Heritability estimates for carcass traits of cattle: a review

We present estimates of heritability for carcass traits of cattle published in the scientific literature. Seventy-two papers published from 1962 to 2004, which reported estimates of heritability for carcass traits, were reviewed. The unweighted means of estimates of heritability for 14 carcass traits by slaughter end point (age, weight, and fat depth) were calculated. Among the three end points, carcass weight, backfat thickness, longissimus muscle area, and marbling score were the carcass traits with the most estimates of heritability (56 相似文献   

Glucose production and glycogen cycle enzyme activities in avian liver explants: procedural optimization

1. There are few studies which both describe the in vitro regulation of glycogen metabolism in nonmammalian animals and list methods to optimize assay conditions for these studies. 2. A mechanical tissue chopper was used to obtain 25-65 mg liver explants from 14- to 28-day old domestic turkeys to determine assay conditions (substrates, buffers, time), regulators (metals, salts and hormones) and points of endogenous regulation of glycogenolysis (protein phosphorylation and enzyme activity). 3. High- and low-bicarbonate-based buffers (Earle's balanced salts, EBSS and Hanks' balanced salts, HBSS, respectively) were used to determine buffer effects. 4. Glucose release into the incubation environment was greater in HBSS than EBSS. Adding HEPES to further buffer conditions did not change release rates. Adding bicarbonate to HBSS resulted in release rates similar to EBSS. 5. Calcium increased glycogenolysis in the presence of absence of equimolar concentrations of EGTA; potassium had no effect. 6. Porcine insulin (100 ng/ml) did not inhibit glycogenolysis; however, glucose release was increased by dibutyryl cyclic AMP. A noted catecholamine-induced increase in in vitro glycogenolysis and phosphorylase activity indicates that points of regulation are under phosphorylation-dephosphorylation regulation.     

Use of chromomycin A3 staining in bovine sperm cells for detection of protamine deficiency

Sperm chromatin integrity is essential for accurate transmission of male genetic information, and normal sperm chromatin structure is important for fertilization. Protamine is a nuclear protein that plays a key role in sperm DNA integrity, because it is responsible for sperm DNA stability and packing until the paternal genome is delivered into the oocyte during fertilization. Our aim was to investigate protamine deficiency in sperm cells of Bos indicus bulls (Nelore) using chromomycin A₃ (CMA₃) staining. Frozen semen from 14 bulls were thawed, then fixed in Carnoy's solution. Smears were prepared and analyzed by microscopy. As a positive control of CMA₃ staining, sperm from one bull was subjected to deprotamination of nuclei. The percentage of CMA₃-positive bovine sperm did not vary among batches. Only two bulls showed a higher percentage of CMA₃-positive sperm cells compared to the others. CMA₃ is a simple and useful tool for detecting sperm protamine deficiency in bulls.     

Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut

Background

Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research.

Findings

The goal of our study was to establish a protocol, using a modified DNA isolation procedure and quality controls, to select decalcified samples suitable for array-CGH testing. Archival paraffin blocks were obtained from 9 different pathology departments throughout Europe, using different fixation, embedding and decalcification procedures, in order to preclude a bias for certain lab protocols. Isolated DNA samples were subjected to direct chemical labelling and enzymatic labelling systems and were hybridised on a high resolution oligonucleotide chip containing 44,000 reporter elements. Genomic alterations (gains and losses) were readily detected in most of the samples analysed. For example, both homozygous deletions of 0.6 Mb and high level of amplifications of 0.7 Mb were identified.

Conclusions

We established a robust protocol for molecular genetic testing of dFFPE derived DNA, irrespective of fixation, decalcification or sample type used. This approach may greatly facilitate further genetic testing on rare tumour entities where archival decalcified, formalin fixed samples are the only source.     

Genomic selection of purebred animals for crossbred performance in the presence of dominant gene action

Background

Genomic selection is an appealing method to select purebreds for crossbred performance. In the case of crossbred records, single nucleotide polymorphism (SNP) effects can be estimated using an additive model or a breed-specific allele model. In most studies, additive gene action is assumed. However, dominance is the likely genetic basis of heterosis. Advantages of incorporating dominance in genomic selection were investigated in a two-way crossbreeding program for a trait with different magnitudes of dominance. Training was carried out only once in the simulation.

