Biomedical subjects

T J Lawlor

Publications and source records attributed to T J Lawlor.

At least 19 recordsLinked to original sources

PubMed2005

Genetic parameters for conformation traits in herds that differ in mean final score and completeness of pedigree and performance data.

The objectives of this study were to assess differences in the heritability of type (conformation) traits between herds that differ in mean final score and completeness of pedigree and performance data and to estimate genetic correlations among these environments. Measurement of subjective characteristics, such as conformation traits, may be more difficult in herds with poor management conditions, and genetic evaluation of sires using data from such herds could lead to inaccurate selection decisions. Furthermore, missing pedigree data is a significant problem in many herds, and a lack of phenotypic data from maternal relatives may reduce the effectiveness of animal model evaluation systems. These hypotheses were examined using type classification scores of 1,728,836 first-parity Holstein cows (from 54,223 sires) that calved from 1993 to 2002 in 24,207 US dairy herds. These data included 480,927 records from progeny test daughters, but only 254,891 (47%) were from dams that had valid sire identification, and only 132,953 (28%) were from dams that had also been classified. Herds were grouped into quartiles by mean classification score, percentage of known maternal grandsires, and percentage of classified dams. Estimated heritability of final score was 0.20 in herds with mean score <74.5, 0.17 in herds with <25% known maternal grandsires, and 0.19 in herds with <18% classified dams. Conversely, estimates were 0.39 in herds with mean score >78.7, 0.35 in herds with 100% known maternal grandsires, and 0.37 in herds with >71% classified dams. Estimated genetic correlations between quartiles ranged from 0.86 to 0.95. Based on this study, it appears that improvements in animal identification and data collection in progeny test herds would lead to greater accuracy and stability of genetic evaluations for conformation traits in US Holstein cattle.

Analysis of Variance↗

PubMed2005

Changing definition of productive life in US Holsteins: effect on genetic correlations.

Data included 392,800 records for cows born between 1995 and 1997. Traits analyzed were milk, fat, and protein yields, somatic cell score, days open (DO), 18 linear type traits, final score, and several measures of longevity. Productive life (PL) was defined as the total number of days in milk up to 84 mo of age with a restriction of 305, 500, or 999 d per lactation (PL(305), PL(500), or PL(999), respectively). Herd life was defined as the total number of days from the first calving date to the last (culling) date. A multiple-trait sire model including the effects of registration status, herd-year, age group, month of calving and stage of lactation, sire, and residual was used for parameter estimation. The average duration of the first lactation was 365 d for survivors and 386 d for culled cows. Lactation lengths for the survivors in the next 3 parities all exceeded 330 d. Heritability estimates of between 0.08 and 0.10 were obtained for all definitions of longevity. As maximum recordable PL was increased from 305 to 999 d per lactation, the genetic correlations with milk production increased (from -0.11 to +0.14) and with DO decreased (-0.62 to -0.27). Formulas for an indirect prediction of PL from correlated traits were developed. As maximum PL per lactation was increased, little change in the weights used to predict the various measures of PL, with the exception of DO was found. As the currently used value of PL(305) does not properly account for the longer lactation lengths that are routinely occurring with today's cows, PL with longer lactations may be preferable in routine evaluation.

Animals↗

PubMed2004

Heritability and correlations for body condition score and dairy form within and across lactation and age.

The objectives of the current study were to investigate the relationship between body condition score (BCS) and dairy form and changes in genetic parameters for BCS and dairy form within and across lactations and age. Body condition score and dairy form were obtained from the Holstein Association USA, Inc. Records were edited to include those cows classified between 24 and 60 mo of age and between 0 and 335 d in milk (DIM). A minimum of 20 daughters per sire and 15 cows per herd-classification visit were required. The dataset consisted of 135,178 records from 119,215 cows. Repeatability, multiple trait, and random regression models were used to analyze the data. All models included fixed effects for herd-classification visit, age within lactations 1, 2, and 3 or higher, and 5th-order polynomials for DIM. Random effects included sire and permanent environment for all models. Random regression models included age at classification nested within sire or DIM and lactation number nested within sire. Genetic variance for both BCS and dairy form was lowest in early lactation and highest in midlactation. Genetic correlations within and across lactations were high. The genetic correlation between DIM 0 in lactation 1 and DIM 305 in lactation 3 was estimated to be 0.77 for BCS and 0.60 for dairy form. The genetic correlation estimate between 30 mo of age at classification and 50 mo of age at classification was 0.94 for both dairy form and BCS. The repeatability models appeared to generate accurate evaluations for BCS or dairy form at all ages and stages of lactation.

