Lawrence R Schaeffer

University of Guelph | UOGuelph · Animal Biosciences

Regular changes in the environment and biological responses generate seasonal patterns in the reproduction in small ruminants. Breeding seasonality is a significant constraint impacting efficiency of lamb production. However, seasonality-related traits present a special peculiarity from a statistical point of view being circular data (day of year r...

Background: Egg production traits are economically important in poultry breeding programs. Previous studies have shown that incorporating genomic data can increase the accuracy of genetic prediction of egg production. Our objective was to estimate the genetic and phenotypic parameters of such traits and compare the prediction accuracy of pedigree-...

An important goal in animal breeding is to improve longitudinal traits; that is, traits recorded multiple times during an individual’s lifetime or physiological cycle. Longitudinal traits were first genetically evalu-ated based on accumulated phenotypic expression, phenotypic expression at specific time points, or re-peatability models. Until now,...

Animal models evolved from sire models and inherited some issues that affected sire models. Those issues include definition and treatment of contemporary groups, accounting for time trends and dealing with animals having unknown parents. The assumptions and limitations of the animal model need to be kept in mind. This review of the animal model wil...

Data were records of daily food intake and milk production, periodic measures of milk composition and all health and reproductive information from 140 multiparous Holstein cows involved in various experiments at the Agriculture Canada dairy research station in Lennoxville, Quebec. Energy concentrations of the total mixed rations were also available...

Abstract Text: Different selection strategies involving genomic data for the swine industry were compared through simulation on their ability to reduce the effects of the PRRS virus. Ten thousand QTL with up to 7 alleles each were assumed to affect 22 traits including resistance to PRRS. The base strategy did not utilize genomic information and i...

Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first relies on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationship with the individual of interest. The second is a ridge-re...

Abstract Text: A genome-wide association study (GWAS) of harvest weight was carried out in an aquaculture population of Atlantic salmon. The 478 fish had EBV for this trait and genotypes for 3,318 SNP. The analysis took into account pedigree relationships among individuals to avoid spurious associations due to population structure. False positives...

Valacta (Sainte-Anne-de-Bellevue, Québec, Canada) is the Canadian Dairy Herd Improvement organization responsible for milk recording in Québec and Atlantic provinces. Up to 14 first-lactation body condition score (BCS) records were collected per cow (average of 2.5 records per cow), allowing the trait to be described by a random regression animal m...

The objective of this research was to estimate daily genetic correlations between longitudinal body condition score (BCS) and health traits by using a random regression animal model in first-lactation Holsteins. The use of indicator traits may increase the rate of genetic progress for functional traits relative to direct selection for functional tr...

A method of approximating estimated breeding values (EBV) from a multivariate distribution of true breeding values (TBV) and EBV is proposed for use in large-scale stochastic simulation of alternative breeding schemes with a complex breeding goal. The covariance matrix of the multivariate distributions includes the additive genetic (co)variances an...

The objectives of this study were to evaluate antibody (AMIR) and cell-mediated immune responses (CMIR), survival, and somatic cell score (SCS) between purebred Holstein (HO) and crossbred Norwegian Red × Holstein (NRHO) first-calf heifers postpartum. Additionally, immune response traits observed as calves in a previous study were correlated with t...

Health traits are of paramount importance for economic dairy production. Improvement in liability to diseases has been made with better management practices, but genetic aspects of health traits have received less attention. Dairy producers in Canada have been recording eight health traits (mastitis (MAST), lameness (LAME), cystic ovarian disease (...

Test-day (TD) records of milk, fat-to-protein ratio (F:P) and somatic cell score (SCS) of first-lactation Canadian Holstein cows were analysed by a three-trait finite mixture random regression model, with the purpose of revealing hidden structures in the data owing to putative, sub-clinical mastitis. Different distributions of the data were allowed...

The objective of this research was to estimate genetic parameters of first-lactation body condition score (BCS), milk yield, fat percentage (Fat%), protein percentage (Prot%), somatic cell score (SCS), milk urea nitrogen (MUN), lactose percentage (Lact%), and fat to protein ratio (F:P) using multiple-trait random regression animal models. Changes i...

Progeny of Holstein females mated to sires of different breeds were genetically evaluated along with their purebred Holstein contemporaries born in the same herds using multiple trait animal models. The resulting estimated breeding values (EBV) of cows were averaged within breed of sire and compared relative to progeny of purebred Holstein sires fo...

Multiple-trait random regression models with recursive phenotypic link from somatic cell score (SCS) to milk yield on the same test day and with different restrictions on co-variances between these traits were fitted to the first-lactation Canadian Holstein data. Bayesian methods with Gibbs sampling were used to derive inferences about parameters f...

