Evaluation and development of animal breeding in Ireland

End of project reportThe primary objectives of this study were: 1) to annually evaluate the pertinence of the Irish dairy cattle breeding index, the Economic Breeding Index (EBI) and where necessary modify, 2) to evaluate the potential of do-it-yourself milk recording as an alternative to current supervised methods of milk recording, and 3) to estimate the level and rate of accumulation of inbreeding in Irish dairy and beef cattle, to quantify its effects on traits of economic importance, and to develop remedial measures to minimise the future accumulation of inbreeding in Ireland

Genetic aspects of calving, growth, and carcass traits in beef cattle

The aim of this thesis was to learn more about the genetic background of calving, growth and carcass traits of beef cattle breeds in Sweden, and to assess the possibility of including calving traits and commercial carcass traits in the genetic evaluation. In addition, the genetic relationship between field-recorded growth rate and daily weight gain at station performance testing was investigated. The breeds studied were Charolais, Hereford and Simmental. Records of birth weight, pre-weaning gain, post-weaning gain, carcass fleshiness grade, carcass fatness grade, carcass weight, calving difficulty score and stillbirth were analysed using linear animal models. The estimated direct heritabilities were moderate to high for birth and carcass weight, moderate for pre- and post-weaning gain, carcass fleshiness and fatness grades, low for calving difficulty score and very low for stillbirth. Maternal heritabilities tended to be lower than the direct ones. Genetic relationships between direct and maternal genetic effects were generally antagonistic. Moderate to high genetic correlations were estimated between post-weaning gain in the field and at the station, showing considerable breed differences, and the added value of station testing was questioned. Genetic relationships were generally weaker between growth traits and both carcass fleshiness and fatness grade than between growth and carcass weight. Male and female birth weights were found to be the same trait genetically, and strong genetic relationships were estimated between birth weight and calving traits. Less than unity genetic correlations between calving difficulty at first and later parities indicated that partly different sets of genes control these traits. Some antagonistic relationships were found between carcass and calving traits. It was concluded that it would be feasible to include commercial carcass records and calving difficulty score in the genetic evaluation, and that both direct and maternal effects should be considered for pre-weaning traits. Information on correlated traits should be used for selection against stillbirth as direct selection would be inefficient due to small progeny group size and very low heritability. Joint genetic evaluation of pre-weaning gain and carcass weight was recommended to reduce selection bias

Identification of SNPs in TG and EDG1 genes and their relationships with carcass traits in Korean cattle (Hanwoo)

Thyroglobulin (TG) gene was known to be regulated fat cell growth and differentiation and the endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene involves blood vessel formation and known to be affecting carcass traits in beef cattle. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) in both TG and EDG1 genes and to analyze the association with carcass traits in Korean cattle (Hanwoo). The T354C SNP in TG gene located at the 3’ flanking region and c.-312A>G SNP located at 3’-UTR of EDG1 gene were used for genotyping the animals using PCR-RFLP method. Three genotypes were identified in T354C SNP in TG gene and only two AA and AG genotypes were observed for the c.-312A>G SNP in EDG1 gene. The results indicated that T354C SNP in TG gene was not significantly associated with carcass traits. However, the c.-312A>G SNP in EDG1 gene had significant effects on backfat thickness (BF) and yield index (YI). These results may provide valuable information for further candidate gene studies affecting carcass traits in Korean cattle and may use as marker assisted selection for improving the quality of meat in Hanwoo. Key words : TG, EDG1, Carcass traits, Hanwo

