Biomedical subjects

G E Shook

Publications and source records attributed to G E Shook.

At least 19 recordsLinked to original sources

PubMed2006

Major advances in determining appropriate selection goals.

Substantial increases of 3,500 kg of milk, 130 kg of fat, and 100 kg of protein per cow per lactation have resulted from improvements in genetics, nutrition, and management during the past 20 yr. At the same time, the interval from calving to conception increased (unfavorable) by 24 d. Genetics has accounted for about 55% of gains in the yield traits and about one-third of the change in interval to conception. Genetic gains in the yield traits and productive life have accumulated to around 1.7 and 1.2 genetic standard deviations since 1980. Unfavorable genetic changes in conception interval since 1980 and somatic cell score since 1990 have accumulated to 1.0 and 0.12 genetic standard deviations. The most important advance in selection indexes has been the introduction of nonyield traits. Advances in selection indexes have gone hand in hand with advances in data collection and genetic evaluation. As new traits were recorded in dairy management databases and as genetic evaluations were developed for these traits, they were incorporated into selection indexes. Until 1994, when somatic cell score and productive life were introduced, selection indexes provided by USDA included only yield traits. In 2000, composite type indexes for udder, feet and legs, and body size were added. Daughter pregnancy rate and service sire- and daughter-calving ease were included in 2003. The lifetime merit indexes introduced in 2003 have, for the first time, resulted in theoretical selection responses in the desired direction for all traits. During this time, the percentage relative economic weights in selection indexes increased from 0 to 45% for the nonyield traits. Selection emphasis on nonyield traits should continue to increase as additional traits (e.g., calf survival, metabolic disease, and male fertility) are introduced in the future. Wide variation exists among countries in traits included in selection indexes and in relative economic weights. Molecular genetic studies have identified many chromosome regions with potentially important major genes for economic traits. Use of DNA markers for genetic improvement is currently limited by lack of precision in marker location. Discovery of major genes will be accelerated by the availability of the bovine genome sequence, comparative genome maps and genome sequences across species, and increased use of breed crosses in molecular studies. As major genes are identified, their effects will be incorporated into genetic evaluations and selection indexes.

Animals↗

PubMed2006

Genetic variation of Mycobacterium avium ssp. paratuberculosis infection in US Holsteins.

The objective of this study was to estimate genetic variability of Mycobacterium avium ssp. paratuberculosis infection in US Holsteins. Blood and fecal samples were collected primarily from daughters of 12 bulls in their second or third lactation. Routine disease testing of the sires documented that they were not infected. Herds without a "suspect" or positive ELISA (sample/positive ratio > or = 0.10) or positive fecal culture test were deleted from the data set. The remaining 4,603 cows from 238 herds and 46 sires were used to estimate heritability of M. paratuberculosis infection. Heritability was estimated with 3 Johne's disease diagnostic tests: 1) fecal culture alone, 2) serum antibody ELISA alone, and 3) both tests (combined) with a positive animal defined as all animals with either a positive fecal culture or ELISA test. Four statistical models were used to estimate heritability: 1) linear (ELISA), 2) threshold (fecal culture and combined), 3) ordered threshold (ELISA), and 4) bivariate linear-threshold (ELISA-fecal culture). A sire model and Bayesian approach using Markov chain Monte Carlo methods were used in each case. Heritability of infection based on the fecal culture test was 0.153 [posterior standard deviation (PSD) = 0.115]. Heritability with the ELISA was 0.159 (PSD = 0.090) with a linear model and 0.091 (PSD = 0.053) with an ordered threshold model. Heritability of the combined tests was 0.102 (PSD = 0.066). Heritability estimates of fecal culture and ELISA with the bivariate model varied slightly from estimates obtained with the univariate models (0.125 and 0.183, respectively), with a corresponding increase in precision (PSD = 0.096 and 0.082, respectively). This study demonstrates that exploitable genetic variation exists in dairy cattle for M. paratuberculosis infection susceptibility.

Animals↗

PubMed2006

Effects of the signal transducer and activator of transcription 1 (STAT1) gene on milk production traits in Holstein dairy cattle.

