Evaluation of genotyping concordance for commercial bovine SNP arrays using quality-assurance samples

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele 'dropout' (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome-wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.

GENOMICS SYMPOSIUM: Using genomic approaches to uncover sources of variation in age at puberty and reproductive longevity in sows

Genetic variants associated with traits such as age at puberty and litter size could provide insight into the underlying genetic sources of variation impacting sow reproductive longevity and productivity. Genomewide characterization and gene expression profiling were used using gilts from the University of Nebraska-Lincoln swine resource population ( = 1,644) to identify genetic variants associated with age at puberty and litter size traits. From all reproductive traits studied, the largest fraction of phenotypic variation explained by the Porcine SNP60 BeadArray was for age at puberty (27.3%). In an evaluation data set, the predictive ability of all SNP from high-ranked 1-Mb windows (1 to 50%), based on genetic variance explained in training, was greater (12.3 to 36.8%) compared with the most informative SNP from these windows (6.5 to 23.7%). In the integrated data set ( = 1,644), the top 1% of the 1-Mb windows explained 6.7% of the genetic variation of age at puberty. One of the high-ranked windows detected (SSC2, 12-12.9 Mb) showed pleiotropic features, affecting both age at puberty and litter size traits. The RNA sequencing of the hypothalami arcuate nucleus uncovered 17 differentially expressed genes (adjusted < 0.05) between gilts that became pubertal early (<155 d of age) and late (>180 d of age). Twelve of the differentially expressed genes are upregulated in the late pubertal gilts. One of these genes is involved in energy homeostasis (), a function in which the arcuate nucleus plays an important contribution, linking nutrition with reproductive development. Energy restriction during the gilt development period delayed age at puberty by 7 d but increased the probability of a sow to produce up to 3 parities ( < 0.05). Identification of pleotropic functional polymorphisms may improve accuracy of genomic prediction while facilitating a reduction in sow replacement rates and addressing welfare concerns.

Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multibreed population

Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was transformed from the USMARC scores to corresponding -scores from the standard normal distribution based on the incidence rate of the USMARC scores. Breed fraction covariates were included to estimate breed differences. Heritability estimates (SE) for BWT direct, CD direct, BWT maternal, and CD maternal were 0.34 (0.10), 0.29 (0.10), 0.15 (0.08), and 0.13 (0.08), respectively. Calving difficulty direct breed effects deviated from Angus ranged from -0.13 to 0.77 and maternal breed effects deviated from Angus ranged from -0.27 to 0.36. Hereford-, Angus-, Gelbvieh-, and Brangus-sired calves would be the least likely to require assistance at birth, whereas Chiangus-, Charolais-, and Limousin-sired calves would be the most likely to require assistance at birth. Maternal breed effects for CD were least for Simmental and Charolais and greatest for Red Angus and Chiangus. Results showed that the diverse biological types of cattle have different effects on both BWT and CD. Furthermore, results provide a mechanism whereby beef cattle producers can compare EBV for CD direct and maternal arising from disjoined and breed-specific genetic evaluations.

Quantitative trait locus mapping and functional genomics of an organophosphate resistance trait in the western corn rootworm, Diabrotica virgifera virgifera

The western corn rootworm, Diabrotica virgifera virgifera, is an insect pest of corn and population suppression with chemical insecticides is an important management tool. Traits conferring organophosphate insecticide resistance have increased in frequency amongst D. v. virgifera populations, resulting in the reduced efficacy in many corn-growing regions of the USA. We used comparative functional genomic and quantitative trait locus (QTL) mapping approaches to investigate the genetic basis of D. v. virgifera resistance to the organophosphate methyl-parathion. RNA from adult methyl-parathion resistant and susceptible adults was hybridized to 8331 microarray probes. The results predicted that 11 transcripts were significantly up-regulated in resistant phenotypes, with the most significant (fold increases ≥ 2.43) being an α-esterase-like transcript. Differential expression was validated only for the α-esterase (ST020027A20C03), with 11- to 13-fold greater expression in methyl-parathion resistant adults (P < 0.05). Progeny with a segregating methyl-parathion resistance trait were obtained from a reciprocal backcross design. QTL analyses of high-throughput single nucleotide polymorphism genotype data predicted involvement of a single genome interval. These data suggest that a specific carboyxesterase may function in field-evolved corn rootworm resistance to organophosphates, even though direct linkage between the QTL and this locus could not be established.

Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII and advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Angus, Charolais, Gelbvieh, Simmental, Limousin and Composite MARC III. Heterosis was further estimated by proportions of British × British (B × B), British × Continental (B × C) and Continental × Continental (C × C) crosses and by breed-specific combinations. Model 1 fitted fixed covariates for heterosis within biological types while Model 2 fitted random breed-specific combinations nested within the fixed biological type covariates. Direct heritability estimates (SE) for birth, weaning ,and yearling weight for Model 1 were 0.42 (0.04), 0.22 (0.03), and 0.39 (0.05), respectively. The direct heritability estimates (SE) of birth, weaning, and yearling weight for Model 2 were the same as Model 1, except yearling weight heritability was 0.38 (0.05). The B × B, B × C, and C × C heterosis estimates for birth weight were 0.47 (0.37), 0.75 (0.32), and 0.73 (0.54) kg, respectively. The B × B, B × C, and C × C heterosis estimates for weaning weight were 6.43 (1.80), 8.65 (1.54), and 5.86 (2.57) kg, respectively. Yearling weight estimates for B × B, B × C, and C × C heterosis were 17.59(3.06), 13.88 (2.63), and 9.12 (4.34) kg, respectively. Differences did exist among estimates of breed-specific heterosis for weaning and yearling weight, although the variance component associated with breed-specific heterosis was not significant. These results illustrate that there are differences in breed-specific heterosis and exploiting these differences can lead to varying levels of heterosis among mating plans.

Genome-wide analysis of TNF-alpha response in pigs challenged with porcine circovirus 2b

Tumor necrosis factor alpha (TNF-α) is a pro-inflammatory cytokine with a role in activating adaptive immunity to viral infections. By inhibiting the capacity of plasmacytoid dendritic cells to produce interferon-α and TNF-α, porcine circovirus 2 (PCV2) limits the maturation of myeloid dendritic cells and impairs their ability to recognize viral and bacterial antigens. Previously, we reported QTL for viremia and immune response in PCV2-infected pigs. In this study, we analyzed phenotypic and genetic relationships between TNF-α protein levels, a potential indicator of predisposition to PCV2 co-infection, and PCV2 susceptibility. Following experimental challenge with PCV2b, TNF-α reached the peak at 21 days post-infection (dpi), at which time a difference was observed between pigs that expressed extreme variation in viremia and growth (P < 0.10). A genome-wide association study (n = 297) revealed that genotypes of 56,433 SNPs explained 73.9% of the variation in TNF-α at 21 dpi. Major SNPs were identified on SSC8, SSC10 and SSC14. Haplotypes based on SNPs from a SSC8 (9 Mb) 1-Mb window were associated with variation in TNF-α (P < 0.02), IgG (P = 0.05) and IgM (P < 0.13) levels at 21 dpi. Potential overlap of regulatory mechanisms was supported by the correlations between genomic prediction values of TNF-α and PCV2 antibodies (21 dpi, r > 0.22), viremia (14-21 dpi, P > 0.29) and viral load (r = 0.31, P < 0.0001). Characterization of the QTL regions uncovered genes that could influence variation in TNF-α levels as well as T- and B-cell development, which can affect disease susceptibility.

The change in differing leukocyte populations during vaccination to bovine respiratory disease and their correlations with lung scores, health records, and average daily gain

Bovine respiratory disease (BRD) is the most economically important disease in U.S. feedlots. Infection can result in morbidity, mortality, and reduced average daily gain. Cheap and reliable genetic methods of prediction and protection from BRD would be highly advantageous to the industry. The immune response may correlate with BRD incidence. Cattle (n = 2,182) were vaccinated against common viral and bacterial pathogens of BRD. Two blood samples were collected, one during booster vaccination and one 21d later, enabling 3 phenotypes for each trait [prebooster (pre), postbooster (post), and delta (post minus pre)]. From the blood samples innate and adaptive responses [counts of white blood cells (WBC), neutrophils, lymphocytes, monocytes, eosinophils, and basophils] were measured. In addition, feedlot ADG and binary traits [health records (HR; 0 = healthy, 1 = ill) and lung scores (LS; collected at harvest; 0 = no lesions, 1 = lesions)] were also recorded. Traits ADG, HR, and LS have all been significantly correlated with infection to BRD. In this investigation we aimed to find correlations between the immune response and ADG, HR, and LS to find an easily measurable trait that would be a good predictor of BRD resistance after vaccination. The results showed an average positive delta for the innate immune response (eosinophils, basophils, neutrophils), whereas the adaptive immune response had an average negative delta (lymphocytes). Overall, we discovered that the immune responses had moderately high heritabilities (h(2); lowest: delta monocytes, 0.21 ± 0.05; greatest: pre lymphocytes: 0.5 ± 0.05), with lymphocytes having the greatest h(2) throughout the study (h(2) ≥ 0.41). All genetic correlations were calculated using bivariate REML models. Although LS did not significantly correlate with any of the immune phenotypes, both ADG (post lymphocytes, -0.24 ± 0.12) and HR (pre eosinophils, -0.67 ± 0.29; delta WBC, -0.5 ± 0.24, and delta lymphocytes, -0.67 ± 0.21) did. All the significant genetic correlations with HR were negative; resistance to BRD appears to be a function of greater delta lymphocytes and WBC. The increase in eosinophils may potentially link its role in decreasing lymphocytes. These results may enable producers to predict if revaccination, quarantine, and breeding of animals is required to reduce the incidence of BRD postvaccination. In addition, immunological phenotypes maybe used to aid genomic selection indices to select animals with greater rates of protection after BRD vaccination.