Associations between the K232A polymorphism in the diacylglycerol-O-transferase 1 (DGAT1) gene and performance in Irish Holstein-Friesian dairy cattle

peer-reviewedSelection based on genetic polymorphisms requires accurate quantification of the effect or association of the polymorphisms with all traits of economic importance. The objective of this study was to estimate, using progeny performance data on 848 Holstein-Friesian bulls, the association between a non-conservative alanine to lysine amino acid change (K232A) in exon 8 of the diacylglycerol-O-transferase 1 (DGAT1) gene and milk production and functionality in the Irish Holstein-Friesian population. The DGAT1 gene encodes the diacylglycerol-O-transferase microsomal enzyme necessary to catalyze the final step in triglyceride synthesis. Weighted mixed model methodology, accounting for the additive genetic relationships among animals, was used to evaluate the association between performance and the K232A polymorphism. The minor allele frequency (K allele) was 0.32. One copy of the K allele was associated (P < 0.001) with 77 kg less milk yield, 4.22 kg more fat yield, 0.99 kg less protein yield, and 1.30 and 0.28 g/kg greater milk fat and protein concentration, respectively; all traits were based on predicted 305-day production across the first five lactations. The K232A polymorphism explained 4.8%, 10.3% and 1.0% of the genetic variance in milk yield, fat yield and protein yield, respectively. There was no association between the K232A polymorphism and fertility, functional survival, calving performance, carcass traits, or any conformation trait with the exception of rump width and carcass conformation. Using the current economic values for the milk production traits in the Irish total merit index, one copy of the K allele is worth €5.43 in expected profitability of progeny. Results from this study will be useful in quantifying the cost-benefit of including the K232A polymorphism in the Irish national breeding programme

Validation and Improvement of the Beef Production Sub-index in Ireland for Beef Cattle

End of project reportThe objectives of the following study were to: a. Quantify the effect of sire genetic merit for BCI on: 1. feed intake, growth and carcass traits of progeny managed under bull or steer beef production systems. 2. live animal scores, carcass composition and plasma hormone and metabolite concentrations in their progeny. b. Compare the progeny of : 1. Late-maturing beef with dairy breeds and 2. Charolais (CH), Limousin (LM), Simmental (SM) and Belgian Blue (BB) sires bred to beef suckler dams, for feed intake, blood hormones and metabolites, live animal measurements, carcass traits and carcass value in bull and steer production systems

The influence of feeding behaviour on growth performance, carcass and meat characteristics of growing pigs

This study investigated the effect of the feeding behaviour on growth performance, and car- cass and meat characteristics of 96 barrows fed ad libitum or restrictively with high or low amino acids (AA) diets according to a 2 7 2 factorial design. The feeding behaviour traits were measured with automated feeders. From 86 kg BW, half of the pigs were given feeds with high indispensable (AA) contents, while the other half received feeds with indispensable AA contents reduced by 9% in early finishing (86\u2013118 kg BW) and by 18% in late finishing (118\u2013145 kg BW). Body lipid and protein retentions were estimated from BW and backfat depth measures recorded at the beginning and end of each period. Pigs were slaughtered at 145 kg BW and carcass and meat quality data were recorded. Phenotypic correlations among feeding behaviours, growth performances, and carcass and meat traits were com- puted from all the data after adjustment for the effects of feeding treatments. As feeding rate was the behavioural trait most highly correlated with performance and carcass traits, the records of each pig were classified into feeding rate tertiles. Then, the data were statistically analysed using a mixed model, which included feed restriction (FR), AA reduction (AAR), the FR 7 AAR interaction and the feeding rate tertile as fixed factors, and pen as a random factor. Pigs eating faster (52.1 to 118.9 g/min) had significantly greater final body weights (16%), average daily weight gains (27%), estimated protein gains (22%), estimated lipid retention (46%), carcass weights (16%), weights of lean cuts (14%), weights of fat cuts (21%), proportions of fat in the carcass (14%), and 4% lower proportions of carcass lean cuts than pigs eating slowly (12.6 to 38.2 g/min). Manipulating the eating rate, through man- agement or genetic strategies, could affect feed intake and subsequent growth perfor- mance, hence carcass quality, but have little influence on feed efficiency