A functional candidate gene approach was used to search for genes affecting milk production traits in Holstein dairy cattle. Signal transducer and activator of transcription 1 (STAT1) was chosen because of its involvement in the development of the mammary gland. Using the pooled genomic DNA sequencing approach, we identified a single nucleotide polymorphism. Genomic DNA was extracted from 1,292 sons obtained from the Cooperative Dairy DNA Repository and from 715 blood samples of daughters of 12 bulls obtained from the University of Wisconsin resource population. Daughter yield deviation data for the sons and yield deviation for the daughters were obtained for milk production traits from the USDA Animal Improvement Programs Laboratory. For the Repository population, allele C was associated with significant increases in milk fat and protein percentages. For the University of Wisconsin population, genotypes CC and CT were associated with significant increases in milk, fat, and protein yields. Results from this study are consistent with previous studies on the role of STAT1 in regulating the transcription of genes involved in milk protein synthesis and fat metabolism.

3' Untranslated Regions↗

PubMed2005

Assessment of the impact of somatic cell count on functional longevity in Holstein and Jersey cattle using survival analysis methodology.

Survival analysis in a Weibull proportional hazards model was used to evaluate the impact of somatic cell count (SCC) on the involuntary culling rate of US Holstein and Jersey cows with first calvings from 1990 to 2000. The full data set, consisting of records from 978,043 Holstein and 250,835 Jersey cows, was divided into subsets (5 for Holsteins and 3 for Jerseys) based on herd average lactation SCC values. Functional longevity (also known as herd life or length of productive life) was defined as days from first calving until culling or censoring, after correcting for milk production. Our model included the time-dependent effects of herd-year-season, parity by stage of lactation interaction, within-herd-year quintile ranking for mature equivalent production, and lactation average SCC (rounded to the nearest 50,000 cells/mL), as well as the time-independent effect of age at first calving. Parameters of the Weibull distribution, as well as variance components for herd-year-season effects, were estimated within each group of herds. Mean failure and censoring times decreased as herd average SCC increased, and a nonlinear relationship was observed between SCC and longevity in all groups. The risk of culling for Holstein cows with lactation average SCC > 700,000 cells/mL was 3.4, 2.7, or 2.3 times greater, respectively, than that of Holstein cows with SCC of 200,000 to 250,000 cells/mL in herds with low, medium, or high average SCC. Likewise, the risk of culling for Jersey cows with lactation average SCC > 700,000 cells/mL was 4.0, 2.9, or 2.2 times greater, respectively, than that of Jersey cows with SCC of 200,000 to 250,000 cells/mL in low, medium, or high SCC herds. These trends may reflect more stringent culling of high SCC cows in herds with few mastitis problems. In addition, cows with lactation average SCC <100,000 cells/mL had a slightly higher risk of culling than cows with SCC of 100,000 to 200,000 cells/mL in both breeds, particularly in herds with high average SCC, where exposure to mastitis pathogens was likely.

Aging↗

PubMed2005

The effect of synchronization on genetic parameters of reproductive traits in dairy cattle.

Genetic evaluation and selection is one strategy for improving female reproductive performance. Many producers use synchronization of ovulation or estrus to manage reproduction. The objective of this study was to examine the effects of reproductive synchronization on genetic parameter estimates of days to first breeding (DFB), days open (DO), and pregnancy rate at 120 d postpartum (PR120). Data were collected from 64 producers participating in an artificial insemination progeny testing program and using Dairy Comp 305 herd management software to record reproductive treatments and events. Data included 18,359 records for DFB and 16,379 records for DO and PR120. Synchronization was classified by breeding codes at time of insemination. The traits DFB and DO were analyzed using a linear model with age at calving, herd-year-season, and parity as fixed effects and sire and residual as random effects. For PR120, a threshold sire model was used with fixed effects as in the DFB and DO models. Three models were applied to the complete data sets of all traits; a base model with no synchronization effect, an expanded model with a fixed synchronization effect, and an interaction model with a random sire by herd management interaction. Herd management categories were based on an individual herd's use of synchronization protocols. Also, data subsets were analyzed separately based on cow synchronization treatment and herd management categories. Synchronized records for DFB had on average 40% higher sire variance and 60% lower residual variance than nonsynchronized records. Heritability for DFB ranged from 0.01 to 0.09. Sire variance was 40% lower for DO and 25% lower for PR120 in first synchronized records than either later-synchronized or nonsynchronized records. Residual variances for DO varied by 3% among cow treatment categories and 14% for herd management categories. Heritabilities ranged from 0.03 to 0.07 for DO and 0.10 to 0.26 for PR120. Including a fixed effect for synchronization in the DO model reduced sire variance by 33% and residual variance by 10%. Sire by herd management interactions were less than 2% of the total variance for all traits. Accounting for synchronization, especially for DFB, may improve accuracy of genetic parameter estimates and animal evaluations.