Genome-wide prediction of age at puberty and reproductive longevity in sows

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1-Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27-28 Mb), SSC8 (36-37 Mb) and SSC12 (1.2-2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities by up to 1.36. The region located on SSC5 harbors non-synonymous alleles in the arginine vasopressin receptor 1A (AVPR1A) gene, a G-protein-coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker-assisted selection programs across populations to increase sow reproductive longevity.

Evolution of starvation resistance in Drosophila melanogaster: measurement of direct and correlated responses to artificial selection

Laboratory selection for resistance to starvation has been conducted under relatively controlled conditions to investigate direct and correlated responses to artificial selection. With regard to starvation resistance, there are three physiological routes by which the trait can evolve: resource accumulation, energy conservation and starvation tolerance. A majority of energetic compounds and macromolecules including triglycerides, trehalose and other sugars, and soluble protein increased in abundance as a result of selection. Movement was additionally investigated with selected males moving less than control males and selected females exhibiting a similar response to selection. Results obtained from this study supported two of the possible evolutionary mechanisms for adaptation to starvation: energy compound storage and conservation. If the response to selection is based on an evolutionarily conserved pattern of genetic correlations (elevated lipid, elevated sugars and reduced movement), then the response to selection is medically relevant and the genetic architecture should be investigated in depth.

Transcriptional profiling of the sperm storage organs of Drosophila melanogaster

The occurrence of female sperm storage across taxa indicates the importance of this complex and dynamic process. Organs responsible for sperm storage (SSOs) and proteins expressed therein, are important in fundamental aspects of reproduction and could play a major role in evolutionary processes such as post-mating sexual selection. Given the essential role of SSOs, it is surprising that the process of sperm storage is so poorly understood. This study investigated the transcriptome of female Drosophila melanogaster SSOs (seminal receptacle and spermathecae). Spermathecae were enriched for proteases and metabolic enzymes while the seminal receptacle was enriched for genes involved in localization, signaling and ion transport. Differences in functional gene categories indicate that these organs play unique roles in sperm storage.

Technical Note: Calculation of standard errors of estimates of genetic parameters with the multiple-trait derivative-free restricted maximal likelihood programs

The multiple-trait derivative-free REML set of programs was written to handle partially missing data for multiple-trait analyses as well as single-trait models. Standard errors of genetic parameters were reported for univariate models and for multiple-trait analyses only when all traits were measured on animals with records. In addition to estimating (co)variance components for multiple-trait models with partially missing data, this paper shows how the multiple-trait derivative-free REML set of programs can also estimate SE by augmenting the data file when not all animals have all traits measured. Although the standard practice has been to eliminate records with partially missing data, that practice uses only a subset of the available data. In some situations, the elimination of partial records can result in elimination of all the records, such as one trait measured in one environment and a second trait measured in a different environment. An alternative approach requiring minor modifications of the original data and model was developed that provides estimates of the SE using an augmented data set that gives the same residual log likelihood as the original data for multiple-trait analyses when not all traits are measured. Because the same residual vector is used for the original data and the augmented data, the resulting REML estimators along with their sampling properties are identical for the original and augmented data, so that SE for estimates of genetic parameters can be calculated.

Estimates of genetic parameters for Holstein cows for test-day yield traits with a random regression cubic spline model

Genetic parameters were estimated with restricted maximum likelihood for individual test-day milk, fat, and protein yields and somatic cell scores with a random regression cubic spline model. Test-day records of Holstein cows that calved from 1994 through early 1999 were obtained from Dairy Records Management Systems in Raleigh, North Carolina, for the analysis. Estimates of heritability for individual test-days and estimates of genetic and phenotypic correlations between test-days were obtained from estimates of variances and covariances from the cubic spline analysis. Estimates were calculated of genetic parameters for the averages of the test days within each of the ten 30-day test intervals. The model included herd test-day, age at first calving, and bovine somatropin treatment as fixed factors. Cubic splines were fitted for the overall lactation curve and for random additive genetic and permanent environmental effects, with five predetermined knots or four intervals between days 0, 50, 135, 220, and 305. Estimates of heritability for lactation one ranged from 0.10 to 0.15, 0.06 to 0.10, 0.09 to 0.15, and 0.02 to 0.06 for test-day one to test-day 10 for milk, fat, and protein yields and somatic cell scores, respectively. Estimates of heritability were greater in lactations two and three. Estimates of heritability increased over the course of the lactation. Estimates of genetic and phenotypic correlations were smaller for test-days further apart.