Aging↗

PubMed2004

Performance of Holstein clones in the United States.

Phenotypic and genetic performance of US Holstein clones from embryo splitting (ETS) and nuclear transfer (ETN) was documented for yield and fitness traits. Holstein Association USA has registered 2319 ETS and 215 ETN clones. The number of male clones has decreased. Animals selected for cloning were slightly superior genetically to population mean for yield traits. For females, mean superiority of pedigree merit of ETS clones was 186 kg for milk, 9 kg for fat, and 7 kg for protein compared with the population for the same birth year; for ETN clones, superiority to the population was 165, 10, and 8 kg. Advantage in pedigree merit for male clones generally was slightly greater. The small pedigree advantage for female clones of <1 standard deviation above breed mean indicates that selection of animals to clone was not based primarily on yield. Yield deviations were lower for ETS clones than for their full siblings, which indicates a possible impact of the technology on performance. Yields were lower for ETN clones than for their noncloned full siblings, but differences were small and based on small numbers of clones. Milk composition for cloned cows was not different from that for the population. Estimated genetic merit based on daughter yield was more similar for male clone pairs with apparent identical genotype than for clone pairs from the same biotechnology but nonidentical as confirmed by blood typing. For ETS clones with confirmed identical genotypes, identical genetic merit should be assigned.

Animals↗

PubMed2004

Genetic correlations among production, body size, udder, and productive life traits over time in Holsteins.

Genetic correlations among milk, fat, and protein yields; body size composite (BSC); udder composite (UDC); and productive life (PL) in Holsteins were investigated over time. The data set contained 25,280 records of cows born in Wisconsin between 1979 and 1993. The multiple trait random regression (MT-RR) animal model included registration status, herd-year, age group, and stage of lactation as fixed effects; additive genetic effects with random regressions (RR) on year of birth using the first-order Legendre polynomial; and residual effects. Heterogeneous residual variances were considered in the model. Estimates of variance components and genetic correlations among traits from MT-RR were compared with those estimated with a multiple trait interval (MT-I) model, which assumed that every 3-yr interval was a separate trait and included the same effects as in the MT-RR model except for the RR. Genetic correlations estimated with MT-RR and MT-I models over time among all traits were compared with correlations among breeding values predicted with the single trait (ST) model without RR. Correlations among breeding values predicted with MT-RR, ST, and MT models were also calculated. Additive genetic and residual variances for all traits except PL increased over time; those for PL were constant. As a result, heritability estimates had no significant changes during the 15 yr. Genetic correlations of PL with milk, fat, protein, and BSC declined to zero or negative; those with UDC remained positive. Correlations among breeding values predicted with ST, MT, and MT-RR models were relatively high for all traits except PL. Genetic correlations between PL and other traits varied over time, with some correlations changing sign. For accurate indirect prediction of PL from other traits, the genetic correlations among the traits need to be re-estimated periodically.

Animals↗

PubMed2004

Correlations among body condition scores from various sources, dairy form, and cow health from the United States and Denmark.

