Gene expression differences in the methionine remethylation and transsulphuration pathways under methionine restriction and recovery with D,L-methionine or D,L-HMTBA in meat-type chickens.

This study examined the molecular mechanisms of methionine pathways in meat-type chickens where birds were provided with a diet deficient in methionine from 3 to 5 weeks of age. The birds on the deficient diet were then provided with a diet supplemented with either D,L-methionine or D,L-HMTBA from 5 to 7 weeks. The diet of the control birds was supplemented with L-methionine from hatch till 7 weeks of age. We studied the mRNA expression of methionine adenosyltransferase 1, alpha, methionine adenosyltransferase 1, beta, 5-methyltetrahydrofolate-homocysteine methyltransferase, 5-methyltetrahydrofolate-homocysteine methyltransferase reductase, betaine-homocysteine S-methyltransferase, glycine N-methyltransferase, S-adenosyl-L-homocysteine hydrolase and cystathionine beta synthase genes in the liver, duodenum, Pectoralis (P.) major and the gastrocnemius muscle at 5 and 7 weeks. Feeding a diet deficient in dietary methionine affected body composition. Birds that were fed a methionine-deficient diet expressed genes that indicated that remethylation occurred via the one-carbon pathway in the liver and duodenum; however, in the P. major and the gastrocnemius muscles, gene expression levels suggested that homocysteine received methyl from both folate and betaine for remethylation. Birds who were switched from a methionine deficiency diet to one supplemented with either D,L-methionine or D,L-HMTBA showed a downregulation of all the genes studied in the liver. However, depending on the tissue or methionine form, either folate or betaine was elicited for remethylation. Thus, mRNA expressions show that genes in the remethylation and transsulphuration pathways were regulated according to tissue need, and there were some differences in the methionine form.

Genetic relationship between leg problems and bone quality traits in a random mating broiler population.

We herein report the genetic association between leg problems and bone quality traits in a random mating broiler control population. The leg problem traits were valgus (VL), varus (VR), and tibial dyschondroplasia (TD), and that of bone quality were shank weight (SW), shank length (SL), shank diameter (SDIAM), tibia weight (TW), tibia length (TL), tibia diameter (TDIAM), tibia density (TDEN), tibia breaking strength (TBS), tibia mineral density (TMD), tibia mineral content (TMC), and tibia ash content (TAC). A threshold-linear mixed model, implemented via a Bayesian approach, was employed for the joint analysis of the traits. Genetic correlations of leg problems with bone quality traits ranged from -0.06 to 0.11 suggesting that genetic relationship between leg problems and quality is weak, and management strategies could better alleviate leg problems than genetic improvement.

Genetic analysis of bone quality traits and growth in a random mating broiler population.

We report the genetic relationship between growth and bone quality traits in a random mating broiler control population. Traits studied were growth rates from week 0 to 4 [body weight gain (BWG) 0 to 4], from week 0 to 6 (BWG 0 to 6), and residual feed intake (RFI) from week 5 to 6 (RFI 5 to 6). Bone quality traits were obtained at 6 weeks of age. These traits were shank weight (SW), shank length (SL), shank diameter (SDIAM), tibia weight (TW), tibia length (TL), and tibia diameter (TDIAM). Likewise, tibia was used to obtain the tibia density (TDEN), tibia breaking strength (TBS), tibia mineral density (TMD), tibia mineral content (TMC), and tibia ash content (TAC). At the phenotypic level, growth traits were positively correlated with most of the bone quality traits except with TDEN and TAC which tended to show unfavorable associations (-0.04 to -0.31). Heritability of bone quality traits ranged from 0.08 to 0.54. The additive genetic associations of growth traits with weight, length, and diameter of shank and tibia were positive (0.37 to 0.80). A similar pattern was observed with TMD and TMC (0.06 to 0.65). In contrast, growth traits showed unfavorable genetic associations with TDEN, TBS, and TAC (-0.03 to -0.18). It was concluded that bone quality traits have an additive genetic background and they can be improved by means of genetic tools. It appears that selection for growth is negatively correlated with some traits involved in the integrity, health, and maturity of leg bones.

Genetic analysis of leg problems and growth in a random mating broiler population.

