height (BH), 205-d weight (WW), and 205-d hip height (WH) by derivative-free REML with an animal model. Model 1 included fixed effects of year, sex, and age of dam. Random effects were additive direct (a) and additive maternal (m) genetic with covariance (a,m), maternal permanent environmental, and residual. Model 2 also included dominance (d) and model 3 included dominance plus additive x additive (a:a) effects. In general, only slight changes occurred in other variance components estimates when day was included in Model 2. However, large estimates of additive x additive genetic variances obtained with Model 3 for 4 out of 24 analyses were associated with reductions in estimates of direct additive variances. Direct (maternal) heritability estimates averaged across herd-line combinations with Model 2 were .53(.11), .42(.04), .27(.12), and .35(.04) for BWT, BH, WW, and WH, respectively. Corresponding covariance (a,m) estimates as fractions of phenotypic variance (sigma p2) were .00, .01, .01, and .06, respectively. For maternal permanent environmental effects in Model 2, average estimates of variances as fractions of sigma p2 across herd-line combinations were .03, .00, .05, and .02, for BW, BH, WW, and WH, respectively. Dominance effects explained, on average, 18, 26, 28, and 11% of total variance for BWT, BH, WW, and WH, respectively. Most of the estimates for additive x additive variances were negligible, except for one data set for BWT, two for BH, and one for WH, where the relative estimates of this component were high (.21 to .45). These results suggest that most of the non-additive genetic variance in the traits studied is accounted for by dominance genetic effects.

Effect of positive genetic trend for mature size on age-of-dam adjustment factors for weaning weight in Angus field records.

Weaning weight and postweaning gain field data from the American Angus Association were used to estimate age-of-dam adjustment factors for 205-d weaning weight. A two-trait model was used to take into account all genetic information available in the breed. Correction factors were developed for age-of-dam categories by sex of calf and management (creep or no creep) within maternal-grandsire birth-year groups. The maternal-grandsire birth-year groups were included to determine the need for updating age-of-dam adjustment factors for weaning weight. The mathematical model for 205-d weight included an overall mean, weaning contemporary group, age of dam by sex of calf and management code within maternal-grandsire birth-year group, animal direct effect, maternal genetic effect, permanent environmental effect, and residual error. The model for postweaning gain included an overall mean, postweaning contemporary group, animal direct effect, and residual error. Age-of-dam additive adjustment factors differed from the current factors used for the Angus breed. Young dams did not receive as large an adjustment as the current Angus adjustments recommended. Grouping the age-of-dam categories by birth year of maternal grandsire yielded different additive adjustment factors for 205-d weight. Noncreep calves tended to have larger age-of-dam adjustments than creep-fed calves did. Results indicate the need to consider including age of dam as a fixed effect in the animal model evaluation, so that adjustment factors may be specific to the genetic changes for growth in the breed.

Genetic parameters for carcass traits estimated from Angus field records.

The American Angus Association has sponsored a carcass evaluation since 1974. The carcass data collected as a part of this program are used by the association to conduct a biannual sire evaluation for carcass merit. This paper presents age-adjustment factors and genetic parameter estimates for carcass traits to be used in the Angus carcass genetic evaluation program. Because of the large range in slaughter ages, age classes were defined as all those animals slaughtered at an age of < or = 480 d and those with a slaughter age > 480 d. Linear and quadratic partial regressions on slaughter age for hot carcass weight (HCW), USDA marbling score (MS), 12th rib longissimus muscle area (LMA), and 12th-rib fat thickness (FT) were estimated within sex and age class. Quadratic age regressions were not significant, nor was the linear age regression coefficient for FT in steers in the > 480-d age class. Heritability estimates for age-constant HCW, MS, LMA, and FT were .31, .26, .32, and .26, respectively. The estimated genetic correlation (rg) between HCW and LMA was .47. The estimated rg between HCW and FT was .38 and between MS and FT was -.13. The linear genetic trends for CWT and LMA were significantly positive at .414 kg/yr and .075 cm2/yr, respectively. The genetic trends for FT and MS were very small but significantly negative at -.004 cm/yr and -.003 units/yr, respectively.