The objective of this research was to estimate the genetic parameters of body condition score (BCS) in the first 3 lactations in Canadian Holstein dairy cattle using a multiple-lactation random regression animal model. Field staff from Valacta milk recording agency (Sainte-Anne-de-Bellevue, QC, Canada) collected BCS from Québec herds several times...

The assumption of a single permanent environmental (PE) effect contributing to every record made by an animal is questioned. An alternative model where new PE effects accumulate with each record made by an animal is proposed. An example is used to illustrate the differences between the traditional model and the proposed model.

Alternative Norwegian sheep breeding schemes were evaluated by stochastic simulation of a breeding population with about 120 000 ewes, considering the gain for an aggregate genotype including nine traits and also the rate of inbreeding. The schemes were: a scheme where both young unproven rams (test rams) and proven rams (elite rams) are used in ar...

As an extension of a former study, the objectives of this study were to evaluate purebred Holstein (HO; n=140) and crossbred Norwegian Red × Holstein (NRFX; n=142) calves for antibody (AMIR) and cell-mediated immune responses (CMIR) as well as survival. Blood was collected on d 0, 14, and 21, and calves were immunized on d 0 and 14 with type 1 (Can...

Finite mixture, multiple-trait, random regression animal models with recursive links between phenotypes for milk yield and somatic cell score (SCS) on the same test-day were applied to first lactation Canadian Holstein data. All models included fixed herd-test-day effects and fixed regressions within region-age at calving-season of calving classes,...

Multiple-trait (MT) finite mixture random regression (MIX) model was applied using Bayesian methods to first lactation test-day (TD) milk yield and somatic cell score (SCS) of Canadian Holsteins, allowing for heterogeneity of distributions with respect to days in milk (DIM) in lactation. The assumption was that the associations between patterns of...

The shape of individual deviations of milk yield for dairy cattle from the fixed part of a random regression test day model (RRTDM) was investigated. Data were 53,217 TD records for milk yield of 6,229 first lactation Canadian Holsteins in Ontario. Data were fitted with a model that included the fixed effects of herd-testdate, DIM interval nested w...

Using spline functions (segmented polynomials) in regression models requires the knowledge of the location of the knots. Knots are the points at which independent linear segments are connected. Optimal positions of knots for linear splines of different orders were determined in this study for different scenarios, using existing estimates of covaria...

Multiple-trait random regression animal models with simultaneous and recursive links between phenotypes for milk yield and somatic cell score (SCS) on the same test day were fitted to Canadian Holstein data. All models included fixed herd test-day effects and fixed regressions within region-age at calving-season of calving classes, and animal addit...

Twice-a-day milking is currently the most frequently used milking schedule in Canadian dairy cattle. However, with an automated milking system (AMS), dairy cows can be milked more frequently. The objective of this study was to estimate genetic parameters for milking frequency and for production traits of cows milked within an AMS. Data were 141,927...

Preadjustment of phenotypic records is an alternative to accounting for the effect of pregnancy within the genetic evaluation model. Variance components used in the Canadian Test-Day Model may need to be re-estimated after preadjusting for pregnancy. The objective of this study was to assess the effect of preadjusting test-day yields on variance co...

Pregnancy has a negative impact on milk production in dairy cattle. Estimates of the effects of pregnancy are required in genetic evaluation models. Test-day records of Ayrshire, Jersey, Brown Swiss, and Guernsey breeds were analyzed phenotypically for the effect of pregnancy using 4 different models. Milk, fat, and protein yields were analyzed sep...

The objective of this study was to compare the immune response of Holstein and Norwegian Red x Holstein calves on 13 commercial Canadian dairy farms. Data were collected on 135 calves, 68 Holstein and 67 Norwegian Red x Holstein calves aged between 2 and 6 mo. The calves were immunized with hen egg white lysozyme to induce antibody-mediated immune...

Random regression models were applied to eight conformation traits (i.e. stature, rump angle, thurl width, rear leg set, rear udder width, rear udder height, udder depth, and fore udder attachment) of Holstein cows from the northeastern United States. Covariates for fixed and random regressions included age and age-squared for six of the traits, an...

Selection of animals based on their BLUP evaluations from an animal model results in animals that are closely related which leads to increased rates of inbreeding. The tendency for higher inbreeding rates is greater at low heritability values. Several attempts have been made to reduce the impact of parent average breeding values from animals evalua...

The success of fine-scale mapping and genomic selection depends mainly on the strength of linkage disequilibrium (LD) between markers and causal mutations. With Lewontin's measure of LD (known as D'), high levels of LD that extend over several million base pairs have been reported in livestock. However, this measure of LD can be strongly biased upw...

Three models for the analysis of functional survival data in dairy cattle were compared using stochastic simulation. The simulated phenotype for survival was defined as a month after the first calving (from 1 to 100) in which a cow was involuntarily removed from the herd. Parameters for simulation were based on survival data of the Canadian Jersey...