Improvement in growth has been widely reported as the cause of increased incidence of leg problems in broiler chickens. We report herein the genetic relationship between growth and leg problems in a random mating broiler control population. The traits studied were valgus (VL), varus (VR), and tibial dyschondroplasia (TD), which were expressed on a binary scale of 0 (normal) and 1 (abnormal); growth rates from 0 to 4 wk (BWG 0-4) and from 0 to 6 wk of age (BWG 0-6); and residual feed intake from 5 to 6 wk of age (RFI 5-6). A threshold-linear mixed model was employed for the joint analysis of the categorical and linear traits. Incidences of VL, VR, and TD were 26, 4, and 2%, respectively. Heritability of leg problems ranged from 0.11 to 0.13. Phenotypic correlations alluded to an unfavorable relationship between growth and leg problems; however, the genetic relationship between growth and leg problems was extremely weak, ranging from 0.01 to 0.08. There is, therefore, a basis for genetic improvement in leg problems. However, improved management practices would also be important to reduce incidence of leg problems in broiler chickens.

Transcriptomic analysis of genes in the nitrogen recycling pathway of meat-type chickens divergently selected for feed efficiency.

The understanding of the dynamics of ammonia detoxification and excretion in uricotelic species is lagging behind ureotelic species. The relative expression of genes involved in nitrogen recycling and feed efficiency in chickens is unknown. The objective of this study was to investigate the transcriptomics differences in key genes in the nitrogen (N) metabolism and purine biosynthesis pathway in a chicken population divergently selected for low (LRFI) or high (HRFI) residual feed intake at days 35 and 42 using duodenum, liver, pectoralis major (P. major) and kidney. There was a significant positive correlation between RFI and fecal N. The purine salvage pathway was activated in the LRFI compared with HRFI at days 42. The birds in the LRFI population attained greater feed efficiency by having lower FI, increasing their protein retention and producing adequate glutamine to maintain growth compared with the HRFI line. To maintain growth, excess N is deaminated mostly to generate purine nucleotides. Generating purine nucleotides primarily from the purine biosynthesis pathway is energetically costly, and to preserve energy, they preferentially generate nucleotides from the purine salvage pathway. The LRFI birds need to generate sufficient nucleotides to maintain growth despite reduced FI that then results in reduced fecal N.

Multitissue transcriptomics demonstrates the systemic physiology of methionine deficiency in broiler chickens.

Methionine (Met) supplementation is common practice in broilers to support nutrition, yet there are gaps in the understanding of its role in systemic physiology. Furthermore, several different Met sources are available that may have different physiological effects. This study evaluated the mode of action of Met deficiency (no Met-supplementation) and supplementation (0.25% DL- or L-Met, 0.41% liquid methionine hydroxy analog-free acid (MHA-FA)), and of Met source (DL-, L- or MHA-FA) in broiler chickens, via host transcriptomics. Biological pathway activation modeling was performed to predict the likely phenotypic effects of differentially expressed genes (DEGs) in tissue samples from the jejunum, liver and breast obtained at 10, 21 and 34/35 d of age from three experiments in a combined analysis. Animal performance data showed that Met deficiency reduced BW, daily BW gain, daily feed intake, and breast yield, and increased feed conversion ratio in all experiments (P < 0.05). Effects of Met deficiency on gene expression were least evident in the jejunum and most evident in the liver and breast, as evidenced by the number of DEG and activated pathways. Activated pathways suggested Met deficiency was associated with inhibited protein turnover, gut barrier integrity, and adaptive immunity functions in the jejunum, that predicted reduced breast yield. There was an interaction with age; in Met-deficient birds, there were 333 DEGs in the jejunum of starter vs finisher birds suggesting young birds were more sensitive to Met deficiency than older birds. In the liver, Met deficiency activated pathways associated with lipid turnover, amino acid metabolism, oxidative stress, and the immune system, whereas in breast, it activated pathways involved in metabolic regulation, hemostasis, the neuronal system, and oxidative stress, again predicting a negative impact on breast yield. In the starter phase, supplementation with DL-Met compared to MHA-FA inhibited gamma-aminobutyric acid activity and oxidative stress in breast tissue. When data from all tissues were integrated, increased expression of a liver gene (ENSGALG00000042797) was found to be correlated with the expression of several genes that best explained variation due to the Met deficiency in jejunum and breast muscle. Some of these genes were involved in anti-oxidant systems. Overall, the findings indicate that impaired growth performance due to Met deficiency results from an array of tissue-specific molecular mechanisms in which oxidative stress plays a key systemic role. Young birds are more sensitive to Met-deficiency and DL-Met was a preferential source of Met than L- or MHA-FA during the starter phase.