Pregnancy rate and first-service conception rate in Angus heifers

The objective of this project was to determine the genetic control of conception rate, or pregnancy percentage in Angus beef heifers. Producers from 6 herds in 5 states provided 3,144 heifer records that included breeding dates, breeding contemporary groups, service sires, and pregnancy check information. Two hundred fourteen sires of the heifers were represented; with 104 sires having less than 5 progeny, and 14 sires having greater than 50 progeny. These data were combined with performance and pedigree information, including actual and adjusted birth weights, weaning weights, and yearling weights, from the American Angus Association database. Heifer pregnancy rate varied from 75 to 95% between herds, and from 65 to 100% between sires, with an overall pregnancy rate of 93%, measured as the percentage of heifers pregnant at pregnancy check after the breeding season. Pregnancy was analyzed as a threshold trait with an underlying continuous distribution. A generalized linear animal model, using a relationship matrix, was fitted. This model included the fixed effects of contemporary group, age of dam, and first AI service sire, and the covariates of heifer age at the beginning of breeding, adjusted birth weight, adjusted weaning weight, and adjusted yearling weight. The relationship matrix included 4 generations of pedigree. The heritability of pregnancy and first-service conception rates on the underlying scale was 0.13 +/- 0.07 and 0.03 +/- 0.03, respectively. Estimated breeding values for pregnancy rate on the observed scale ranged from -0.02 to 0.05 for sires of heifers. Including growth traits with pregnancy rate as 2-trait analyses did not change the heritability of pregnancy rate. As expected for a reproductive trait, the heritability of pregnancy rate was low. Because of its low heritability, genetic improvement in fertility by selection on heifer pregnancy rate would be expected to be slow.

Effects of supplementation of whole corn germ on reproductive performance, calf performance, and leptin concentration in primiparous and mature beef cows

A 2-yr study using primiparous and multiparous, spring-calving, crossbred beef cows was conducted to evaluate the effects of supplemental whole corn germ on reproductive performance, calf performance, and serum leptin concentrations. Each year, cows were blocked by age and BCS and assigned randomly to one of three treatments: PRE (n = 115) cows received 1.14 kg/d (DM basis) of whole corn germ for approximately 45 d before calving; POST (n = 109) cows were fed 1.14 kg/d of whole corn germ for approximately 45 d after calving; and control cows (n = 118) were fed similar energy and protein from dry-rolled corn (1.82 kg of DM/d) for 45 d before and after calving. Additionally, PRE cows were grouped with controls after calving, and POST cows were grouped with control cows before calving, so that corn germ-supplemented cows received the control supplement in the alternate feeding period. Cow BW (538 +/- 13 kg) and BCS (5.4 +/- 0.13) did not differ among treatments at any time during the experiment. Calf birth weight (39 +/- 2 kg), weaning weight (225 +/- 7 kg), and age-adjusted weaning weight (234 +/- 8 kg) did not differ because of dam supplementation regimen. Treatment did not affect the proportion of cows exhibiting ovarian luteal activity before the start of the breeding season (67%) or pregnancy rate (91%). The interval from exposure to bulls until subsequent calving did not differ (P = 0.16) among PRE (298 +/- 2.3 d), POST (303 +/- 2.6 d), and control (304 +/- 2.3 d) cows. Leptin concentrations did not differ among treatments and were 2.15 +/- 0.75, 1.88 +/- 0.76, and 1.91 +/- 0.75 ng/mL for control, POST, and PRE cows, respectively. Age and week relative to calving influenced leptin concentration. Primiparous cows had similar leptin concentrations to 3-yr-old and mature cows for wk -7 and -6 relative to calving, but lower (P < 0.10) concentrations than mature cows for wk -5, and lower (P < 0.05) concentrations than either 3-yr-old or mature cows for wk -4 to +7 relative to calving. Serum leptin was correlated with BCS (P < 0.0001; r = 0.35) at initiation of the feeding period and was correlated with BCS (P = 0.02; r = 0.12) and weight (P < 0.01; r = 0.14) at the completion of the supplement period, but it was not correlated with initial BW or interim BCS. Calving interval was not correlated (P > 0.12) with weekly measures of serum leptin concentration. Supplementing beef cows with whole corn germ had no effect on cow performance, calf performance, or serum leptin concentrations of cows.

Genetic Evaluation of Dairy Cattle with Test-Day Models with Autoregressive Covariance Structures and with a 305-d Model

