Dairy Records Processing Center Research Articles

Genetic parameters and trends for Johne's disease in US Holsteins: An updated study

Johne's disease (JD) is an infectious enteric disease in ruminants, causing substantial economic loss annually worldwide. This work aimed to estimate JD's genetic parameters and the phenotypic and genetic trends by incorporating recent data. It also explores the feasibility of a national genetic evaluation for JD susceptibility in Holstein cattle in the United States (US). The data were extracted from a Johne's disease data repository, maintained at the Council on Dairy Cattle Breeding (CDCB), and initially supplied by 2 dairy records processing centers. The data comprised 365,980 Holstein cows from 1,048 herds participating in a voluntary control program for JD. Two protocol kits, Idexx Paratuberculosis Screening Ab Test (IDX) and Parachek® 2 (PCK), were used to analyze milk samples with the Enzyme-Linked Immunosorbent Assay (ELISA) technique. Test results from the first 5 parities were considered. An animal was considered infected if it had at least one positive outcome. The overall average of JD incidence was 4.72% in these US Holstein cattle. Genotypes of 78,964 SNP markers were used for 25,000 animals randomly selected from the phenotyped population. Variance components and genetic parameters were estimated based on 3 models, namely, a pedigree-only threshold model (THR), a single-step threshold model (ssTHR), and a single-step linear model (ssLR). The posterior heritability estimates of JD susceptibility were low to moderate: 0.11 to 0.16 based on the 2 threshold models and 0.05 to 0.09 based on the linear model. The average reliability of estimated breeding values of JD susceptibility using single-step analysis for animals with or without phenotypes varied from 0.18 (THR) to 0.22 (ssLR) for IDX and from 0.14 (THR) to 0.18 (ssTHR and ssLR) for PCK. Despite no prior direct genetic selection against JD, the estimated genetic trends of JD susceptibility were negative and highly significant (P-value <0.01). The correlations of bulls' predicted transmitting abilities with economically important traits such as milk yield, milk protein, milk fat, somatic cell score, and mastitis were low, indicating a non-overlapping genetic selection process with traits in current genetic evaluations. Our results suggest the feasibility of reducing the JD incidence rate by incorporating it into the national genetic evaluation programs.

Use of early lactation days open records for genetic evaluation of cow fertility.

National genetic evaluations for cow fertility were introduced by the USDA in February, 2003. These evaluations, reported as daughter pregnancy rate, are based on days open. One requirement of the evaluation system is that lactations be at least 250 d in milk (DIM) to be included for analysis. The objective of this research was to develop a predictor of days open, usable in genetic evaluation, to allow for earlier predicted transmitting abilities (PTA), especially for young bulls. The final prediction equation included an overall intercept, the effects of lactation and calving ease score, the linear and quadratic effects of age at calving, and a regression on days open based on last breeding. Data used for estimation were breeding records from 4 dairy records processing centers for the years 1995 through 1998. Genetic correlations were > or =0.91 by d 130, and phenotypic means of predicted days open were in agreement with means for final days open, indicating that the predictions were phenotypically unbiased. Comparison of mean PTA based on actual and predicted days open indicated no bias in PTA, and correlations between PTA were > or =0.92 by d 130. The earlier use of data increased reliability by about 5% for sires between the ages of 4 and 5 yr. The USDA began using predicted days open for records that are at least 130 DIM in national evaluations starting November, 2003.