Analysis of Variance↗

PubMed2004

Identification of an ovulation rate QTL in cattle on BTA14 using selective DNA pooling and interval mapping.

Increased twinning incidence in beef cattle has the potential to improve production efficiency. However, phenotypic selection for twinning rate is difficult because of the trait's low heritability and the long time interval necessary to collect phenotypic records. Therefore, this trait and the correlated trait of ovulation rate are ideal candidates for marker-assisted selection. The objective of this study was to complete a genome-wide search for ovulation rate quantitative trait loci (QTL) in two related sire families. The families (paternal halfsib sires 839802 and 839803) were from a population of cattle selected for ovulation rate at the USDA Meat Animal Research Center, Clay Center, Nebraska. Putative ovulation rate QTL have previously been identified in the 839802 family on chromosomes 7 and 19; however, marker coverage in the original scan was not complete. This study fills the gaps in marker coverage of the earlier study by adding approximately 60 informative microsatellites to each sire family. Each family was genotyped using selective DNA pooling. Sons and daughters were included in either the high or low pool based on their estimated breeding value deviations from the mid-parent average (EBVMD) for ovulation rate. Approximately 40% (839802) and 26% (839803) of available progeny comprised the high and low pools combined. Pooled typing revealed possible associations (nominal P < 0.05) between ovulation rate and marker genotype for 11 and 15 microsatellites in the 839802 and 839803 families, respectively. Subsequent interval mapping strengthened support for the presence of an ovulation rate QTL on BTA14 (chromosome-wise P < 0.02).

Animals↗

PubMed1998

Bayesian analysis via Gibbs sampling of susceptibility to intramammary infection in Holstein cattle.

A Bayesian analysis was undertaken to assess the susceptibility of Holsteins to mastitis from 120 to 305 d in milk. Data included 595 lactations from 267 cows. The response variable was presence or absence of intramammary infection; explanatory variables were period and season of calving, somatic cell score, and cow. The logistic model adopted had period and season of calving and the regression on somatic cell score with vague prior distributions, and cow effects had a normal prior with unknown variance sigma u2, which, in turn, had a gamma prior. Implementation was by Gibbs sampling. Posterior densities of location parameters were unimodal and symmetric. The probability of intramammary infection of a sample cow was skewed. The posterior distribution of sigma u2 was skewed also. Gibbs samples of sigma u2 had high lag correlations, which gave an effective sample ranging between 47 and 117 from a chain of size 3000. There were differences between estimates of sigma u2 found using Gibbs sampling and those obtained using approximations. The low information content arising from the small size of the data and the binary nature of the response are reasons for such differences. A sensitivity analysis revealed influences of hyperparameters of the prior distribution of sigma u2 on inferences about this parameter.

Animals↗

PubMed1997

Factors affecting susceptibility to intramammary infection and mastitis: an approximate Bayesian analysis.