This study compared genetic evaluations from 3 test-day (TD) models with different assumptions about the environmental covariance structure for TD records and genetic evaluations from 305-d lactation records for dairy cows. Estimates of genetic values of 12,071 first-lactation Holstein cows were obtained with the 3 TD models using 106,472 TD records. The compound symmetry (CS) model was a simple test-day repeatability animal model with compound symmetry covariance structure for TD environmental effects. The ARs and ARe models also used TD records but with a first-order autoregressive covariance structure among short-term environmental effects or residuals, respectively. Estimates of genetic values with the TD models were also compared with those from a model using 305-d lactation records. Animals were genetically evaluated for milk, fat, and protein yields, and somatic cell score (SCS). The largest average estimates of accuracy of predicted breeding values were obtained with the ARs model and the smallest were with the 305-d model. The 305-d model resulted in smaller estimates of correlations between average predicted breeding values of the parents and lactation records of their daughters for milk and protein yields and SCS than did the CS and ARe models. Predicted breeding values with the 3 TD models were highly correlated (0.98 to 1.00). Predicted breeding values with 305-d lactation records were moderately correlated with those with TD models (0.71 to 0.87 for sires and 0.80 to 0.87 for cows). More genetic improvement can be achieved by using TD models to select for animals for higher milk, fat, and protein yields, and lower SCS than by using models with 305-d lactation records.

Genetic parameters for stayability, stayability at calving, and stayability at weaning to specified ages for Hereford cows1

Genetic parameters for stayability to six ages (ST1, . . ., ST6), for five measures of stayability to calving (SC2, . . ., SC6), and for five measures of stayability to weaning (SW2, . . ., SW6), were estimated using records of 2,019 Hereford cows collected from 1964 to 1979 from a selection experiment with a control line and three lines selected for weaning weight, yearling weight, and an index of yearling weight and muscle score. The model included birth year of the cow as a fixed effect and the cow's sire as a random effect. Analyses were performed with 1) a generalized linear mixed model for binary data using a probit link with a penalized quasi-likelihood function, and 2) with a linear mixed model using REML. Genetic trends were estimated by regressing weighted means of estimated transmitting abilities (ETA) of sires by birth year of their daughters on birth year. Environmental trends were estimated by regressing solutions for year of birth on birth year. Estimates of heritability (SE) for ST were between 0.09 (0.08) and 0.30 (0.14) for threshold model and between 0.05 (0.04) and 0.19 (0.09) for linear model. Estimates of heritability from linear model analyses transformed to an underlying normal scale were between 0.09 and 0.35. Estimates of heritability (SE) for SC were between 0.29 (0.10) and 0.39 (0.11) and between 0.18 (0.09) and 0.25 (0.08) with threshold and linear models. Estimates of heritability transformed to an underlying normal scale were between 0.30 and 0.40. Estimates of heritability (SE) for SW were between 0.21 (0.14) and 0.47 (0.19) and between 0.12 (0.08) and 0.26 (0.12) with threshold and linear models, respectively. Estimates of heritability transformed to an underlying normal scale were between 0.21 and 0.50. Estimates of genetic and environmental trends for all lines were nearly zero for all traits. Correlations between ETA of sires for stayability to specific ages, for stayability to calving, and for stayability to weaning with threshold and linear models ranged from 0.09 to 0.82, from 0.68 to 0.90, and from 0.67 to 0.87, respectively. Selection for stayability would be possible in a breeding program and could be relatively effective as a result of the moderate estimates of heritability, which would allow selection of sires whose daughters are more likely to remain longer in the herd. Selection for weaning and yearling weights resulted in little correlated response for any of the measures of stayability.

Evaluation of Autoregressive Covariance Structures for Test-Day Records of Holstein Cows: Estimates of Parameters

The objective of this study was to compare test-day (TD) models with autoregressive covariance structures for the estimation of genetic and environmental components of variance for milk, fat and protein yields, and somatic cell score (SCS) in Holstein cows. Four models were compared: model I (CS model) was a simple TD repeatability animal model with compound symmetry covariance structure for environmental effects, model II (ARpe model) and model III (ARe model) had first-order autoregressive covariance structures for TD permanent or residual environmental effects, respectively, and model IV (305-d model) was a simple animal model using 305-d records. Data were 106,472 first-lactation TD records of 12,071 Holstein cows calving from 1996 through 2001. Likelihood ratio tests indicated that ARpe and ARe models fit the data significantly better than the CS model. The ARe model resulted in slightly smaller estimates of genetic variance and heritability than did the CS model. Estimates of residual variance were always smaller with the CS model than with the ARe model with the autoregressive covariance structure among TD residual effects. Estimates of heritability with different TD models were in the range of 0.06 to 0.11. The 305-d model resulted in estimates of heritability in the range of 0.11 to 0.36. The autoregressive covariance structure among TD residual effects may help to prevent bias in heritability estimates for milk, fat and protein yields, and SCS.