The objectives of this study were to estimate genetic correlations among body condition scores (BCS) from various sources, dairy form, and measures of cow health. Body condition score and dairy form evaluated during routine type appraisal was obtained from the Holstein Association USA, Inc. A second set of BCS was obtained from Dairy Records Managements Systems (DRMS) and was recorded by producers that use PCDART dairy management software. Disease observations were obtained from recorded veterinarian treatments in several dairy herds in the United States. Estimated breeding values for diseases in Denmark were also obtained. Genetic correlations among BCS, dairy form, and cow health traits in the United States were generated with sire models. Models included fixed effects for age, DIM, and contemporary group. Random effects included sire, permanent environment, herd-year season for health traits, and error. Predicted transmitting abilities (PTA) for BCS and dairy form were correlated with estimated breeding values for disease in Denmark. The genetic correlation estimate between BCS from DRMS and BCS from the Holstein Association USA, Inc., was 0.85. The genetic correlation estimate between BCS and a composite of all diseases in the United States was -0.79, and PTA for BCS was favorably correlated with an index of resistance to disease other than mastitis in Denmark (0.27). Dairy form was positively correlated with a composite of all diseases in the United States (0.85) and was unfavorably correlated with an index for resistance to disease other than mastitis in Denmark (-0.29). Adjustment for protein yield PTA had a minimal affect on correlations between PTA for BCS or dairy form and disease in Denmark. Selection for higher body condition or lower dairy form with continued selection for yield may slow deterioration in cow health as a correlated response to selection for increased yield.

Animals↗

PubMed2004

Body condition scores and dairy form evaluations as indicators of days open in US Holsteins.

The objectives of this study were to estimate genetic correlations among body condition score (BCS), dairy form, milk yield, and days open in US Holsteins and investigate the potential of using BCS or dairy form evaluations as early indicators of days open. Dairy form and BCS obtained from the Holstein Association USA, Inc., were merged with mature equivalents (ME) for milk yields and days open data from AIPL-USDA. Cows were required to be classified between 24 and 60 mo of age, before 335 d in milk (DIM) and have ME milk of at least 4537 kg. A minimum of 20 daughters per sire and 10 cows per herd-classification visit (HV) or herd-year-season of calving (HYS) were required. The final data set included 159,700 records. Heritabilities and correlations among dairy form, BCS, milk yield, and days open were estimated with multiple trait sire models. Fixed effects included age at classification for dairy form and BCS, age at calving for milk yield, HV for dairy form and BCS, HYS for milk yield and days open, DIM within lactation group for dairy form and BCS and lactation group for milk yield and days open. Correlations among dairy form, BCS, and days open were generated with and without a ME milk covariable. Correlations between ME milk and days open were generated with and without covariables for dairy form or BCS. Random effects included sire and error. The genetic correlation estimates of days open with dairy form, BCS, and ME milk were 0.48, -0.30, and 0.38, respectively. The genetic correlation estimate between days open and dairy form was 0.38 after adjustment for ME milk, whereas the genetic correlation between days open and BCS was -0.24 after adjustment for ME milk. Combining dairy form evaluations with days open evaluations for 19 recently proven bulls resulted in an average increase of 0.06 for reliability of days open evaluations. The addition of BCS evaluations did not increase reliability when dairy form observations were available.

Aging↗

PubMed2003

Heritabilities and correlations among body condition score, dairy form and selected linear type traits.

The objectives of this study were to estimate the heritability of body condition score (BCS) with data that could be used to generate genetic evaluations for BCS in the US, and to estimate the relationship among BCS, dairy form and selected type traits. Body condition score and linear type trait records were obtained from Holstein Association USA Inc. Because BCS was a new trait for classifiers, scoring distribution and accuracy was not normal. Records from 11 of 29 classifiers were eliminated to generate a data set that should represent BCS data recorded in the future. Edited data included 128,478 records for analysis of first lactation cows and 207,149 records for analysis of all cows. Heritabilities and correlations were estimated with ASREML using sire models. Models included age at calving nested within lactation, 5th order polynomials of DIM, fixed herd-classification visit effects and random sire and error. Genetic correlation estimates were generated between first lactation data that had records from 11 classifiers removed and data with no classifiers removed. Genetic correlation estimates were 0.995 and above between data with and without classifiers removed for scoring distributions, but heritability estimates were higher with the classifiers edited from the data. Heritability estimates for type traits and final score were similar to previously reported estimates. The heritability estimate for BCS was 0.19 for first lactation cows and 0.22 for all cows. The genetic correlation estimate for first lactation cows between BCS and dairy form was -0.73, whereas the genetic correlation estimate between BCS and strength was 0.72. Genetic correlation estimates were nearly identical when cows from all lactations were included in the analyses. Body condition score had a genetic correlation with final score closer to zero (0.08) than correlations of final score with dairy form, stature or strength.