Phenotypic Trends in Incidence of Stillbirth for Holsteins in the United States

The objectives for this study were to determine 1) if there was a trend in stillbirths for the U.S. Holstein population, 2) if stillbirths are the same trait in primiparous and multiparous cows, and 3) what was the role of dystocia in stillbirths. A sample of 666,341 births from the MidStates Dairy Records Processing Center and the National Association of Animal Breeders was used to examine the influence of sire, herd, year, season, sex of calf, parity of dam, calving ease, and gestation length on the survival of the calf. Parity was scored as an ordered variable (1, 2, 3+). Calving ease was scored on a scale of 1 (no assistance) to 3+ (needed assistance). An increasing trend in stillbirths was found in primiparous and multiparous cows. The percentage of stillborn calves in primiparous cows increased from 9.5 in 1985 to 13.2 in 1996. Stillbirths in multiparous cows increased from 5.0 to 6.6% from 1985 to 1996. Variation about the trend was greater in primiparous cows than in multiparous cows. Dystocia was a major determinant of stillbirth incidence, but the association was stronger in primiparous cows. Sex of calf had different associations with stillbirth incidence in primiparous and multiparous cows. Gestation length and season of birth also had significant associations with stillbirth incidence. Logistic regression models with fixed and random effects were fit to the data to preserve the binary nature of the stillbirth response. The expected probability of stillbirths for an average herd and sire was 10% for primiparous cows and 5% for multiparous cows. Replacement of stillborn calves is a substantial cost to the dairy industry at more than $125.3million per year. Because of the increasing incidence of stillbirths, these costs have increased by $75.9million from 1985 to 1996.

Interactions among Factors Affecting Stillbirths in Holstein Cattle in the United States

Each year about 7% of the Holstein calves born in the United States die within 48h of birth. The exact cause of death is unknown. The purpose of this article is to examine the complex interactions among factors (e.g., parity, season of birth, dystocia, year) contributing to stillbirth rates. A modified chi-squared automated interaction detection algorithm was used to develop classification trees explaining the most likely sequence of factors that result in a stillborn calf. The data were 666,341 births from the MidStates Dairy Records Processing Center and the National Association of Animal Breeders.Primiparous and multiparous cows clearly differ in the rate of stillbirths, 11.0 and 5.7%, respectively. Dystocia followed parity as the next most important factor within both primiparous and multiparous cows. In primiparous cows, season, year of birth, or gestation length ranked third as an important predictor for dystocia equal to 1, 2, or 3+, respectively. Gestation length ranked third in importance among the factors that affect stillbirth rates for all levels of dystocia in multiparous cows. Among multiparous cows needing assistance (dystocia 3+), stillbirth rates were greatest for shorter gestations less than the average of 280 d, 55.3% for −15 to −12 d, 45.5% for −11 to −9 d, 33.7% for −8 to −5 d, 23.8% for −4 to 13 d, and 35.4% for 14 to 15 d. Gestation length pinpointed the time when stillbirths occurred, as indicated by the increase from 23.8% stillbirth rate among calves born at or above the mean gestation length to 55.3% for those calves born −15 to −12 d below the mean gestation. Further investigation of the relationship between stillbirth rates and gestation length is needed to develop a more complete understanding of the biological processes resulting in the loss of calves at birth.Primiparous cows and multiparous cows were best analyzed separately. In multiparous cows, the third most influential factor was gestation length at all levels of dystocia. Among births needing assistance, gestation lengths of −4 to 13 d had similar stillbirths rates of 23.8%. The analysis procedure also defined three intervals below the mean with significantly different stillbirth rates; −15 to −12 d (55.3%), −11 to −9 d (45.0%), and −8 to −5 d (33.7%) This suggest that gestation length did not have a linear, quadratic, or exponential trend in relation to stillbirths.

Estimation of Relative Economic Value for Herd Life of Dairy Cattle from Profile Equations

Lifetime records of 122,679 cows from 7557 herds, obtained from Mid States Dairy Records Processing Center (Ames, IA), were used to determine net income and net income for the planning horizon. With a planning horizon of five lactations for each cow, the estimated profit from the replacements was credited to each cow not surviving until fifth calving. Net income was defined as lifetime income minus costs. Net income for the planning horizon was defined as net income plus profit from replacements within the planning horizon. Income was from the sale of milk, calves, and culled cows. Costs were included for heifer rearing, feed, labor, and breeding. Longer herd life yielded greater profit for net income and net income for the planning horizon. The rate of increase in profit for longer herd life was reduced for net income for the planning horizon, which accounts for profit from cows replacing a culled cow compared with profit from net income. The relative economic value (phenotypic standard deviation basis) of production to herd life was 0.18:1 for net income and 0.46:1 for net income for the planning horizon. The relative value for herd life was overestimated by about 2.5 times when profit from replacements was not considered. Values for production relative to herd life increased for high milk prices and low feed prices. Lower prices for culled cows in combination with high prices for milk and feed increased the relative economic value of production.