Performance and carcass traits of progeny of Limousin sires differing in genetic merit

peer-reviewedGenetic indices for growth and carcass classification are published for beef sires used in Ireland for artificial insemination (AI). The objective of this study was to compare growth and carcass traits of progeny of Limousin sires of low and high genetic index for growth. A total of 70 progeny (42 males and 28 females) out of predominantly Holstein-Friesian cows by 7 AI Limousin sires were reared together to slaughter. The 7 sires were classified as low (n=3) or high (n=4) index based on their published genetic index for growth. The male progeny were reared entire and all animals were slaughtered at about 20 months of age. Carcasses were classified for conformation and fatness, and a rib joint (ribs 6 to 10) was separated into fat, muscle and bone. Growth rate did not differ significantly between the index groups but tended to be higher for the high index progeny. This higher growth rate, combined with a significantly higher kill out proportion, resulted in carcass weight andcarcass weight per day of age being significantly higher for the high index progeny. Carcass conformation and fat class were not affected by genetic index, nor was the composition of the rib joint. Compared with males, females had a significantly lower growth rate and kill out proportion and, consequently, had a significantly lower carcass weight. The proportions of fat and bone in the rib joint were significantly higher, and the proportion of muscle was significantly lower for females than for males. It is concluded that carcass weight reflected sire group genetic index for growth but feed intake, carcass classification and rib joint composition were not affected

Herd-specific random regression carcass profiles for beef cattle after adjustment for animal genetic merit

Abattoir data are an important source of information for the genetic evaluation of carcass traits, but also for on-farm management purposes. The present study aimed to quantify the contribution of herd environment to beef carcass characteristics (weight, conformation score and fat score) with particular emphasis on generating finishing herd-specific profiles for these traits across different ages at slaughter. Abattoir records from 46,115 heifers and 78,790 steers aged between 360 and 900 days, and from 22,971 young bulls aged between 360 and 720 days, were analysed. Finishing herd-year and animal genetic (co)variance components for each trait were estimated using random regression models. Across slaughter age and gender, the ratio of finishing herd-year to total phenotypic variance ranged from 0.31 to 0.72 for carcass weight, 0.21 to 0.57 for carcass conformation and 0.11 to 0.44 for carcass fat score. These parameters indicate that the finishing herd environment is an important contributor to carcass trait variability and amenable to improvement with management practices

Comparison of alternative approaches to single-trait genomic prediction using genotyped and non-genotyped Hanwoo beef cattle.

BackgroundGenomic predictions from BayesA and BayesB use training data that include animals with both phenotypes and genotypes. Single-step methodologies allow additional information from non-genotyped relatives to be included in the analysis. The single-step genomic best linear unbiased prediction (SSGBLUP) method uses a relationship matrix computed from marker and pedigree information, in which missing genotypes are imputed implicitly. Single-step Bayesian regression (SSBR) extends SSGBLUP to BayesB-like models using explicitly imputed genotypes for non-genotyped individuals.MethodsCarcass records included 988 genotyped Hanwoo steers with 35,882 SNPs and 1438 non-genotyped steers that were measured for back-fat thickness (BFT), carcass weight (CWT), eye-muscle area, and marbling score (MAR). Single-trait pedigree-based BLUP, Bayesian methods using only genotyped individuals, SSGBLUP and SSBR methods were compared using cross-validation.ResultsMethods using genomic information always outperformed pedigree-based BLUP when the same phenotypic data were modeled from either genotyped individuals only or both genotyped and non-genotyped individuals. For BFT and MAR, accuracies were higher with single-step methods than with BayesB, BayesC and BayesCπ. Gains in accuracy with the single-step methods ranged from +0.06 to +0.09 for BFT and from +0.05 to +0.07 for MAR. For CWT, SSBR always outperformed the corresponding Bayesian methods that used only genotyped individuals. However, although SSGBLUP incorporated information from non-genotyped individuals, prediction accuracies were lower with SSGBLUP than with BayesC (π = 0.9999) and BayesB (π = 0.98) for CWT because, for this particular trait, there was a benefit from the mixture priors of the effects of the single nucleotide polymorphisms.ConclusionsSingle-step methods are the preferred approaches for prediction combining genotyped and non-genotyped animals. Alternative priors allow SSBR to outperform SSGBLUP in some cases