M. Vinsky

Accuracy of predicting genomic breeding values for residual feed intake in Angus and Charolais beef cattle.

In beef cattle, phenotypic data that are difficult and/or costly to measure, such as feed efficiency, and DNA marker genotypes are usually available on a small number of animals of different breeds or populations. To achieve a maximal accuracy of genomic prediction using the phenotype and genotype data, strategies for forming a training population to predict genomic breeding values (GEBV) of the selection candidates need to be evaluated. In this study, we examined the accuracy of predicting GEBV for residual feed intake (RFI) based on 522 Angus and 395 Charolais steers genotyped on SNP with the Illumina Bovine SNP50 Beadchip for 3 training population forming strategies: within breed, across breed, and by pooling data from the 2 breeds (i.e., combined). Two other scenarios with the training and validation data split by birth year and by sire family within a breed were also investigated to assess the impact of genetic relationships on the accuracy of genomic prediction. Three statistical methods including the best linear unbiased prediction with the relationship matrix defined based on the pedigree (PBLUP), based on the SNP genotypes (GBLUP), and a Bayesian method (BayesB) were used to predict the GEBV. The results showed that the accuracy of the GEBV prediction was the highest when the prediction was within breed and when the validation population had greater genetic relationships with the training population, with a maximum of 0.58 for Angus and 0.64 for Charolais. The within-breed prediction accuracies dropped to 0.29 and 0.38, respectively, when the validation populations had a minimal pedigree link with the training population. When the training population of a different breed was used to predict the GEBV of the validation population, that is, across-breed genomic prediction, the accuracies were further reduced to 0.10 to 0.22, depending on the prediction method used. Pooling data from the 2 breeds to form the training population resulted in accuracies increased to 0.31 and 0.43, respectively, for the Angus and Charolais validation populations. The results suggested that the genetic relationship of selection candidates with the training population has a greater impact on the accuracy of GEBV using the Illumina Bovine SNP50 Beadchip. Pooling data from different breeds to form the training population will improve the accuracy of across breed genomic prediction for RFI in beef cattle.

Phenotypic and genetic relationships of feed efficiency with growth performance, ultrasound, and carcass merit traits in Angus and Charolais steers

Feed efficiency is of particular importance to the beef industry, as feed costs represent the single largest variable cost in beef production systems. Selection for more efficient cattle will lead to reduction of feed related costs, but should not have adverse impacts on quality of the carcass. In this study, we evaluated phenotypic and genetic correlations of residual feed intake (RFI), RFI adjusted for end-of-test ultrasound backfat thickness (RFIf), and RFI adjusted for ultrasound backfat thickness and LM area (RFIfr) with growth, ultrasound, and carcass merit traits in an Angus population of 551 steers and in a Charolais population of 417 steers. In the Angus steer population, the phenotypic and genetic correlation of RFI with carcass merit traits including HCW, carcass backfat, carcass LM area, lean meat yield, and carcass marbling were not significant or weak with correlations coefficients ranging from -0.0007 ± 0.05 to 0.18 ± 0.21. In the Charolais steer population, the phenotypic and genetic correlations of RFI with the carcass merit traits were also weak, with correlation coefficients ranging from -0.07 ± 0.06 to 0.19 ± 0.18, except for the genetic correlation with carcass average backfat, which was moderate with a magnitude of 0.42 ± 0.29. Inclusion of ultrasound backfat thickness in the model to predict the expected daily DMI for maintenance explained on average an additional 0.5% variation of DMI in the Angus steers and 2.3% variation of DMI in the Charolais steer population. Inclusion of both the ultrasound backfat and LM area in the model explained only 0.7% additional variance in DMI in the Angus steer population and only 0.6% in the Charolais steer population on top of the RFIf model. We concluded that RFIf adjusted for ultrasound backfat at the end of the test will lead to decreases of both the phenotypic and genetic correlations with carcass backfat and marbling score to a greater extent for late-maturing beef breeds such as Charolais than for early-maturing beef breeds such as Angus. However, further inclusion of ultrasound LM area on top of the final ultrasound backfat in the model of calculating RFI had little effect in reducing the correlations of RFI with the carcass merit traits.