Dairy producers value DHIA milk testing, but some deterred by cost

A survey was conducted to assess the attitudes of past and current members of the California Dairy Herd Improvement Association (CDHIA) toward the DHIA program. Members placed importance on service and production data. Northern and southern DHIA members rated their local DHIA supervisor high with regard to knowledge and service. All regions rated their local DHIA management high with regard to knowledge and service. Over 50% of the northern and southern DHIA members rated laboratory service high. All regions were satisfied with the service of the dairy records processing centers. Cost and the dairies' adoption of on-farm milk-weight meters and/or computers were the most frequently cited reasons for discontinuing DHIA membership. Based on information collected in this survey, CDHIA members continue to look to DHIA records for production and management information.

A Knowledge-Based Mastitis Evaluation Tool for Dairy Management Advisors

A decision aid has been developed to evaluate mastitis data retrieved electronically from two of nine U.S. regional dairy records processing centers. The program was developed for ease of use for inexperienced and experienced field persons assisting farmers with mastitis problems. Heuristic rules to diagnose herd mastitis problems were collected and incorporated into the system from various domain experts. This expert system imports database files for individual cows and queries the user for appropriate herd management information. It allows users to select mastitis control schemes with various degrees of aggressiveness and teaches commonly accepted mastitis control practices.

Correlations Among Somatic Cell Scores of Milk Within and Across Lactations and Linear Type Traits of Jerseys

Genetic and phenotypic correlations were estimated for means of log2 SCC (somatic cell scores) from the first 305 d, the first 75 d, the first 150 d, 76 to 305 d, and 151 to 305 d of lactation for first and second lactations using REML. Somatic cell scores from the Dairy Records Processing Center in Raleigh, North Carolina for 31,180 Jersey cows sired by 411 bulls were used for analyses. Correlations between sire evaluations for somatic cell scores from this study and linear type traits from the American Jersey Cattle Club were also calculated. The model used for analyses of the somatic cell score means included herd-year of calving, age at first calving, sire, and residual. Heritability estimates for the means ranged from .05 to .15 (.12 for 305-d mean for first lactation). Genetic correlations among the somatic cell score means within first and within second lactation were≥.79. The genetic correlation between the 305-d mean from first and second lactation was .90. The smallest genetic correlation across lactations was .68. Somatic cell scores measured at various times were under similar genetic control. Phenotypic correlations were usually much smaller than genetic correlations. Correlations were small between sire evaluations for somatic cell scores measured in first lactation and linear type traits; the largest correlations were between somatic cell scores and dairy form and between somatic cell scores and teat length. Most correlations between sire evaluations for somatic cell scores measured in second lactation and linear type traits were similar to the correlations between somatic cell scores in first lactation and linear type traits. However, in second lactation the negative correlations were larger between somatic cell scores and fore udder attachment and udder depth. Lower scores for dairy form (less angularity), shorter teats, tighter fore udders, and higher udders were associated with lower somatic cell scores, especially somatic cell scores measured in second lactation.

Dairy Herd Improvement: Meeting the Information Needs of the Dairy Industry Through a Totally Integrated Cooperative

The New Zealand dairy industry comprises 2.5million dairy cows milked in 14,600 herds. Dairy herd improvement has been restructured over the past 8 yr into a single legal entity operating as a farmer cooperative company. The cooperative encompasses the national milk records operations; a single dairy records processing center with an associated national animal database; the development, management, and calculation of sire and cow evaluations; and the deployment of scientific and technical resources for research and development of products and services. Also included is 1) the operation of the country's largest progeny-testing program, an artificial breeding, semen, and inseminating service commanding 80% of the artificial insemination market, and 2) the management of the industry's farm extension service. The extension service and the marginal cost of developing and operating sire and cow evaluations are funded through an industry grant. All other operations, including farm management information, are fully funded by users. The totally integrated operation allows cost-effective utilization of personnel, facilities, and equipment. Industry management information is made available to the industry, universities, and research organizations without charge.