Animals↗

PubMed2002

Analysis of age-specific predicted transmitting abilities for final scores in Holsteins with a random regression model.

Conformation final scores obtained by the Holstein Association were used in this study. Five subsets were sampled from the original complete data, which contained about 7 million records, and (co)variance components for additive genetic, permanent environmental, and residual effects were estimated with a multiple-trait (MT) model at different ages of cows and with a random regression model. Transmitting abilities were predicted with the random-regression (RR) model and with the repeatability model for the national evaluation, using the entire data set. The RR model included fixed and random regressions on age at classification for additive genetic and permanent environmental effects. Additive genetic and residual variances estimated with the MT model increased with aging. Genetic correlations between age groups decreased with their distance. Heritability and repeatability estimates with the RR model were 0.27 and 0.88 on average, increasing with cow's age. Correlations between transmitting abilities predicted with the RR model at various ages and with the repeatability model were in the range of 0.89 to 0.99. In the 1980s, predicted transmitting abilities (PTA) of sires increased with their daughters' age, but in 1991 and 1995, the PTA decreased. In general, sires whose daughters were evaluated at mature ages tended to have higher PTA. For sires and cows, genetic trends estimated from the repeatability model and from the RR model were similar. The low genetic trend of cows at 60 mo for recent years was due to many grade cows that had only single records and little pedigree information.

Aging↗

PubMed1999

Supply of genetic information--amount, format, and frequency.

The volume and complexity of genetic information is increasing because of new traits and better models. New traits may include reproduction, health, and carcass. More comprehensive models include the test day model in dairy cattle or a growth model in beef cattle. More complex models, which may include nonadditive effects such as inbreeding and dominance, also provide additional information. The amount of information per animal may increase drastically if DNA marker typing becomes routine and quantitative trait loci information is utilized. In many industries, evaluations are run more frequently. They result in faster genetic progress and improved management and marketing opportunities but also in extra costs and information overload. Adopting new technology and making some organizational changes can help realize all the added benefits of the improvements to the genetic evaluation systems at an acceptable cost. Continuous genetic evaluation, in which new records are accepted and breeding values are updated continuously, will relieve time pressures. An online mating system with access to both genetic and marketing information can result in mating recommendations customized for each user. Such a system could utilize inbreeding and dominance information that cannot efficiently be accommodated in the current sire summaries or off-line mating programs. The new systems will require a new organizational approach in which the task of scientists and technicians will not be simply running the evaluations but also providing the research, design, supervision, and maintenance required in the entire system of evaluation, decision making, and distribution.

Animals↗

PubMed1998

Effect of full sibs on additive breeding values under the dominance model for stature in United States Holsteins.

Differences in breeding values between dominance and additive models were examined theoretically and with field data. Data included 5.2 million records on stature from 3.0 million US Holsteins. The largest full-sib family had 29 animals, and 7% of all animals had at least one full sib. The dominance model, which accounted for dominance covariances, included the following effects: management, age, stage of lactation, permanent environment, animal additive, and parental dominance (one-quarter of dominance variance) as well as a regression coefficient for inbreeding percentage. Two reduced models were also assumed; in the first, the parental dominance effect was removed, and, in the second, the inbreeding regression coefficient was also removed. The correlations between breeding values in the three models were > 0.999, but breeding values of some animals from full-sib families changed > 5 standard deviations of parental dominance. The largest changes were observed for parents with large numbers of full-sib progeny, with limited information from parents, and without individual performance records. On average, the differences were up to four times larger for cows than for bulls and up to five times larger for dams than for sires. The greatest differences in breeding values between the dominance and the additive models were observed for dams with full-sib progeny, female full sibs, and low reliability bulls with full sibs in the extended family. Animals with large amounts of additive information as progeny-tested bulls were influenced little by the inclusion of dominance. Animals with a large proportion of information coming from animals with dominance relationships, such as cows originating via embryo transfer changed the most.

Animals↗

PubMed1998

Blood groups and milk and type traits in dairy cattle: after forty years of research.