Genetic evaluation for growth, body composition, feed efficiency, and leg soundness.

A multiple trait linear-threshold model was used to analyze data for BW, residual feed intake, breast meat yield (BMY), conformation score (CS), area (AR), tibial dyschondroplasia, valgus, varus, and rotated tibia. Leg soundness traits were considered as binary responses. At the liability scale, the model included the fixed effects of flock-week of hatch, and sex of the bird and the genetic additive effect, and the error terms as random. The random maternal effect was included in the model only for BW. A full Bayesian implementation of the model was straightforward even though large number of traits and missing records were present. As expected, binary traits have the lowest heritability. Heritability ranged from 0.12 for tibial dyschondroplasia to 0.44 for BMY. Genetic correlations between BW and conformation traits were moderate to high. Residual feed intake was negatively correlated with BW (-0.15), AR (-0.13), BMY (-0.04), and CS (-0.12). Genetic correlation between leg soundness traits were generally low and negative with the exception of the correlation between valgus and varus (-0.70) and between varus and rotated tibia (-0.39). Genetic correlations between BW, BMY, CS, and AR with leg soundness traits were in general negative and low in magnitude. Thus, selecting for improved leg soundness will have minimal effect on BW and carcass traits. Furthermore, genetic improvement in residual feed intake will result in improvements in carcass traits. Simultaneous genetic improvement in leg soundness and innovative husbandry practices should improve broiler welfare without significant adverse effects on production efficiency.

Genotype by environment interaction in response to cold stress in a composite beef cattle breed.

Extreme weather conditions such as cold stress influence the productivity and survivability of beef cattle raised on pasture. The objective of this study was to identify and evaluate the extent of the impact of genotype by environment interaction due to cold stress on birth weight (BW) and weaning weight (WW) in a composite beef cattle population. The effect of cold stress was modelled as the accumulation of total cold load (TCL) calculated using the Comprehensive Climate Index units, considering three TCL classes defined based on temperature: less than -5°C (TCL5), -15°C (TCL15) and -25°C (TCL25). A total of 4221 and 4217 records for BW and WW, respectively, were used from a composite beef cattle population (50% Red Angus, 25% Charolais and 25% Tarentaise) between 2002 and 2015. For both BW and WW, a univariate model (ignoring cold stress) and a reaction norm model were implemented. As cold load increased, the direct heritability slightly increased in both BW and WW for TCL5 class; however, this heritability remained consistent across the cold load of TCL25 class. In contrast, the maternal heritability of BW was constant with cold load increase in all TCL classes, although a slight increase of maternal heritability was observed for TCL5 and TCL15. The direct and maternal genetic correlation for BW and maternal genetic correlation for WW across different cold loads between all TCL classes were high (r > 0.99), whereas the lowest direct genetic correlations observed for WW were 0.88 for TCL5 and 0.85 for TCL15. The Spearman rank correlation between the estimated breeding value of top bulls (n = 79) using univariate and reaction norm models across TCL classes showed some re-ranking in direct and maternal effects for both BW and WW particularly for TCL5 and TCL15. In general, cold stress did not have a big impact on direct and maternal genetic effects of BW and WW.

The Effect of Increased Temperatures on Viability, Morphology, Infectivity, and Development of Eimeria tenella.

Commonly found in backyard and commercial poultry production, coccidiosis, caused by Eimeria species, presents a self-limiting intestinal infection based on the number of ingested oocysts. Heat stress (HS) is one of the major environmental stressors in poultry, predisposing broiler chickens to immunosuppression and rendering them susceptible to diseases. There are suggestions that HS reduces Eimeria oocyst shedding in chickens; however, the relationship between HS and coccidiosis is not well elucidated. The objective of this study was to investigate the effect of temperature on viability, morphology, infectivity, and development of Eimeria tenella in vitro, and merozoite production and oocyst shedding in vivo. In vitro exposure of sporozoites to 55 C for at least 60 min reduced sporozoites viability as shown by morphological changes and rendering them unable to invade Mardin-Darbi bovine kidney (MDBK) cells. Intracellular development of merozoites was significantly reduced by an increase in 2 C in the optimal temperature of incubation in vitro. Most importantly, the induction of HS in the live chickens caused significantly lower lesion scores, reduced merozoite production, and oocyst shedding, resulting in a much less severe disease outcome.