Genetic Prediction for Calving Ease in the United States: Data, Models, and Use by the Dairy Industry

Dystocia of Holsteins has a major economic impact on the dairy cattle industry. Genetic evaluation of AI sires for calving ease is sponsored by the National Association of Animal Breeders. The AI organizations and dairy records processing centers collect data from herds that have progeny of AI bulls. Genetic predictions of merit for calving ease have been available for Holstein AI bulls in the US since 1978. A threshold model was implemented during 1988. The threshold model adjusts for the effects of herd-year, season, sex of calf, parity, and birth-year group of sire to predict the genetic merit of each sire for calving ease. Pedigree information from sires, sons, and grandsons is also included in the analysis to improve the reliability of genetic predictions for bulls that have pedigree data available. Each sire's genetic prediction for calving ease is reported as the expected percentage of difficult births of primiparous cows. National in scope, genetic predictions for calving ease are used internationally by breeders of dairy cattle to minimize the risk of difficult births of primiparous cows and to increase the use of AI for young cows.

Relationship of Somatic Cell Score and Linear Type Trait Evaluations of Holstein Sires

Genetic evaluations of Holstein bulls for mean somatic cell score were compared with their standardized transmitting abilities for linear type traits. Based on first lactation daughter information from five dairy records processing centers, PTA for somatic cell scores for 712 sires ranged from –.50 to .56. Standardized transmitting abilities for 14 type traits were provided for these bulls by the Holstein Association. Mean transmitting abilities for udder traits were negative for the 100 bulls with highest PTA and positive for the 100 bulls with lowest PTA for somatic cell score. For all bulls, correlations of PTA for somatic cell score with udder trait evaluations were negative (–.31 for fore udder attachment, –.28 for udder depth, –.21 for front teat placement, –.17 for rear udder width, –.16 for udder cleft, and –.13 for rear udder height). The best five-trait model to predict PTA for somatic cell score consisted of transmitting abilities for fore udder attachment, thurl width, strength, dairy form, and body depth (R2 = .142). If PTA for milk yield was included with evaluations for type traits, it replaced dairy form in the model. Inclusion of quadratic terms did not contribute greatly to prediction of PTA for somatic cell score. Selection for higher, more firmly attached udders should contribute to reducing somatic cell scores.

Genetic Evaluation of Holstein Bulls for Somatic Cells in Milk of Daughters

Lactational means of somatic cell score from sample days of primiparous DHI cows were analyzed to compare dairy records processing centers for data properties, to examine effects of age at calving and month of calving on somatic cell score, and to calculate preliminary PTA of sires for somatic cell scores. Five processing centers contributed data but differed substantially with respect to availability of records in progress, DIM on last sample day, and length of time that data were submitted. Highest lactational means of somatic cell score tended to be in short lactations for young cows but in long lactations for older cows. Regions of the country differed substantially for effect of month of calving on lactational means of somatic cell score, but lactational means of somatic cell scores increased with age at calving for all dairy records processing centers. Standardized yields of milk, fat, and protein were included as multiple traits with somatic cell score for analysis. Heritability of somatic cell score was .08 to .16 for individual processing centers and .10 across processing centers. Phenotypic correlations of somatic cell score with yield traits were negative, but genetic correlations were positive. Selection for decreased somatic cell score on a national basis should be possible and would seem advisable to decrease mastitis infections. Response may be slow, however, because of antagonistic genetic relationships with the yield traits, which have great economic importance.

The Effect of Herd Milk Production on Scoring Dairy Herd Improvement Performance Measures

Objectives of this research were to convert DHI performance measures into percentile scores based on expected values at a producer's rolling herd average and to compare performance with percentile scores based on means of all herds. Holstein herd data from the Minnesota Dairy Records Processing Center were used to derive regression coefficients to predict expected values of DHI management variables from three forms of rolling herd average 4% FCM. Variables were converted to percentiles using expected parameter value, assumption of normal distribution, and the mean square error of the prediction equation as an estimate of the variance.With some exceptions in reproductive categories, expected values for DHI performance measures at the mean rolling herd average were generally better than expected values in lower producing herds and worse than expected values in higher producing herds. Absolute values for the 75th percentile of performance measures based on the mean of all herds translated to percentiles of 54 to 82 when scoring was based on expected values at the 75th percentile of rolling herd average. Electronically importing DHI data and converting to percentiles based on rolling herd average allowed for comparison of DHI performance measures with similar rather than all herds.