This study addresses the utility of 11 blood groups as selection aids in Holstein breeding schemes and considers issues inherent to the approach of resolving quantitative variation into components that are due to quantitative trait loci. The data consisted of predicted transmitting abilities of 22,614 bulls, first lactation information on 1,924,171 cows, and type scores on 447,800 cows. Linear models were fitted under male half-sib designs, female half-sib designs, and granddaughter designs as well as under the assumption of direct effects of the markers. The evolution of allele frequencies through time was determined, and previous research results were synthesized according to criteria of consistency of biological significance. The inconsistency of results across studies and analytical designs alludes to the importance of the intrinsic nonadditivity of genetic and biological phenomena to quantitative trait locus detection and marker-assisted selection. In our analyses, three associations met the criteria of consistency--a C blood group effect on rump angle, an L effect on milk yield and composition traits, and an S effect on milk fat yield. The M locus appears to be directly associated with effects on milk and protein yields. An enhanced understanding of the biochemical and physiological bases of quantitative genetics should be a long-term objective of this type of genetic analysis.

Animals↗

PubMed1998

Trait-based analysis in dairy cattle using blood group polymorphisms.

The potential of trait-based analysis to detect quantitative trait loci was investigated using blood group polymorphisms as the marker systems and milk and type traits in Holstein cattle as the quantitative traits. Within large half-sib families, animals were ranked on their predicted transmitted abilities or phenotypes, and blood group allele frequencies were compared between the upper and lower 5% tails of the distributions. Genotype frequencies within large families were also examined for evidence of selection. All of the major effects that had previously been detected using linear model analyses were identified by the trait-based analyses of a C blood group effect on rump angle, an L effect on milk yield and composition traits, an S effect on milk fat yield, and a direct effect of the M locus on milk and protein yields. These results provide additional support for the biological validity of these associations and also demonstrate the utility of trait-based analysis for the detection of quantitative trait loci within existing dairy breeding programs. However, just as in the linear model analyses, an analytical strategy should be utilized that allows the identification of the effects that are consistent across environments and genetic backgrounds.

Alleles↗

PubMed1998

Use of linear type and production data to supplement early predicted transmitting abilities for productive life.

Genetic evaluations for the length of productive life based on actual DHIA culling data have been available in the US since January 1994. Although substantial genetic variation in productive life exists, the reliability of selection is often low, particularly for recently progeny-tested bulls having daughters that have not yet had an opportunity to be culled. Correlated production and conformation traits, which have higher heritability than productive life and are available earlier in life, may be used to enhance evaluations of productive life for young bulls that have little or no direct culling information available. Genetic correlations between productive life and milk, fat, dairy form, and udder traits ranged from +0.22 to +0.46. The maximum reliability of the indirect prediction of productive life from 16 correlated type and production traits was 0.56, and the maximum reliability from a subset of 10 traits was 0.51. Indirect information about productive life that was derived from type and production traits was combined with actual culling information to increase the total amount of available information for many recently progeny-tested bulls. The procedures described herein for enhancing direct evaluations for the productive life of dairy sires with indirect information about production and type were implemented by the USDA Animal Improvement Programs Laboratory and the Holstein Association USA in July 1994.

Animals↗

PubMed1997

Dominance models with method R for stature of Holsteins.

Estimates of variance components were obtained with method R for several additive and dominance models. The data included 301,960 records for first parity and 280,040 records for later parities of Holsteins. The single-record model included effects of management, regression on inbreeding percentage, age at calving, stage of lactation, and additive and dominance effects. The repeatability model included these effects in addition to permanent environment. For the single-record model, estimates were 46% of the total variance for additive variance, 12% of total variance for dominance variance, and -0.06 for the regression coefficient on inbreeding. In the repeatability model, the variance for permanent environment was estimated at 5%; other estimates were similar. When the dominance effect was eliminated, the estimate of the variance for permanent environment increased to 17% for the repeatability model. Elimination of stage of lactation increased regression on inbreeding to 0.09 and the estimate of dominance variance to 17% in the single-record model. The same change increased the estimate of additive variance to 64% for the repeatability model. Elimination of regression on inbreeding or stage of lactation had a small effect on the estimates. The presence or absence of the dominance effect had little influence on additive variance. In the absence of dominance, the estimate of the permanent environment effect included the dominance effect. Estimates of variances with method R are very sensitive to age adjustments. With the adjustments, the estimates of the dominance and additive variances are consistent.