Estimates of genetic parameters for fatty acids in brisket adipose tissue of Canadian commercial crossbred beef steers

Heritability and genetic and phenotypic correlations between 15 individuals and 10 groups of fatty acids with a concentration greater than 0.5% in the brisket adipose tissue of 223 Angus and Charolais based crossbred commercial steers were estimated using univariate and bivariate animal models. Individual saturated fatty acids were low to moderately heritable, with heritability estimates ranging from 0.05 (C16:0) to 0.31 (C15:0). Individual monounsaturated fatty acids were low to moderately highly heritable ranging from 0.04 (9c C17:1 and 11c C18:1) to 0.51 (9c C14:1). Polyunsaturated fatty acid C18:2n-6 was moderately heritable (0.17). Among groups of fatty acids, heritability estimates ranged from 0.03 for branched chain fatty acid (BCFA) and n-6/n-3 to 0.16 for n-6 and Health Index. A range of low (0.00) to high (1.00) phenotypic and genetic correlations was observed among the 25 fatty acids considered in this study. In general, fatty acids such as conjugated linoleic acid (CLA) and 11t C18:1, with potential health benefits, showed significant antagonistic correlations with unhealthy fatty acids such as C14:0 and C16:0. The results from this study provide insight into the direct genetic control of host genes on fatty acid composition of beef tissues and will facilitate designs of genetic selection and/or genetic based diet management to improve fatty acid composition in beef cattle.

Phenotypic and genetic relationships of feeding behavior with feed intake, growth performance, feed efficiency, and carcass merit traits in Angus and Charolais steers1

Feeding behavior traits including daily feeding duration (FD), daily feeding head down time (HD), average feeding duration per feeding event (FD_AVE), average feeding head down time per feeding event (HD_AVE), feeding frequency (FF), and meal eating rate (ER) were analyzed to estimate their phenotypic and genetic correlations with feed intake, growth performance, residual feed intake (RFI), ultrasound, and carcass merit traits in Angus and Charolais finishing steers. Heritability estimates for FD, HD, FD_AVE, HD_AVE, FF, and ER were 0.27 ± 0.09 (SE), 0.25 ± 0.09, 0.19 ± 0.06, 0.11 ± 0.05, 0.24 ± 0.08, and 0.38 ± 0.10, respectively, in the Angus population and 0.49 ± 0.12, 0.38 ± 0.11, 0.31 ± 0.09, 0.29 ± 0.10, 0.43 ± 0.11, and 0.56 ± 0.13, respectively, in the Charolais population. In both the Angus and Charolais steer populations, FD and HD had relatively stronger phenotypic (0.17 ± 0.06 to 0.32 ± 0.04) and genetic (0.29 ± 0.17 to 0.54 ± 0.18) correlations with RFI in comparison to other feeding behavior traits investigated, suggesting the potential of FD and HD as indicators in assessing variation of RFI. In general, feeding behavior traits had weak phenotypic correlations with most of the ultrasound and carcass merit traits; however, estimated genetic correlations of the feeding behavior traits with some fat deposition related traits were moderate to moderately strong but differed in magnitude or sign between the Angus and Charolais steer populations, likely reflecting their different biological types. Genetic parameter estimation studies involving feeding behavior traits in beef cattle are lacking and more research is needed to better characterize the relationships between feeding behavior and feed intake, growth, feed utilization, and carcass merit traits, in particular with respect to different biological types of cattle.

Accuracy of predicting genomic breeding values for carcass merit traits in Angus and Charolais beef cattle

Accuracy of predicting genomic breeding values for carcass merit traits including hot carcass weight, longissimus muscle area (REA), carcass average backfat thickness (AFAT), lean meat yield (LMY) and carcass marbling score (CMAR) was evaluated based on 543 Angus and 400 Charolais steers genotyped on the Illumina BovineSNP50 Beadchip. For the genomic prediction within Angus, the average accuracy was 0.35 with a range from 0.32 (LMY) to 0.37 (CMAR) across different training/validation data-splitting strategies and statistical methods. The within-breed genomic prediction for Charolais yielded an average accuracy of 0.36 with a range from 0.24 (REA) to 0.46 (AFAT). The across-breed prediction had the lowest accuracy, which was on average near zero. When the data from the two breeds were combined to predict the breeding values of either breed, the prediction accuracy averaged 0.35 for Angus with a range from 0.33 (REA) to 0.39 (CMAR) and averaged 0.33 for Charolais with a range from 0.18 (REA) to 0.46 (AFAT). The prediction accuracy was slightly higher on average when the data were split by animals birth year than when the data were split by sire family. These results demonstrate that the genetic relationship or relatedness of selection candidates with the training population has a great impact on the accuracy of predicting genomic breeding values under the density of the marker panel used in this study.

Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle1

Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.

Short Communication: Association analyses of a single nucleotide polymorphism in the promoter of OLR1 with growth, feed efficiency, fat deposition, and carcass merit traits in hybrid, Angus and Charolais beef cattle.