Susceptibility to IMI and to mastitis in Holstein cows was studied using logistic mixed effects models and an approximate Bayesian analysis. Dichotomous response variables were the presence or absence of IMI, caused by any microorganism. IMI caused by Staphylococcus spp. or Corynebacterium spp., and clinical mastitis caused by any microorganism at specific lactation stages. Data included 619 lactation records from 282 cows. Fixed explanatory variables in the model were period, season and age at calving, lactation number, log-transformed SCC, and a joint effect of age and log SCC. Because random cow effects were assumed to be normally distributed and to have an unknown variance, this parameter was estimated by approximate marginal maximum likelihood. Results from the Bayesian analysis were contrasted with maximum likelihood estimates obtained from a fixed effects logistic model that ignored cow effects. Posterior mode and maximum likelihood estimates of location parameters were similar, although standard errors of the maximum likelihood estimates understated uncertainty. The IMI status during a previous lactation was a poor predictor of IMI status in subsequent lactations, and susceptibility increased as SCC increased. Interlactation (logit scale) repeatability estimates of susceptibility ranged from 0.22 to 0.23. A Taylor series expansion was used to approximate correlations between lactations on a binary scale. These correlations depended on associated fixed effects and ranged between 0.12 and 0.18, which were lower than correlations using the logit scale.

Animals↗

PubMed1996

Effects of age on milk yield: time trends and method of adjustment.

Multiplicative adjustment factors for age that were used in the US from 1974 through 1994 were developed from performance records of the 1960s. Rapid genetic improvement and improved management may have altered the relationship between lactation yield and calving age. The purpose of this study was 1) to examine changes in age effects on lactation milk yield over time; 2) to compare multiplicative, additive, or a combined method to adjust records for calving age; and 3) to examine effect of adjustment method on estimates of genetic trend. Data were complete lactation records (n = 765,413) of 383,011 Holsteins from Wisconsin DHI. An animal model was used with fixed effects for herd-year and month of calving by period by age-lactation class and with random effects for EBV, permanent environment, and error. Correction factors were applied additively, multiplicatively, and in combinations. The combination of additive and multiplicative adjustments that minimized heterogeneity of standard deviations within age class was considered to be optimal. The increase in yield that was associated with advancing age and lactation number was greater during recent years than during earlier years. Heterogeneity of standard deviations within age class was nearly minimum with additive adjustment for lactations 1 to 3. For lactations 4 and 5, heterogeneity was not sensitive to method of adjustment; however, multiplicative adjustment was near the optimum. The genetic trend from records with multiplicative adjustment was substantially greater than additive and optimal adjustments, especially during recent years.

Aging↗

PubMed1994

Nutrient requirements and feed costs associated with genetic improvement in production of milk components.

Dietary requirements for NEL and absorbed true protein were summarized for marginal production of milk components because of genetic improvement through selection. Shelled corn and soybean meal were used to meet marginal nutrient requirements and were assigned variable concentrations of absorbed true protein, depending on rumen-available energy and protein. Mean ratios among national averages for shelled corn to milk prices and soybean meal to milk prices (DM: standardized milk, dollars per kilogram) over a recent 25-yr period were .52 and 1.20, respectively. Stability of these relationships over time permits estimation of feed costs from milk price as prices inflate. Feed costs per kilogram of component, expressed as kilograms of standardized milk with equivalent value, were 1.00 for lactose, 1.89 for fat, and 3.49 for protein. Costs of milk protein were higher if production of absorbed true protein was limited by rumen-available energy, suggesting that selection for fat or lactose, in addition to protein, may be beneficial. High feed costs for milk protein indicate a need for adequate compensation to producers for milk protein and consideration of feed costs during selection. A net value index is proposed that considers feed costs associated with marginal production of individual milk components.

Animal Feed↗

PubMed1994

Selection on somatic cell score to improve resistance to mastitis in the United States.

Increased genetic susceptibility to mastitis has accompanied the rapid genetic increase in milk yield, and genetic selection for mastitis resistance should be considered. Somatic cell score is recommended as an indicator trait to achieve genetic improvement for mastitis resistance. Heritability of somatic cell score is around 10%, and genetic correlation between somatic cell score and clinical mastitis is around .6 to .8. Selection for lower somatic cell score is consistent with the goal of maximizing genetic improvement for total economic merit and should be included in breeding programs. National genetic evaluations for somatic cells scores will use the same animal models and methods as are currently used for milk yield traits. Reliabilities of PTA for somatic cell scores will be smaller than for yield traits because of lower heritability and availability of records from fewer cows. Several forms are proposed for reporting genetic evaluations of somatic cells to producers, and advantages and disadvantages are discussed. Using somatic cell scores for breeding decisions would marginally decrease genetic gain for milk yield and increase total economic merit. Optimal selection indexes would slow the rate of increase in mastitis, rather than decrease its incidence.