The estimation of (co)variance components for multiple traits with maternal genetic effects was found to be influenced by population structure. Two traits in a closed breeding herd with random mating were simulated over nine generations. Population structures were simulated on the basis of different proportions of dams not having performance record...

Genome-wide estimated breeding values can be computed from the simultaneous estimates of the effects of small intervals of DNA throughout the genome on a trait or traits of interest. Small intervals or segments of DNA can be created by the use of thousands of single nucleotide polymorphisms (SNP) available in panels of 10, 25 and 50 thousand SNP. A...

The effects of additive, dominance, additive by dominance, additive by additive and dominance by dominance genetic effects on age at first service, non-return rates and interval from calving to first service were estimated. Practical considerations of computing additive and dominance relationships using the genomic relationship matrix are discussed...

Robust procedures for estimation of breeding values were applied to multiple-trait random regression test-day (TD) model to reduce the influence of outliers on inferences. Robust estimation methods consisted of correcting selected observations (defined as outliers) in the process of solving mixed-model equations in such a way that 'new' observation...

The shape of individual deviations of milk yield for dairy cattle from the fixed part of a random regression test day model (RRTDM) was investigated. Data were 53,217 TD records for milk yield of 6,229 first lactation Canadian Holsteins in Ontario. Data were fitted with a model that included the fixed effects of herd-testdate, DIM interval nested w...

The aim of this study was to develop the linear haplotype sharing transmission disequilibrium test (LHS-TDT) method and combine this method with the simple regression method to estimate the precision of QTL positions in granddaughter designs. This precision was determined by Monte Carlo simulation in granddaughter designs. A single bi-allelic QTL a...

Animals can be genotyped for thousands of single nucleotide polymorphisms (SNPs) at one time, where the SNPs are located at roughly 1-cM intervals throughout the genome. For each contiguous pair of SNPs there are four possible haplotypes that could be inherited from the sire. The effects of each interval on a trait can be estimated for all interval...

The performance of several transmission disequilibrium tests (TDT) for detection of quantitative trait loci (QTL) in data structures typical of outbred livestock populations were investigated. Factorial mating designs were simulated with 10 sires mated to either 50 or 200 dams, each family having five or eight full sibs. A single marker and QTL, bo...

Legendre polynomials of orders 3 to 8 in random regression models (RRM) for first-lactation milk production in Canadian Holsteins were compared statistically to determine the best model. Twenty-six RRM were compared using LP of order 5 for the phenotypic age-season groupings. Variance components of RRM were estimated using Bayesian estimation via G...

The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL va...

Abstract The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio...

Pedigree information and test-day records for the first 3 parities of Milking Shorthorn dairy cattle from 5 countries were analyzed. After editing, the data included 1,018,528 test-day records from 68,653 cows. A multiple-lactation random regression test-day model with Legendre polynomials of order 4 and a Bayesian method were used to estimate vari...

Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE an...

Age at first insemination, days from calving to first insemination, number of services, first-service nonreturn rate to 56 d, days from first service to conception, calving ease, stillbirth, gestation length, and calf size of Canadian Holstein cows were jointly analyzed in a linear multiple-trait model. Traits covered a wide spectrum of aspects rel...

Multiple lactation random regression model was applied to test-day records of milk, fat and protein yields in the first three lactations of the Czech Holstein breed. Data included 9 583 cows, 89 584, 44 207 and 11266 test-day records in the first, second and third lactation, respectively. Milk, fat and protein in the first three lactations were ana...

Genetic evaluation strategies were studied using simulated data for three lactation traits in each of two importing and two exporting countries, each running a typical progeny test program. Conversion (CNV), multiple-trait across-country evaluation (MACE) and global animal model (GAM) strategies were considered. Base populations were either unselec...

A two-dimensional random regression model with regressions on days in milk (DIM) and parity number was applied to lactational milk yields in Chinese Simmental cattle. Random regressions were fitted for additive genetic and permanent environmental effects using a two-dimensional polynomial on DIM and parity number. A total of 4340 lactational milk y...

The objectives of this study were to estimate the heritability of locomotion score and estimate the genetic and phenotypic correlations of locomotion score with milk production (150-day milk), body condition score (BCS), and selected conformation traits. Data were collected from 26 herds that were visited in October and December of 1997. During tho...

The main objective of this study was to estimate genetic relationships between lactation persistency and reproductive performance in first lactation. Relationships with day in milk at peak milk yield and estimated 305-d milk yield were also investigated. The data set contained 33,312 first-lactation Canadian Holsteins with first-parity reproductive...

Two robust estimation procedures were applied to a random regression test-day model to reduce the effects of test-day records that are generally labelled as outliers. One robust procedure consisted of estimating residuals (actual observation minus predicted) from the genetic evaluation model, computing the standard deviation of residuals across all...