Results

When the dominance variance and heterosis were large and overdominance was present, a dominance model including both additive and dominance SNP effects gave substantially greater cumulative response to selection than the additive model. Extra response was the result of an increase in heterosis but at a cost of reduced purebred performance. When the dominance variance and heterosis were realistic but with overdominance, the advantage of the dominance model decreased but was still significant. When overdominance was absent, the dominance model was slightly favored over the additive model, but the difference in response between the models increased as the number of quantitative trait loci increased. This reveals the importance of exploiting dominance even in the absence of overdominance. When there was no dominance, response to selection for the dominance model was as high as for the additive model, indicating robustness of the dominance model. The breed-specific allele model was inferior to the dominance model in all cases and to the additive model except when the dominance variance and heterosis were large and with overdominance. However, the advantage of the dominance model over the breed-specific allele model may decrease as differences in linkage disequilibrium between the breeds increase. Retraining is expected to reduce the advantage of the dominance model over the alternatives, because in general, the advantage becomes important only after five or six generations post-training.

Conclusion

Under dominance and without retraining, genomic selection based on the dominance model is superior to the additive model and the breed-specific allele model to maximize crossbred performance through purebred selection.     

The natural frequency of the foot-surface cushion during the stance phase of running

Researchers have reported on the stiffness of running in holistic terms, i.e. for the structures that are undergoing deformation as a whole rather than in terms of specific locations. This study aimed to estimate both the natural frequency and the viscous damping coefficient of the human foot-surface cushion, during the period between the heel strike and the mid-stance phase of running, using a purposely developed one degree-of-freedom inverted pendulum state space model of the leg. The model, which was validated via a comparison of measured and estimated ground reaction forces, incorporated a novel use of linearized and extended Kalman filter estimators. Investigation of the effect of variation of the natural frequency and/or the damping of the cushioning mechanism during running, using the said model, revealed the natural frequency of running on said foot-surface cushion, during the stance phase, to lie between 5 and 11 Hz. The "extended Kalman filter (EKF)" approach, that was used here for the first time to directly apply measured ground forces, may be widely applicable to the identification process of combined estimation of both unknown physiological state and mechanical characteristics of the environment in an inverse dynamic model.     

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation

Background

Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.

Methods

Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values.

Results

Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied.

Conclusions

These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.     

Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model

Background

Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line.

Methods

The following traits were analyzed: egg production, egg weight, egg color, shell strength, age at sexual maturity, body weight, albumen height, and yolk weight. Predictions appropriate for early or late selection were compared. A total of 2,708 birds were genotyped for 23,356 segregating SNP, including 1,563 females with records. Phenotypes on relatives without genotypes were incorporated in the analysis (in total 13,049 production records).The data were analyzed with a Reduced Animal Model using a relationship matrix based on pedigree data or on marker genotypes and with a Bayesian method using model averaging. Using a validation set that consisted of individuals from the generation following training, these methods were compared by correlating EBV with phenotypes corrected for fixed effects, selecting the top 30 individuals based on EBV and evaluating their mean phenotype, and by regressing phenotypes on EBV.

Results

Using high-density SNP genotypes increased accuracies of EBV up to two-fold for selection at an early age and by up to 88% for selection at a later age. Accuracy increases at an early age can be mostly attributed to improved estimates of parental EBV for shell quality and egg production, while for other egg quality traits it is mostly due to improved estimates of Mendelian sampling effects. A relatively small number of markers was sufficient to explain most of the genetic variation for egg weight and body weight.     

Context-dependent development of sexual ornamentation: implications for a trade-off between current and future breeding efforts

Allocation of resources into the development of sexual displays is determined by a trade-off between the competing demands of current reproduction and self-maintenance. When reproduction overlaps with acquisition of sexual ornamentation, such as in birds with a yearly post-breeding moult, such a trade-off can be expressed in elaboration of sexual traits used in subsequent matings. In turn, selection for elaboration of sexual ornaments should favour resolution of this trade-off through a modification of the ornaments' development, resulting in variable and life history-dependent development of sexual displays. Here we examined a novel hypothesis that the trade-off between current reproduction and development of sexual ornamentation in the house finch (Carpodacus mexicanus) can be mediated by the shared effects of prolactin - a pituitary hormone that regulates both parental care and moult in this species. We compared developmental variation in sexual ornamentation between breeding, nonbreeding, and juvenile males and examined the relative contribution of residual levels of prolactin and individual condition during moult to the acquisition of sexual ornamentation. Males that invested heavily in parental care entered post-breeding moult in lower condition and later in the season, but their higher plasma prolactin was associated with shorter and more intense moult ultimately resulting in equal or greater elaboration of sexual ornamentation compared with nonparental males. Elaboration of sexual ornamentation of nonparental males that entered moult in greater condition, but with lower prolactin, was produced by longer and earlier moult and by lesser overlap in moult between sexual ornaments. Ornamentation of juvenile males that acquire sexual ornamentation for the first time was closely associated with physiological condition during moult. We discuss the implications of such context-dependent ontogenies of sexual ornamentation and resulting differences in condition-dependence of sexual traits across life history stages on the evolution of female preference for elaborated sexual displays.