Ant colony optimization as a method for strategic genotype sampling.

A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK(P)), the probability of assigning true alleles (AK(G)) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A(-1)). Comparisons of these two methods showed that ACO yielded an increase in AK(P) ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A(-1), with different pedigree sizes and structures.

Genetic determination of the onset of heat stress on daily milk production in the US Holstein cattle.

Existence of individual variation in the onset of heat stress for daily milk yield of dairy cows was assessed. Data included 353,376 test-day records of 38,383 first-parity Holsteins from a random sample of US herds. Three hierarchical models were investigated. Model 1 inferred the value of a temperature-humidity index (THI) at which mean yield began to decline as well as the extent of that decline. Model 2 assumed individual variation in yield decline beyond a common THI threshold. Model 3 additionally assumed individual variation for the onset of heat stress. Deviance information criteria indicated the superiority of model 3 over model 2. For model 2, genetic correlation between milk yield in the absence of heat stress and the THI threshold for heat stress was -0.4 (0.11) [marginal posterior mean (marginal posterior standard deviation)]. For model 3, genetic correlations were -0.53 (0.05) between milk yield and THI threshold and -0.62 (0.08) between milk yield and yield decay beyond the THI threshold. Total standard deviation (sum of additive genetic and permanent environmental standard deviations) for the THI threshold was 3.95 (0.06), and more than half of that variation had an additive genetic origin [56% (5%)]. Because of the high genetic correlation [0.95 (0.03)] between yield decay and THI threshold with model 3, using only one of them as a selection criterion for heat tolerance would modify the other in the desired direction.

BMP4 promotes formation of primitive vascular networks in human embryonic stem cell-derived embryoid bodies.

The vasculature develops primarily through two processes, vasculogenesis and angiogenesis. Although much work has been published on angiogenesis, less is known of the mechanisms regulating the de novo formation of the vasculature commonly called vasculogenesis. Human embryonic stem cells (hESC) have the capability to produce all of the cells of the body and have been used as in vitro models to study the molecular signals controlling differentiation and vessel assembly. One such regulatory molecule is bone morphogenetic protein-4 (BMP4), which is required for mesoderm formation and vascular/hematopoietic specification in several species. However, hESC grown in feeder-free conditions and treated with BMP4 differentiate into a cellular phenotype highly expressing a trophoblast gene profile. Therefore, it is unclear what role, if any, BMP4 plays in regulating vascular development in hESC. Here we show in two National Institutes of Health-registered hESC lines (BG02 and WA09) cultured on a 3D substrate of Matrigel in endothelial cell growth medium-2 that the addition of BMP4 (100 ng/ml) for 3 days significantly increases the formation and outgrowth of a network of cells reminiscent of capillary-like structures formed by mature endothelial cells (P<0.05). Analysis of the expression of 45 genes by quantitative real time-polymerase chain reaction on a low-density array of the entire culture indicates a rapid and significant downregulation of pluripotent and most ectodermal markers with a general upregulation of endoderm, mesoderm, and endothelial markers. Of the genes assayed, BMPR2 and RUNX1 were differentially affected by exposure to BMP4 in both cell lines. Immunocytochemistry indicates the morphological structures formed were negative for the mature endothelial markers CD31 and CD146 as well as the neural marker SOX2, yet positive for the early vascular markers of endothelium (KDR, NESTIN) and smooth muscle cells (alpha-smooth muscle actin [alpha SMA]). Together, these data suggest BMP4 can enhance the formation and outgrowth of an immature vascular system.

Effect of heat stress on amino acid digestibility and transporters in meat-type chickens.