First-lactation milk yield test-day records of Canadian Holsteins were analyzed by single-trait random regression test-day models that assumed normal or Student's-t distribution for residuals. Objectives were to test the performance of the robust statistical models that use heavy-tailed distributions for the residual effect. Models fitted were: Gau...

Random regression models (RRM) have become common for the analysis of longitudinal data or repeated records on individuals over time. Applications in animal breeding research are emphasized while recognizing that RRM are used in many biological situations including human health. The best known application of RRM has been to genetic evaluation of da...

A limiting factor in the analysis of non-additive genetic models has been the ability to compute the inverses of non-additive genetic covariance matrices for large populations. Also, the order of the equations was equal to the number of animals times the number of non-additive genetic effects that were included in the model. This paper describes a...

Single- and multiple-country random regression models were applied to estimate genetic parameters for first-lactation test-day milk yield of cows from four countries: Australia, Canada, Italy, and New Zealand. Selected countries represented a wide range of production systems and environments. Milk production in Canada and Italy is based mainly on i...

This book contains 16 chapters. Topics covered are: patents, trade secrets and other forms of intellectual property rights; advent of animal patents: innovation and controversy in the engineering and ownership of life; economics of patents; access to data and intellectual property; global intellectual property: international developments in animal...

First-lactation milk yield test-day records on cows from Australia, Canada, Italy, and New Zealand were analyzed by single- and multiple-country random regression models. Models included fixed effects of herd-test day and breed composition-age at calving-season of calving by days in milk, and random regressions with Legendre polynomials of order fo...

Genetic parameters of calving ease in first and second parities of Canadian Holsteins were estimated using a Bayesian approach. Multiple-trait calving ease records on 94 925 cows (no missing records) were analyzed with a threshold model. The model included a fixed effect for sex of calf and random effects of herd–year–season, sire of cow, and sire...

Bayesian (via Gibbs sampling) and empirical BLUP (EBLUP) estimation of fixed effects and breeding values were compared by simulation. Combinations of two simulation models (with or without effect of contemporary group (CG)), three selection schemes (random, phenotypic and BLUP selection), two levels of heritability (0.20 and 0.50) and two levels of...

INTRODUCTION Recently, there has been considerable interest in random regression (RR) models (Schaeffer and Dekkers, 1994) because of their flexibility and ability to describe individual gene expression at different time points (Swalve, 2000, Jensen, 2001). A key element in a RR model is the function submodel for the random regressions, which can r...

Abstract Bayesian (via Gibbs sampling) and empirical BLUP (EBLUP) estimation of fixed effects and breeding values were compared by simulation. Combinations of two simulation models (with or without effect of contemporary group (CG)), three selection schemes (random, phenotypic and BLUP selection), two levels of heritability (0.20 and 0.50) and two...

Stochastic simulation was used to study the effect on selection response of accounting for inbreeding versus ignoring it in the construction of the inverse of the relationship matrix used in mixed model equations (MME) to obtain BLUP of breeding values. Three different heritabilities of 0.10, 0.25, and 0.50 and two different family structures were...

1 Introduction In the analysis of large amounts of data to obtain BLUP, large sets of mixed model equations must be solved iteratively, which can involve considerable computing time. In real life, solutions are required only periodically for breeders to choose the best individuals, so that computing time is not usually a limiting factor. In simulat...

Hierarchical models were fitted to first lactation test day milk yields of Canadian Holstein cows. Models included Wilmink’s lactation curve and herd-test date effects in the first stage, and herd–year–season of calving, region–age–season of calving and animal genetic effects in the second stage of the hierarchy, using various combinations of these...

A model for the genetic evaluation of dairy bulls and cows for subjectively scored conformation traits using random contemporary groups is proposed. Variance parameters for the random factors of the model were estimated for 14 traits in Jersey cattle. Three alternatives for reducing the influence of parent averages on estimated breeding values were...

A multiple trait, multiple country, international evaluation model is described for dairy or beef cattle. Such a model is necessary so that countries with estimated breeding values for several subtraits from a within-country multiple trait model do not have to combine those values into one single trait. A multiple trait de-regression step is necess...

We implemented statistical models of Bayesian inference that included direct and maternal genetic effects for genetic parameter estimation of categorical traits by Gibbs sampling. The estimation errors and variances of estimates of animal versus sire and maternal grandsire models, of linear versus threshold models, of single-trait versus multiple-t...

The objective of the study was to calculate phenotypic relationships between energy balance in early lactation and health and reproduction in that lactation. Data were 26,701 daily records of dry matter intake and milk production, periodic measures of milk composition and body weight, and all health and reproductive information from 140 multiparous...

Two computing algorithms for solving mixed model equations for a multiple lactation, multiple trait random regression test day model were compared. The model for each trait (yields of milk, fat, and protein, and somatic cell scores in the first three lactations) included fixed contemporary groups, fixed regressions within levels of time–region–age–...