Animal Husbandry↗

PubMed1993

Genetic improvement of mastitis through selection on somatic cell count.

Heredity influences both clinical mastitis and somatic cell score. Intramammary infection is the major cause of elevated somatic cell score. A nationwide program of genetic evaluation of dairy cattle for somatic cell score is being developed. Proper selection of artificial insemination sires, considering their genetic merit for both milk production and somatic cell score, will reduce the genetic increase in mastitis susceptibility that accompanies selection for high production.

Animals↗

PubMed1993

Metabolizable energy and absorbed protein requirements for milk component production.

Metabolic pathways of milk component synthesis were used to estimate metabolizable energy and absorbed protein requirements for lactation. Amounts of ATP and AA used for synthesis of each component from absorbed substrates were determined. Coefficients were adjusted to account for additional inefficiencies and to define requirements in terms of dietary supply based on NRC energy requirements and N balance data. Assuming that 10% of glucose required was derived from AA, metabolizable energy and absorbed protein requirements were 6.02 Mcal and .136 kg/kg of lactose, 13.43 Mcal and .127 kg/kg of fat, and 7.57 Mcal and 1.069 kg/kg of protein, respectively; an additional .144 Mcal/kg of milk was required for milk volume. For production of milk containing 4.8% lactose, 3.5% fat, and 3.3% protein, absorbed protein required for lactose and fat may account for 14.1 and 9.6%, respectively, of total absorbed protein required for milk production. Efficiency of protein utilization for milk protein synthesis may be as high as 90% when 10% of glucose requirements must be supplied by AA. Expressing nutrient requirements for lactation on a component basis enables calculation of requirements for milk production of any composition and does not rely on correlations between major milk components.

Absorption↗

PubMed1992

Prediction of mastitis using milk somatic cell count, N-acetyl-beta-D-glucosaminidase, and lactose.

The objectives of this work were 1) to examine the responsiveness of SCC, lactose concentration, and NAGase activity in milk to changes in bacteriological status and 2) to develop models for predicting bacteriological status of mammary glands. Data included 550 cows in 10 commercial herds. Natural logarithm NAGase and log cell count were most responsive to changes in bacterial status. The log NAGase was relatively more effective in identifying major from minor pathogen infections, whereas log SCC was better able to differentiate between infected and uninfected classes. Non-transformed NAGase, SCC, and lactose were considerably less responsive to infection status. Logistic regression of bacterial status on herd, lactation number, milk, log SCC, log NAGase, and stage of lactation was performed. The least significant variables were removed in a stepwise process. Final predictors of infection status were herd, log SCC, and log NAGase. The role of log SCC was to discriminate infection from no infection, whereas log NAGase discriminated major from minor pathogens. The log NAGase, alone or in combination with log SCC, added substantially to the detection power of the model. Chi-square goodness of fit tests found no significant differences between observed and predicted infection probabilities. Substitution of herd averages for log SCC and log NAGase for the herd variables resulted in significant differences between predicted and observed herd infection probabilities.

Acetylglucosaminidase↗

PubMed1991

Reproductive performance in genetic lines selected for high or average milk yield.

Genetic lines were created by selection of service sires differing by approximately 450 kg of milk for estimated transmitting ability. High line sires were selected from the best available proven sires. Selection continued over 24 yr with up to eight generations of selection. Records from 708 nulliparous, 575 first parity, and 437 second parity animals were analyzed. High milk yield was associated with longer days open and calving intervals in both first and second parities. A 1000-kg increase in 305-d milk production was associated with average increases in both days open and calving interval of around 7 d in first parity and 13 d in second parity and with average increases in days to first detected estrus of 4.5 d in first parity. Difference between genetic lines for milk yield was 804 kg in first parity and 772 kg in second parity. Days open and calving interval were less for the average line in both parities and differed by 10 d in second parity. Other reproductive differences were small or insignificant. Selection for yield has affected reproductive fitness modestly.