Impact of candidate sire number and sire relatedness on DNA polymorphism-based measures of exclusion probability and probability of unambiguous parentage

Genetic paternity testing can provide sire identity data for offspring when females have been exposed to multiple males. However, correct paternity assignment can be influenced by factors determined in the laboratory and by size and genetic composition of breeding groups. In the present study, DNA samples from 26 commingled beef bulls and their calves from the Nebraska Reference Herd-1 (NRH1), along with previously reported Illinois Reference/Resource Families data, were used to estimate the impact of sire number and sire relatedness on microsatellite-based paternity testing. Assay performance was measured by exclusion probabilities and probabilities of unambiguous parentage (PUP) were derived. Proportion of calves with unambiguous parentage (PCUP) was also calculated to provide a readily understandable whole-herd measure of unambiguous paternity assignment. For NRH1, theoretical and observed PCUP values were in close agreement (85.3 and 85.8%, respectively) indicating good predictive value. While the qualitative effects on PUP values of altering sire number and sire relatedness were generally predictable, we demonstrate that the impacts of these variables, and their interaction effects, can be large, are non-linear, and are quantitatively distinct for different combinations of sire number and degree of sire relatedness. In view of the potentially complex dynamics and practical consequences of these relationships in both research and animal production settings, we suggest that a priori estimation of the quantitative impact of a given set of interacting breeding group-specific and assay-specific parameters on PUP may be indicated, particularly when candidate sire pools are large, sire relatedness may be high, and/or loci numbers or heterozygosity values may be limiting.

Laying hen behavior. 1. Effects of cage type and startle stimuli

The well-being of commercial laying hens plays an important role in egg production. Behaviors such as pacing, displaced preening, increased aggression, and redirected activities have been associated with stress in poultry. This study was conducted to determine whether two strains of commercial layers, reported to differ in level of excitability, behave differently in two types of commercial cages. DeKalb Delta and Hy-Line W36 hens, 40 to 45 wk of age, were housed six to eight per cage in open or solid-sided cages, at an equal density between cages. For each strain, there were six cages per cage type for a total of 24 cages. In the first five experiments, behavioral data were obtained at a distance of 1 m by instantaneous or scan sampling. These experiments included hen behavior in both types of cages with and without the presence of frustrating or startle conditions. Some significant differences in behavior existed within experiments but not consistently among all experiments. Sampling method did not affect reliability of data collection. Two trials were then conducted to determine whether the length of time to return to normal activity after a startle stimulus is influenced by the cage type or strain. In the first startle experiment, DeKalb hens returned to normal activity more quickly than did Hy-Line hens (P = 0.07); this strain difference was not found when the experiment was repeated. Cage type did not appear to affect the behavior of birds adversely, although neither cage type appeared to confer an advantage. No clear differences were found in behavior by strain or by strain within cage.

Applicaitons in survival analysis

Survival or failure time traits such as herd life and days open are both important economically and pose a number of challenges to an analysis based on linear mixed models. The main features of a survival trait are that it is the time until some event occurs, and some of the observations are censored. Survival models and the associated estimation procedures provide a flexible means of modeling survival traits. In this paper I will discuss the application of survival analysis based on the Weibull distribution. The components that make up a survival model will be presented along with their interpretation. Issues related to the model construction and estimation will be presented.

Parameter estimates for direct, maternal, and grandmaternal genetic effects for birth weight and weaning weight in Hereford cattle

Birth and weaning weights adjusted for age of dam from four lines of Hereford cattle were analyzed to determine the relationships among grandmaternal, maternal, and direct genetic effects. Three lines were selected for 1) weaning weight (WWL), 2) yearling weight (YWL), and 3) an index of yearling weight and muscle score (IXL). The fourth line was an unselected control line (CTL). Numbers of observations ranged from 1,699 (CTL) to 2,811 (WWL), and number of animals in the pedigree file ranged from 2,266 to 3,192. Two animal models were used to obtain estimates by REML using an average information method. Model 1 included random direct and maternal genetic, permanent maternal environmental, and residual environmental effects, and fixed sex x year effects. Model 2 additionally included random grandmaternal genetic and permanent grandmaternal environmental effects. For birth weight, Models 1 and 2 gave almost identical estimates for direct and maternal heritability, and for the fraction of variance that was due to maternal permanent environmental effects. Estimates for grandmaternal heritability could be obtained only for IXL (.03) and CTL (.01). For weaning weight, estimates for direct heritability were similar from both models. Estimates for maternal heritability from Model 1 were .18, .20, .13, and .20, and corresponding estimates from Model 2 were .34, .31, .13, and .34 for WWL, YWL, IXL, and CTL, respectively. For IXL, estimates for variances that were due to grandmaternal genetic and grandmaternal permanent environmental variances could not be obtained and were set to zero. Grandmaternal heritability estimates for WWL, YWL, and CTL were .05, .09, and .12. Estimates of correlations between direct and maternal genetic effects were -.13, -.44, -.11, and -.26 for WWL, YWL, IXL, and CTL. Estimates of correlations between direct and grandmaternal genetic effects were .21, .83, and .55, and those between maternal and grandmaternal genetic effects were -.99, -.84, and -.76 for WWL, YWL, and CTL, respectively. These results indicate that grandmaternal effects may be important for weaning weight and that maternal heritability may be underestimated if grandmaternal effects are not included in the model.