Aging↗

PubMed1994

Adjustment for heterogeneous variance in genetic evaluations for conformation of United States Holsteins.

A method was developed to account for heterogeneous phenotypic variance for final type (conformation) score within herd-year-month-classifier subclasses for national genetic evaluations of US Holsteins. Phenotypic variances decreased 3.5-fold as within-subclass means increased from 70 to 89 points, and variances increased slightly over time and with increases in subclass size and proportion of registered animals. A model containing known management characteristics was fitted to phenotypic standard deviations within subclass, and resulting solutions were used to estimate the prior variance for each subclass. Prior estimates and phenotypic variance estimates within subclass were combined using Bayesian methods, resulting in posterior estimates that contained more information than either the prior estimates or the within-subclass statistics. Observations were standardized to a common variance using the mean of the posterior density of the phenotypic standard deviation within subclass. Moderate changes in PTA occurred for low reliability bulls, bulls with many progeny in a single herd, and foreign bulls subjected to positive assortative mating. Significant increases occurred in PTA of superior cows in subclasses with high means. Incorporation of a heterogeneous variance adjustment into national genetic evaluations should increase fairness of selection among cows and young bulls and may increase the rate of genetic gain from female selection.

Aging↗

PubMed1992

Genetic parameters of conformation traits, milk yield, and herd life in Holsteins.

Genetic parameters were estimated simultaneously for 5 herd-life traits, 15 conformation (type) traits, and milk yield measured in first lactation for 128,601 Holstein cows. Heritabilities of all traits were higher in registered than in grade cows. Genetic correlations of linear type traits with first lactation yield ranged from -.48 for udder depth to .54 for dairy form. Genetic correlations among milk yield and herd-life traits were all positive except for milk-corrected herd life in grade cows. Udder traits had largest absolute genetic correlations with herd-life traits, followed by body traits and feet and leg traits. Some traits associated with body size and foot angle differed between registered and grade cows. Estimates of genetic trends from obtained parameters revealed greatest progress for milk yield from single-trait selection but also the largest changes for some type traits and milk-corrected herd life in an undesirable direction. Relative milk to type ratios of between 2:1 and 3:1 yielded 90% of the gain in milk yield with no change or slight improvement in type traits and functional herd life. Selection for type traits associated with herd life appears to be warranted to improve days of functional herd life or to decrease involuntary culling of dairy cows.

Animals↗

PubMed1992

Use of reproductive technology to estimate variances and predict effects of gene interactions.

Advanced reproductive techniques are creating the large numbers of close relatives needed to study gene interactions. Identical triplets, a set of 26 full sisters, a family of 4215 three-quarter sisters (same sire and maternal grandsire), a family of 76,698 half sisters, and 1.6 million granddaughters of Round Oak Rag Apple Elevation now have lactation records. Similarity of closest relatives might be explained by similar nonadditive as well as additive genetic merit. The 23,015 families of full sisters with mean family size of 3 provide nearly as much information about dominance variation as do the 55,779 families of three-quarter sisters with mean family size of 13; the 79 families of clones provide little information by comparison. Hypothetically, REML analysis of all US Holstein data could provide estimates of dominance and additive x additive variance with standard errors approximately 1% of phenotypic variance, but estimates of any higher order interactions would have standard errors greater than 10%. The tilde-hat approximation proved to be incompatible with animal models but was used for sire-maternal grandsire analysis of 765,868 first lactation records. Dominance variance was estimated as 3.5% of phenotypic variance for milk and 3.3% for fat with standard error of 4.2%. With constant data set size, variances are estimated most precisely if family sizes equal 1 plus ratio of within-family to between-family variance. An animal model evaluation including dominance relationships for 581,670 animals was computed, but gene interactions from distant ancestor pairs were ignored. Mating advice and improved additive predictions, especially for clones, could be obtained by including dominance in models.

Animals↗