The present study was conducted to investigate the effect of heat stress (HS) on performance, digestibility, and molecular transporters of amino acids in broilers. Cobb 500 chicks were raised from hatch till 13 d in floor pens. At d 14, 48 birds were randomly and equally divided between a control group (25°C) and a HS treatment group (35°C). Birds in both treatment classes were individually caged and fed ad libitum on a diet containing 18.7% CP and 3,560 Kcal ME/Kg. Five birds per treatment at one and 12 d post treatment were euthanized and the Pectoralis major (P. major) and ileum were sampled for gene expression analysis. At d 33, ileal contents were collected and used for digestibility analysis. Broilers under HS had reduced growth and feed intake compared to controls. Although the apparent ileal digestibility (AID) was consistently higher for all amino acids in the HS group, it was not significant except for hydroxylysine. The amino acid consumption and retention were significantly lower in the HS group when compared to the control group. Meanwhile, the retention of amino acids per BWG was higher in the HS group when compared to the control group except for hydroxylysine and ornithine. The dynamics of amino acid transporters in the P. major and ileum was influenced by HS. In P. major and ileum tissues at d one, transporters SNAT1, SNAT2, SNAT7, TAT1, and b0,+AT, were down-regulated in the HS group. Meanwhile, LAT4 and B0AT were down-regulated only in the P. major in the treatment group. The amino acid transporters B0AT and SNAT7 at d 12 post HS were down-regulated in the P. major and ileum, but SNAT2 was down-regulated only in the ileum and TAT1 was down-regulated only in the P. major compared with the control group. These changes in amino acid transporters may explain the reduced growth in meat type chickens under heat stress.

Genomic prediction of continuous and binary fertility traits of females in a composite beef cattle breed.

Reproduction efficiency is a major factor in the profitability of the beef cattle industry. Genomic selection (GS) is a promising tool that may improve the predictive accuracy and genetic gain of fertility traits. There is a wide range of traits used to measure fertility in dairy and beef cattle including continuous (days open), discrete (pregnancy status), and count (number of inseminations) responses. In this study, a joint analysis of age of puberty (AOP), age at first calving (AOC), and the heifer pregnancy status (HPS) was performed. Data used in this study consisted of records from 1,365 Composite Gene Combination (CGC; 50% Red Angus, 25% Charolais, 25% Tarentaise) first parity females born between 2002 and 2011. The pedigree file included 5,374 animals. A total of 3,902 animals were genotyped with different density SNP chips (3K to 50K SNP). Animals genotyped with low-density arrays were imputed to higher density (BovineSNP50 BeadChip) using FImpute. Data were analyzed using univariate and multivariate classical quantitative models (pedigree based) and univariate genomic approaches. For the latter, 3 different Bayesian methods (BayesA, BayesB, and BayesCπ) were implemented and compared. Estimates of heritabilities using univariate and multivariate analyses based on pedigree relationships ranged between 0.03 (for AOC) to 0.2 (AOP). Heritability of pregnancy status was 0.15 and 0.09 using the univariate and multivariate analyses, respectively. Genetic correlation between pregnancy status and the other 2 traits was low being 0.08 with age at puberty and -0.10 with age at first calving. Heritability estimates were slightly higher using genomic rather than average additive relationships. The accuracy of genomic prediction was similar across the 3 Bayesian methods with higher accuracies for age of puberty than the age at first calving likely due to the higher heritability of the former. The prediction of the binary pregnancy status measured using the area under the curve increased by 27% to 29% compared to a random classifier. Due to the small size of the data, all estimates have large posterior standard deviations and results should be interpreted with caution.

Random regression models for male and female fertility evaluation using longitudinal binary data.

A longitudinal Bayesian threshold analysis of insemination outcomes was carried out using 2 random regression models with 3 (Model 1) and 5 (Model 2) parameters to model the additive genetic values at the liability scale. All insemination events of first-parity Holstein cows were used. The outcome of an insemination event was treated as a binary response of either a success (1) or a failure (0). Thus, all breeding information for a cow, including all service sires, was included, thereby allowing for a joint evaluation of male and female fertility. An edited data set of 369,353 insemination records from 210,373 first-lactation cows was used. On the liability scale, both models included the systematic effects of herd-year, month of insemination, technician, and regressions on age of service sire and milk yield during the first 100 d of lactation. The random effects in the model were the 3 or 5 random regression coefficients specific to each cow, the permanent effect of the cow, and the service sire effect. Using Model 1, the estimated heritability of an insemination outcome decreased from 0.035 at d 50 to 0.032 at d 140 and then increased continuously with DIM. The genetic correlations for insemination success at different time points ranged from 0.83 to 0.99, and their magnitude decreased with an increase in the interval between inseminations. A similar trend was observed for heritability and genetic correlations using Model 2. However, the average estimate of heritability was much higher (0.058) than those obtained using Model 1 or a repeatability model. In addition, the estimated genetic correlations followed the same trend as Model 1, but were lower and with a higher rate of decrease when the interval between inseminations increased. The posterior mean of service sire variance was 0.01 for both models, and permanent environmental variance was 0.05 and 0.02 for Models 1 and 2, respectively. Model comparison based on the Bayes factor indicated that Model 1 was more plausible, given the data.