Effect of wheat straw treated with alkali on ruminal function and lactational performance of dairy cows

Two experiments were conducted to evaluate the effects of wheat straw treated with alkali on ruminal function and lactational performance of dairy cows. In Experiment 1, four ruminally fistulated Holsteins cows (X = 57 d of lactation) were fed four diets that contained 0, 20, 30, or 40% (dry basis) wheat straw treated with 3% NaOH plus 3% Ca(OH)2 in a 4 x 4 Latin square. The diets contained 60, 40, 30, and 20% (dry basis) prebloom alfalfa haylage to result in a 60: 40 ratio of forage to concentrate. In Experiment 2, 12 (X = 149 d of lactation) midlactation Holstein cows were fed diets containing 0 or 20% treated wheat straw to measure lactational performance during a 12-wk period. In Experiment 1, no effect of diet was observed on ruminal pH, osmolality, digestion of neutral detergent fiber of straw, or 4% fat-corrected milk. However, the dry matter intake of cows fed diets containing the two highest concentrations of treated straw was depressed and was associated with a significant body weight loss. The ruminal rate of passage of treated straw was not affected by diet; however, rate of passage of alfalfa haylage decreased when straw was included in the diet. In Experiment 2, no effect on cow performance was observed when straw treated with alkali was included at 20% of the diet. Inclusion of up to 20% wheat straw treated with 3% NaOH plus 3% Ca(OH)2 in diets of lactating cows resulted in ruminal function and performance that were similar to those of cows fed diets that contained alfalfa haylage only.

Acute high environmental temperature and calcium-estrogen relationship in the hen

Much is known about the effects of high environmental temperature (HT) on egg production, but very little is understood about the mechanisms that underlie them. Two experiments were conducted to examine the effects of acute heat stress on circulating estradiol, on calcium uptake by gut tissue, on bone resorption, and on the dynamic relationship between estradiol and calcium in the hen during one ovulatory cycle. In one study, hens were moved individually and randomly into a hot [HT: temperature (T) = 35 C, relative humidity (RH) = 50%; n = 18] or a control, thermoneutral (TN: T = 23 C, RH = 50%; n = 18) environment immediately after a mid-sequence oviposition and brachial vein cannulation. Blood samples (2 mL) were collected every 3 h for 21 h for ionized calcium (Ca2+) and pH determinations and from which aliquots were frozen for 17 beta-estradiol (E2), total calcium (TCa), and inorganic P analysis. Excreta and urine were assayed for TCa and hydroxyproline (OHPr), respectively. A second study was conducted to determine the effects of HT (T = 35, H = 50%, 12 h) vs TN (T = 23 C, RH = 50%, 12 h) on the ability of duodenal cells to take up calcium (CaT). Blood pH and calcium responded to HT as expected (pH increased, Ca2+ decreased, and TCa decreased) and the cyclic pattern of Ca2+ in blood was abolished. The ratio of Ca2+:TCa decreased sharply at approximately the onset of shell calcification in control hens, but in HT hens there was no clear change in the ratio of any point in the cycle. The pattern of E2 typical of hens under normal conditions was significantly depressed in plasma of HT hens. Calcium uptake by duodenal epithelial cells of HT hens was lower than in TN hens. There was a clear inverse correlation between blood Ca2+ and urine OHPr in TN hens (r2 = -73, P = 0.0021) but not in HT hens (r2 = -27, P = 0.32). In addition to alterations in acid-base balance and the status of Ca2+, diminished ability of duodenal cells to transport calcium may be a critical factor in the detrimental effects of heat stress on egg production (numbers), eggshell characteristics, and skeletal integrity often documented in the laying hen.

N-acetyl-beta-D-glucosaminidase as a marker of renal damage in hens

Urinary N-acetyl-beta-D-glucosaminidase (NAG) is an early physiological indicator of renal damage in several mammalian species. A study was conducted to confirm occurrence of NAG in hen urine, to establish baseline urinary NAG in laying hens, and to assess the feasibility of using the enzyme as a marker of renal damage in hens. Hy-Line hens were used in a completely randomized block design in the first part of the study. Urine was collected at 4 to 6, 6 to 10, 10 to 14, and 14 to 18 h, and serum at 4, 6, 10, and 14 h postoviposition, and assayed by spectrophotometry for NAG. Kidney tissue from additional hens was assayed histochemically for NAG. Serum NAG (range: 0.11 to 0.14 mU/mg protein) was found to be several orders of magnitude lower than urine NAG (6.44 to 12.27 mU/mg protein). Urine NAG increased from 4 to 6 h through 14 to 18 h, indicating that time of collection is critical in order to utilize the enzyme as a valid marker for laying hens. A preliminary study with five hens indicated that 10 d of treatment with liquid cholecalciferol (D3) supplement (three times the recommended level) were not enough to detect renal damage on the basis of significant changes in urine (NAG, but elevated urine NAG was detected at 40 d of D3-supplementation. Overall the results indicate that NAG in urine of laying hens is a potentially useful diagnostic marker of renal damage.