Expert System for Evaluation of Reproductive Performance and Management

A microcomputer expert system for dairy herd reproductive management was developed using an expert system shell and Turbo Pascal. The expert system initially examines the broad areas of days open, days to first breeding, detection of estrus, and conception rate to determine whether a problem exists. Interpretations ranging from “excellent” to “severe” were established for each trait. The system then selects an area for evaluation that has the largest negative influence on days open. Once an area has been selected for further evaluation, the expert system utilizes information from the user and DHI reports developed by the Dairy Records Processing Center in Raleigh, NC. These reports identify problems with conception categorized by production, parity, service number, days in milk, breed, and service sire. In addition, questions are presented by the expert system to isolate problems of accuracy of data, use of natural service, semen handling, AI technique, detection of estrus, signs of estrus, and other management areas. Recommendations and suggestions are given. Ten commercial herds having a conception rate less than 40% were evaluated by the expert system and by an extension reproduction specialist who supplied information for the system. Of 100 areas investigated, the expert system and extension specialist identified 47 as potential problem areas, agreeing on 85% of them. Most discrepancies resulted from the specialist applying a less restrictive standard when values were close to a preselected threshold.

National genetic improvement programs for dairy cattle in the United States2

Rate of genetic improvement for milk yield has been increasing in recent years. Cows born in 1986 were about 135 kg superior in breeding value for milk yield to those born in 1985. Over 2.2 million cows contribute new data to genetic evaluations for production traits annually. These evaluations are computed with an animal model that provides best linear unbiased predictions of transmitting abilities for milk, fat, and protein yields and fat and protein percentages. The model includes effects of management group, permanent environment, herd-sire interaction, and animal genetic merit. Unknown-parent groups represent the genetic merit of base populations defined by birth year and sex. Type appraisal data are collected by breed associations and are evaluated with a sire model. Holstein cow evaluations are computed using scores from all appraisals and a multitrait model; evaluations for other breeds are computed using all appraisal scores, a repeatability model, and a single-trait system. Dystocia data are collected by individual AI organizations and dairy records processing centers; they are analyzed by a categorical-trait sire model at Iowa State University with support from the National Association of Animal Breeders. The AI organizations have been extremely important in increasing rate of genetic progress by increasing numbers of young bulls sampled, increasing selection intensity of bull dams through multiple ovulation and embryo transfer, and shortening generation interval through the use of younger cows and some virgin heifers as bull dams. (ABSTRACT TRUNCATED AT 250 WORDS)

Production Losses from Mastitis: Carry-Over from the Previous Lactation

The study examined whether elevation in SCC in the second lactation was associated with reduced milk production in the third lactation. Lactation records from 10,705 Holstein cows from 770 herds were taken from the Dairy Records Processing Center at Raleigh. Cows in the data set were selected so that no SCC test in the first lactation was elevated above a linear score of 4.5 (no mastitis in the first lactation). Using actual and mature equivalent milk production in the first lactation as a baseline, effects of elevated SCC on production in the second and third lactations were examined using linear regression. The effect of high SCC during a cow's current lactation was found to be essentially the same as previously reported by other investigators. An increase in the lactation average linear score of 1.0 was associated with a decrease of approximately 200kg of milk per lactation. Limited carry-over effect of elevated SCC during the second lactation was found in the third lactation. For third lactation milk production, the effect of increased SCC during the preceding (second) lactation was only about 20 to 30% as much as the effect of SCC increases in the third lactation.