Vinsky, M., Islam, K., Chen, L. and Li, C. 2013. Short Communication: Association analyses of a single nucleotide polymorphism in the promoter of OLR1 with growth, feed efficiency, fat deposition, and carcass merit traits in hybrid, Angus and Charolais beef cattle. Can. J. Anim. Sci. 93: 193-197. A single nucleotide polymorphism (SNP) in the promoter region of oxidized low density lipoprotein (lectin-like) receptor 1 (OLR1) (c. -495 T>C) was identified and analyzed for associations with 10 traits related to growth, feed efficiency, body fat deposition and carcass merit traits in hybrid (n=456), Angus (n=567) and Charolais (n=423) beef cattle populations. Significant allele substitution effect (P=0.023) was found for residual feed intake (RFI) in the Angus population. The allele “C”, which had a frequency of 0.24 in the Angus population, was associated with decreased RFI. The Angus steers with the “CC” genotype had a lower RFI value (i.e., more efficient) than the Angus steers carrying the ‘TT’ genotype. The SNP was also found to have significant dominance effects on final ultrasound rib-eye area (FUREA) (P=0.0004) and carcass rib-eye area (CREA) (P=0.009) in the Angus steer population. The Angus steers with the “CT” genotype had smaller rib-eye areas of both ultrasound and carcass measures than the average of the steers with the homozygous genotypes. However, the SNP did not show significant associations with the traits examined in either the hybrid or the Charolais steer population at P<0.05. OLR1 plays a role in lipid metabolism, and analyses of transcript binding site based on the transcription element search system revealed that the “T” allele of the c.-495T>C SNP introduces a presumptive binding site for CCAAT/enhancer binding protein alpha (C/EBPa). However, further investigation is required to delineate the possible regulatory role of the SNP on growth and efficiency of energy utilization in relation to different biological types of beef cattle.

Phenotypic and genetic relationships of residual feed intake measures and their component traits with fatty acid composition in subcutaneous adipose of beef cattle

Feed efficiency is of particular interest to the beef industry because feed is the largest variable cost in production and fatty acid composition is emerging as an important trait, both economically and socially, due to the potential implications of dietary fatty acids on human health. Quantifying correlations between feed efficiency and fatty acid composition will contribute to construction of optimal multiple-trait selection indexes to maximize beef production profitability. In the present study, we estimated phenotypic and genetic correlations of feed efficiency measures including residual feed intake (RFI), RFI adjusted for final ultrasound backfat thickness (RFIf); their component traits ADG, DMI, and metabolic BW; and final ultrasound backfat thickness measured at the end of feedlot test with 25 major fatty acids in the subcutaneous adipose tissues of 1,366 finishing steers and heifers using bivariate animal models. The phenotypic correlations of RFI and RFIf with the 25 individual and grouped fatty acid traits were generally low (<0.25 in magnitude). However, relatively stronger genetic correlation coefficients of RFI and RFIf with PUFA traits including the -6:-3 ratio (0.52 ± 0.29 and 0.45 ± 0.31, respectively), 18:2-6 (0.45 ± 0.18 and 0.40 ± 0.19, respectively), -6 (0.43 ± 0.18 and 0.38 ± 0.19, respectively), PUFA (0.42 ± 0.18 and 0.36 ± 0.20, respectively), and 9-16:1 (-0.43 ± 0.20 and -0.33 ± 0.22, respectively) were observed. Hence, selection for low-RFI or more efficient beef cattle will improve fatty acid profiles by lowering the content of -6 PUFA, thus reducing the ratio of -6 to -3 along with increasing the amount of 9-16:1. Moderate to moderately high genetic correlations were also observed for DMI with 9-14:1 (-0.32 ± 0.17) and the sum of CLA analyzed (SumCLA; -0.45 ± 0.21), suggesting that selection of beef cattle with lower DMI will lead to an increase amount of 9-14:1 and SumCLA in the subcutaneous adipose tissue. However, unfavorable genetic correlations were detected for ADG with 11-18:1 (-0.38 ± 0.23) and SumCLA (-0.73 ± 0.26), implying that selection of beef cattle with a better growth rate will decrease the contents of healthy fatty acids 11-18:1 and SumCLA. Therefore, it is recommended that a multiple-trait selection index be used when genetic improvements of fatty acid composition, feed efficiency, feed intake, and growth are important in the breeding objective.

Additional file 2: of Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle

List of significant single nucleotide polymorphisms (SNP) for 81 fatty acid composition traits in subcutaneous adipose (SQ). Results include trait name, SNP name, chromosome, position on the UMD3.1 genome assembly, alleles, allele substitution effect, percentage of total genetic variance explained, and posterior probability of inclusion of SNP. (CSV 24 kb)