Multi-generational imputation of single nucleotide polymorphism marker genotypes and accuracy of genomic selection.

Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval increases, the imputation accuracies decay, although not at an alarming rate. In absence of updating of the reference population, accuracy of GEBVs decays substantially in one or two generations at the rate of 20% to 25% per generation. When the reference population is updated by 1% or 5% every generation, the decay in accuracy was 8% to 11% after seven generations using true and imputed genotypes. These results indicate that imputed genotypes provide a viable alternative, even after several generations, as long the reference and training populations are appropriately updated to reflect the genetic change in the population.

Longitudinal multiple-trait versus cumulative single-trait analysis of male and female fertility and hatchability in chickens.

The objective of the current study was to compare the performances of a longitudinal multipletrait (MT) and cumulative single-trait (ST) best linear unbiased prediction (BLUP) analyses for eggs set (E), percentage fertility (F), and percentage hatched of fertile eggs (H) based on rank correlations of hens and roosters (ROO). Longitudinal data consisted of weekly records, and the ST analysis used cumulative records of the 3 traits. Comparisons were carried out using simulated data, in which true values assigned during the simulation were compared with estimates obtained from MT and ST analyses. Two methods were used to calculate breeding values and ROO effects. Weekly E records equal to zero were assumed as valid records, and missing weekly F and H records were predicted in MT analysis. However, missing F and H were not included in the cumulative record. Weekly E, F, and H records were converted to a cumulative record following a procedure used by a commercial broiler company. Further, ST models were developed to evaluate hens and ROO separately as currently practiced in the industry. There was virtually no difference in hen rank correlations between true and predicted breeding values obtained from MT (0.64) and ST (0.62) analyses for E, thus suggesting that hens would rank similarly when weekly or cumulative data were used for genetic evaluation of E. With ST analysis, rank correlations between true and estimated hen breeding values decreased, compared with MT analysis, by 74 and 75% for F and H, respectively. For F (H), the rank correlation between true and estimated ROO effects were 0.64 (0.67) and 0.17 (0.12) with MT and ST analyses, respectively. The results suggested that longitudinal MT BLUP, which handles missing records, was better at estimating true hen and ROO effects than ST BLUP. Therefore, it was recommended that the MT BLUP method be used for genetic evaluation of hens and ROO for E, F, and H.

Genetic properties of residual feed intakes for maintenance and growth and the implications of error measurement.

A procedure for estimating residual feed intake (RFI) based on information used in feeding studies is presented. Koch's classical model consists of using fixed regressions of feed intake on metabolic BW and growth, and RFI is obtained as the deviation between the observed feed intake and the expected intake for an individual with a given weight and growth rate. Estimated RFI following such a procedure intrinsically suffers from the inability to separate true RFI from the sampling error. As the latter is never equal to 0, estimated RFI is always biased, and the magnitude of such bias depends on the ratio between the true RFI variance and the residual variance. Additionally, the classical approach suffers from its inability to dissect RFI into its biological components, being the metabolic efficiency (maintaining BW) and growth efficiency. To remedy these problems we proposed a procedure that directly models the individual animal variation in feed efficiency used for body maintenance and growth. The proposed model is an extension of Koch's procedure by assuming animal-specific regression coefficients rather than population-level parameters. To evaluate the performance of both models, a data simulation was performed using the structure of an existing chicken data set consisting of 2,289 records. Data was simulated using 4 ratios between the true RFI and sampling error variances (1:1, 2:1, 4:1, and 10:1) and 5 correlation values between the 2 animal-specific random regression coefficients (-0.95, -0.5, 0, 0.5, and 0.95). The results clearly showed the superiority of the proposed model compared to Koch's procedure under all 20 simulation scenarios. In fact, when the ratio was 1:1 and the true genetic correlation was equal to -0.95, the correlation between the true and estimated RFI for animals in the top 20% was 0.60 and 0.51 for the proposed and Koch's models, respectively. This is an 18% superiority for the proposed model. For the bottom 20% of animals in the ranking, the superiority was 17%. Even when the ratio of variances was 10:1, the superiority of the proposed model was around 6%.