Genetic parameter estimates and expected progeny differences for mature size in Angus cattle.

Mature size records collected on Angus cows of 5 to 12 yr of age were used to estimate heritabilities, genetic correlations, and EPD for mature weight and mature height. A total of 256 sires were evaluated using mature size data collected on 2,732 daughters. Data were analyzed using REML procedures with a two-trait sire model to estimate sire and error variances for mature weight and height. Models with and without adjustment of weight for body condition score were investigated. The linear model for weight and height included fixed herd-year-month the records were taken, sire genetic group, random sire, and residual error. Using unadjusted mature weights, heritabilities were .48 +/- .10 for weight and .83 +/- .11 for height. When condition score adjustments were made, heritability estimates were .45 +/- .10 for weight and .83 +/- .11 for height. Genetic (phenotypic) correlations between weight and height were .78(.58) for adjusted data and .66(.54) with no adjustment. Spearman rank correlations between sire EPD for adjusted and unadjusted data were .94 for weight and .99 for height. Two-trait models of mature cow weight with immature weights (birth weight, 205-d weight, 365-d weight) were used to assess genetic relations among mature and immature cow weights. Genetic correlations between mature weight and immature weights were .57 with birth weight, .62 with 205-d weight, and .45 with 365-d weight.

Adjusting weight for body condition score in Angus cows.

Weight, height, and body condition score data supplied by the American Angus Association were used to determine the effect of body condition score on cow weight and to compute condition score adjustment factors. Single records on 11,301 cows for weight and 7,769 cows for height were collected at or near weaning, at which time a subjective condition score (9-point scale) was taken. Limited information on extreme scores 1 and 9 allowed only scores 2 through 8 to be included in the analysis. Cows were grouped into age classes corresponding to 2, 3, 4, 5, 6, 7 to 10, and 11+ yr of age. The mathematical model for a weight record included effects of fixed herd, year-month the record was collected, cow age, body condition score, and a random residual error term. The model for height excluded the condition score effect. Effects of herd, year-month, and cow age were highly significant (P less than .0001) for weight and height. Body condition score was a significant source of variation in weight (P less than .0001) and accounted for 16% of the total variation. Adjustment factors for weight (kilograms) by condition score were +116 (score 2), +91 (score 3), +69 (score 4), +39 (score 5), 0 (score 6), -40 (score 7), and -86 (score 8).

Genetic parameters for nuclear and nonnuclear inheritance in three synthetic lines of beef cattle differing in mature size.

Genetic parameters for nuclear and cytoplasmic genetic effects were estimated from preweaning growth data collected on three synthetic lines of beef cattle differing in mature size. Lines of small-, medium-, and large-framed calves were represented in each of two research herds (Rhodes and McNay). Variance components were estimated separately by herd and size line for birth weight and 205-d weight (WW) by REML with an animal mode using an average of 847 and 427 calf records from Rhodes and McNay, respectively. Model 1 included effects of fixed year, sex of calf, age of dam, and random additive direct (a), additive maternal genetic (m), covariance (a,m), permanent environment affecting the dam, and residual error. Model 2 differed from Model 1 by including random cytoplasmic lineage effects and by ignoring permanent environmental effects. Model 1--direct (maternal) heritability estimates for birth weight at Rhodes were .62(.03) for small, .67(.06) for medium, and .30(.11) for large lines. Genetic correlations between direct and maternal effects for birth weight were .67, -.16, and .48 for the respective size groups. For WW at Rhodes, direct (maternal) heritability estimates were .30(.29), .30(.14), and .10(.16) for small, medium, and large lines, respectively, with genetic correlations of -.34 (small), -.12 (medium), and .17 (large). Heritability estimates at McNay were similar to those at Rhodes, except that maternal genetic heritabilities for WW were smaller (.10, small; .01, medium; .00, large). Model 2--estimates for nuclear genetic effects were consistent with the estimates from Model 1. Cytoplasmic variance accounted for 0 to 5% of the total random variance in birth weight. For WW, cytoplasmic variance was negligible at Rhodes and accounted for 4% of the total random variance in the large line at McNay, averaging less than the permanent environment. Results failed to indicate that cytoplasmic variance was important for preweaning performance.