Heterogeneity of variance by sire breed, sex, and dam breed in 200- and 365-day weights of beef cattle from a top cross experiment

The nature of the heterogeneity of variance for 200- and 365-d weights by sex, sire breed, and dam breed subclasses was studied. Data consisted of records for weaning (n = 7,829) and yearling (n = 7,367) weights of progeny from 673 and 672 sires, respectively, from 22 breeds that have been evaluated in the Germ Plasm Evaluation Program at the U.S. Meat Animal Research Center, Clay Center, NE. Sires were mated to Hereford and Angus cows. Each trait was analyzed separately. Three studies were undertaken separately to investigate heterogeneity due to the different factors (i.e., sire breed, sex, or dam breed). Only data from seven sire breeds were used to study the factor sire breed, but all data (22 sire breeds) were used to study the factors sex and dam breed. In each study, three sire and dam models with records of animals of the four sex x dam breed combinations considered different traits and with the same model equation, but covariance structures for random effects (sires, dams, and residuals) of increasing generality were fitted. First, (co)variances across subclasses were assumed equal. Second, correlations and fractions of phenotypic variance were assumed equal but phenotypic variance differed by sire breed, sex, or dam breed as appropriate. Third, variances and covariances were different for each subclass of the factor under study. Variance components were estimated by derivative-free REML. Models for each trait and each factor were compared through likelihood ratio tests. For both traits, variances differed (P < .02) in scale, but not as fractions of phenotypic variance (P > .10), by sire breed and sex subclasses. Variances were not different (P > .10) by dam breed subclasses, either in scale or as fractions of phenotypic variance. Estimates of correlations among genetic effects on weights of calves from different sex-dam breed subclasses were at least .85. Across all sex, sire breed, and dam breed subclasses, pooled estimates of sire and dam variances as fractions of phenotypic variance were, respectively, .06 and .39 for weaning weight and .11 and .24 for yearling weight. The conclusion is that the assumption of equal phenotypic variances among sire breeds and between sexes may not be appropriate in genetic evaluations.

Estimating energy needs of pediatric patients with burns

Recent reports indicate that formulas used to estimate the energy needs of pediatric patients with burns overestimate the energy consumption that results in maintenance of body weight in these patients. The purpose of this project was to determine which of four formulas (identified as Boston, Galveston, UCSD original, or UCSD modified) most accurately estimated the energy consumption needed to maintain body weight in pediatric patients with burns. The medical records of 12 subjects, 1 to 12 years of age, who maintained body weight (within +/- 10% of dry weight) were reviewed retrospectively. Analysis of variance was used to compare the patients' energy intakes with their estimated energy needs by use of each of the four formulas. All four formulas overestimated the energy intakes that resulted in maintenance of body weight (p < 0.05), but the estimate that used the Galveston formula was closest to actual energy consumption.

Estimating milk, fat, and protein lactation curves with a test day model

Test day models were used to estimate lactation curves for milk, fat, protein, fat percentage, and protein percentage and to study the influence of age, season, and herd productivity on Holstein lactation curves. Random effects of lactation within herd and fixed effects of herd test date were absorbed. Fixed effects of cow's age on test day and either DIM (57 divisions) by parity (1, 2, greater than or equal to 3) class or season of calving (winter or summer) by DIM by parity class were estimated. Lactation curves for yield traits derived from DIM solutions were flatter for first versus later lactation, even without addition of age effects. Differences between lactation curves for the two seasons were slight, suggesting that most observed seasonal differences are caused by seasonal productivity accounted for by herd test date effects. At peak, winter calving cows yielded slightly more milk of similar fat percentage but of lower protein percentage than those calving in summer. Data were also partitioned into nine subsets based on rolling herd milk and fat percentage. Lactation curves for yield traits, but not percentage traits, varied with rolling herd milk. Lactation curves for fat yield and percentage varied with rolling herd fat percentage.

Phenotypic and genetic variability of estimated growth curve parameters in mice

Data from 1,919 outbred ICR mice were used to examine the potential usefulness of growth curve parameters as selection criteria for altering the relationship between body weight and age. A logistic growth function was used to model growth through 12 weeks of age. Estimates of asymptotic weight (A), maximum growth rate (r) and age at point of inflection (t(*)) were obtained by nonlinear least-squares. A log transformation was also used to stabilize residual variance. Phenotypic and genetic parameters were estimated for the estimated growth curve parameters and for body weights at 2, 3, 4.5, 6, 8 and 12 weeks of age. Heritabilities of estimated growth curve parameters (obtained with and without a log transformation, respectively) were: A (0.28±0.07, 0.28±0.07), r (0.35±0.07, 0.53±0.09) and t(*) (0.41±0.08, 0.44±0.08). Estimated genetic correlations suggest that t(*) may be useful in selecting for rapid early growth without increasing mature weight.