Simulation study of teat score in first-parity Gelbvieh cows: parameter estimation.

Teat scores from 9,598 first-parity Gelbvieh cows were used to investigate the adequacy of grouping approaches to decrease score misclassifications or inconsistencies as well as to simplify the data collection process. The procedure was tested using simulated data and then validated using teat score records of Gelbvieh cattle. First-parity cows were considered to be 4 yr of age or younger at first calving, did not have multiple records within 280 d, and were at least 50% Gelbvieh. Producers scored cows within 24 h of parturition. Teat score, a subjective measure of teat size, ranged from 0 (very large) to 50 (very small). A linear mixed model that included herd-year, month of calving, and age at calving as systematic effects; regression on the percentage of Gelbvieh; and additive breeding values (BV) and residual as random effects was used to generate the data. Simulated data were analyzed using one of three scoring methods: all values (S50), 10 classes (S10), and five classes (S5). The 10 classes were formed by subdividing every five scores into a single class starting at score zero. Similarly, the five classes were formed by combining every 10 scores into one class. The average Pearson correlations, based on five replicates, between the true and estimated BV (systematic effects) were 0.36 (0.85), 0.35 (0.89), and 0.32 (0.87) using S50, S10, and S5, respectively. Average correlations between estimated BV (systematic effects) were 0.97 (0.95), 0.89 (0.92), and 0.92 (0.97) based on S50 and S10, S50 and S5, and S10 and S5, respectively. Field data were used to validate the simulation procedure. The field data were categorized into 10 classes (F10) and five classes (F5) as described for the simulated data. Pearson correlations between estimated BV (systematic effects) were 0.99 (0.93), 0.93 (0.88), and 0.93 (0.96), based on F50 with F10, F50 with F5, and F10 with F5, respectively. The extremely high correlations between predicted BV based on S50, S10, S5, F50, F10, with F5 suggest that a simplified score classification method could be adopted without compromising the expected genetic progress for the trait under consideration. Furthermore, the difference in corresponding Pearson correlations across the field and simulated data might suggest the presence of some inconsistencies or misclassifications of the actual scoring system.

Comparison of methods for handling censored records in beef fertility data: simulation study.

A simulation study was conducted to compare methods for handling censored records for days to calving in beef cattle data. Days to calving was defined as the time, in days, between when a bull is turned out in the pasture and the subsequent parturition. Simulated data were generated to have data structure and genetic relationships similar to an available field data set. Records were simulated for 33,176 daughters of 4,238 sires. Data were simulated using a mixed linear model that included the fixed effects of contemporary group and sex of calf, linear and quadratic covariates for age at mating, and random effects of animal and residual error. Two methods for handling censored records were evaluated, and two censoring rates of 12 and 20% were applied to assess the influence of higher censoring rates on inferences. Censored records were assigned penalty values on a within-contemporary group basis under the first method (DCPEN). Under the second method (DCSIM), censored records were drawn from their respective predictive distributions. A Bayesian approach via Gibbs sampling was used to estimate variance components and predict breeding values. Posterior means (PM) and standard deviations (SD) of additive genetic variance for DCPEN at 12 and 20% censoring were 23.2 (3.7) and 21.0 (3.6), respectively, whereas the same estimates for DCSIM at 12 and 20% censoring were 23.7(3.3) and 21.9 (3.4), respectively. In all cases, the true value of the genetic variance was within the high posterior density (HPD) interval (95%). The PM (SD) of residual variance for DCPEN at 12 and 20% censoring were 415.7 (4.7) and 440.0 (4.8) respectively, whereas the same estimates for DCSIM at 12 and 20% censoring were 371.0 (4.3) and 365.4 (4.4), respectively. The true value of the residual variance was within the HPD (95%) for DCSIM, but it was outside this interval for DCPEN at both censoring rates, indicating a systematic bias for this parameter. Bayes Factor and Deviance Information Criteria were used for model comparisons, and both criteria indicated the superiority of the DCSIM method. However, little difference was observed between the two methods for correlations between true breeding values and posterior means of animal effects for sires, indicating that no major reranking of sires would be expected. This finding suggests that either censored data handling technique can be successfully used in a genetic evaluation for days to calving.