Animals↗

PubMed1990

Response to recombinant bovine somatotropin in dairy cows with different genetic merit for milk production.

Thirty-nine multiparous cows obtained from two genetic lines were utilized to determine the effect of genetic merit on lactation response to long-term administration of recombinant bST. Cow index ranged from -70 to 456 (mean = 183) and -494 to -88 (mean = -288) kg milk for high and low genetic groups, respectively. Cows were blocked by calving date and randomly assigned to treatment within genetic group. Treatments were 0, 10.3, 20.6, and 30.9 mg somatotropin injected daily from wk 14 through 44 postpartum. Cows were fed one of two total mixed rations. Diet 1 (NE1 = 1.65 Mcal/kg, CP = 18%, and ADF = 22%) was fed from start of lactation to at least 4 wk after initiation of treatment. Cows were switched to diet 2 (NE1 = 1.56 Mcal/kg, CP = 16%, and ADF = 27%) when milk output fell below 25 kg/d. Forty-four week lactation yields were 9800 and 9447 kg milk; 364 and 354 kg fat; and 322 and 309 kg protein for high and low genetic groups, respectively. Milk, milk fat, or protein yield due to somatotropin did not differ between genetic groups. Increasing dosage of bST increased milk, 4% FCM, fat, and protein yields in a linear fashion. Percentages of fat and protein of milk were similar for all treatment groups. Body weight changes were not significantly different among treatments, but condition score changes decreased linearly with increasing dose of bST. Long-term treatment with recombinant bST had no apparent effect on incidence of health problems or reproduction.

Animals↗

PubMed1990

Genotype by environment interaction and genetic correlations among parities for somatic cell count and milk yield.

Lactation measures of somatic cell concentration and total SCC production were developed. Data were separated into three parity groups. Within parity, five data sets were created: four subsets by herd-year average SCC, and one with all records. Records on lactation SCC, total SCC production, and 305-d milk were analyzed by a sire model separately in each subset within parity. Variance components estimates were by REML. For SCC and total SCC production, heritability estimates averaged .12 and were lowest in the highest level of herd-year average SCC. Estimates of genetic correlation between SCC and total SCC production were over .95; between SCC and 305-d milk were around .25 in first and -.15 in later parities; between total SCC and 305-d milk were around .50 in first and .15 in later parities. Product-moment correlations between sire effects in different levels of herd-year average SCC were obtained. Ratios of product-moment correlations to their expected value were above .80 for all traits in all parities. High ratios indicated little genotype by environment interaction. A sire by herd interaction was fitted in the model and accounted for less than 2% of total phenotypic variance for SCC and total SCC production, and 4% for 305-d milk. Estimates of genetic correlation of first with later parities were .71 to .86 for all traits. Between second and third parity genetic correlation estimates were around unity for all traits. Records from all parities should be used for sire evaluation.

Animals↗

PubMed1989

Selection for disease resistance.

Approaches to disease control are prioritized. Genetic improvement could reduce need for treatment and culling but would not reduce the need for proper management and sanitation. Results of several studies indicate that disease incidence and cost increases with selection for milk yield. The large array of disease resistance mechanisms in animals suggests a large number of loci are involved in disease resistance. A few loci, e.g., the major histocompatibility complex, may account for a major portion of genetic variance in disease. Rate of genetic gain from selection for a major locus alone or in combination with performance is discussed. Four criteria for including traits in a breeding program are outlined, and each is discussed with respect to disease. In spite of low heritabilities for disease traits, genetic variation for disease incidence is economically important and justifies including disease in breeding programs. An industry-wide standard for recording and accumulating field data for disease is lacking. Institutional relationships among segments of the animal breeding and animal health industries are needed to facilitate genetic improvement for disease resistance.

Animals↗