Relationship between Herd Management Practices in the Midwest on Milk and Fat Yield

A dairy management survey was conducted in fall 1985 and spring 1986 in the nine-state area served by the Midstates Dairy Records Processing Center in Ames, IA. The questionnaire, consisting of 57 questions with 254 possible choices, was used to survey dairy producers on DHI testing in Arkansas, Illinois, Iowa, Kansas, Missouri, Nebraska, North Dakota, Oklahoma, and South Dakota. The questions covered housing pactices, milking equipment and practices, feeding regimens, calf rearing and feeding, feed additives, various management categories, and artificial insemination usage.The survey responses were merged with the 1985 year end rolling herd production averages from the processing center. A completely fixed model was fit for all 254 potential responses. The greatest differences among solutions were found in the feeding categories with some of the major differences associated with type of grain and forage fed. Feed additives showed the next largest difference among categories with feed ingredients, such as distillers grain, whole cottonseed, and buffers being associated with higher herd averages. There was a positive association between the length of time a producer had been on DHI and herd averages. Herds using a total AI program had herd averages 506kg higher than those using only a beef bull.

Ordered Categorical Sire Evaluation for Dystocia in Holsteins

New statistical procedures for analysis of ordered categorical data were investigated. In using the standardized threshold model, scores are transformed to estimate unknown boundary points and fixed and random effects on an underlying scale of continuous response. The model for calving ease included sex of calf, parity of dam, and the unknown boundary points as fixed effects; herd-year-seasons and sires were random. Data were 5029 dystocia scores on a scale of 1 to 5 collected from June 1982 to January 1984 through the Mid-States Dairy Records Processing Center. The predicted probability of a difficult birth by an average sire indicated that twice as many males as females are born with difficulty. Difficult births declined between first and second parity by a factor of 5. Herd-year-seasons accounted for 13.3% of the variance and sires 3.2%. Heritability on the underlying scale was higher (.147) than on the observed scale (.061). Rank correlations among the threshold model sire solutions and best linear unbiased predictions were .94 when herd-year-seasons were fixed, .98 with random herd-year-seasons, and .99 with normalized scores. Predicted percentage of difficult births for all sires in the analysis ranged from 6 to 18%.

Reporting of Dystocia Scores and Effects of Dystocia on Production, Days Open, and Days Dry from Dairy Herd Improvement Data

Dystocia and livability scores are collected through the Mid-States Dairy Records Processing Center. Thirty-four percent of the cows had dystocia scores reported. Least difficult births were scored 1 and the most difficult births scored 5. Days open in first parity were 14 d greater for births scored 5 versus 1. The differences were larger in later parities. There were 26 more d open in second parity and 19 more d open in third and greater parities for score 5 versus 1. Differences between cows scored 5 versus 1 were 465kg milk and 20.7kg milk fat in first lactations, 576kg milk and 20.9kg milk fat in second lactations, and 725kg milk and 25kg milk fat in third and greater lactations. Cows produced more in lactations following an easy birth. Frequency of difficult births was less in lactations other than the first.

Projection of Protein Yield to 305 Days

Lactation records with at least 305 d in milk, information on milk and protein yields at each sample day, and completion dates during 1984 were obtained from the dairy records processing center in Provo, UT. Most of the 180,323 Holstein and 11,685 Jersey records were from Colorado, Idaho, Maryland, Ohio, Utah, and Washington. Protein yield between last sample day and 305 d was regressed on product of milk yield between last sample day and 305 d, protein percentage from partial record or at last sample day, and a quadratic function of days in milk. This function estimated a factor for each day of lactation to adjust last sample day or partial lactation protein percentage to expected protein percentage for remainder of lactation. Errors from projection with average percentage of partial records had smaller variance at less than 240 d in milk than did those from projection with last sample day percentage. For records with less than 240 d in milk, partial lactation protein percentage was adjusted by a quadratic function of days in milk jointed at 50 and 140 d. For records with 240 d or more in milk, last sample day protein percentage was adjusted by a quadratic without joint points. No difference between factors for first and later lactations was found. Holstein and Jersey factors were applied to records completed during 1982 and 1983 in addition to previously analyzed 1984 data to determine projection errors for partial records of 150 to 304 d in milk. Standard deviations of projection errors showed a linear decline from 15.1kg for Holsteins and 12.6kg for Jerseys for the 150 to 159-d group to almost 0 at 304 d.