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PubMed2026

Integrating genomic additive relationship matrices improves the efficiency in diploid banana breeding.

Partitioning of genetic variance into additive and non-additive components using the pedigree-based best linear unbiased prediction (P-BLUP) model is possible because of the family structure and replicated clones in clonally propagated crops, but this model may overestimate these components. However, the genomic best linear unbiased prediction (G-BLUP) method, which integrates the genetic relationship through molecular marker information reduces the overestimation. Alternatively, a combination of the P-BLUP and G-BLUP, sourcing to create a hybrid matrix that estimates hybrid best linear unbiased prediction (H-BLUP), is proposed. We investigated if integrating molecular information into the clonal model could improve the partitioning of the variance components leading to more accurate estimates of genetic parameters and prediction accuracy of breeding values of 14 key traits in diploid banana. In this study, we used clones of 14 full-sib families from a factorial mating design of four female and five diploid male banana (Musa acuminata) parents, generated at the International Institute of Tropical Agriculture in Arusha. The genomic-based relationship matrices were constructed using a set of 2792 filtered single-nucleotide polymorphism markers. Additive variance and heritability derived from G-BLUP and H-BLUP models reduced bias compared to the P-BLUP model. The H-BLUP estimated the highest prediction accuracies for yield-related and cycling traits, while the P-BLUP model had the highest prediction accuracy estimates for agronomic traits. The use of marker-based models enhances the accuracy of predicting breeding values, contributing to accurate estimates of genetic gain while paving a way for further genomic exploration in diploid banana breeding programs.

Journal Article↗

PubMed2003

Genotype x environment interaction for milk production of daughters of Australian dairy sires from test-day records.

In Australia, dairy farming is carried out in environments that vary in many ways, including level of feeding and climate variables such as temperature and humidity. The aim of this study was to assess the magnitude of genotype x environment interactions (GxE) on milk production traits (milk yield, protein yield, and fat yield) for a range of environmental descriptors. The environment on individual test days was described by herd size (HS), average herd protein yield (AHTDP), herd test-day coefficient of variation for protein yield (HTDCV), and temperature humidity index (THI). A sire random regression model was used to model the response of a sire's daughters to variation in the environment and to calculate the genetic correlation between the same traits measured in two widely different environments. Using test-day records, rather than average lactation yields, allowed exploitation of within-cow variation as well as between-cow variation at different levels of AHTDP, and led to more accurate estimates of sire breeding values for "response to environment." The greatest GxE observed was due to variation in AHTDP, with a genetic correlation of 0.78 between protein yield when AHTDP = 0.54 kg and protein yield when AHTDP = 1.1 kg (the 5th and 95th percentile of the distribution of AHTDP). The GxE was also observed for THI, with a genetic correlation of 0.90 between protein yield at the 5th and 95th percentile of THI. The use of response to environment estimated breeding values to improve the accuracy of international sire evaluations is discussed.

Animals↗

PubMed1999

Solving large mixed linear models using preconditioned conjugate gradient iteration.

Continuous evaluation of dairy cattle with a random regression test-day model requires a fast solving method and algorithm. A new computing technique feasible in Jacobi and conjugate gradient based iterative methods using iteration on data is presented. In the new computing technique, the calculations in multiplication of a vector by a matrix were recorded to three steps instead of the commonly used two steps. The three-step method was implemented in a general mixed linear model program that used preconditioned conjugate gradient iteration. Performance of this program in comparison to other general solving programs was assessed via estimation of breeding values using univariate, multivariate, and random regression test-day models. Central processing unit time per iteration with the new three-step technique was, at best, one-third that needed with the old technique. Performance was best with the test-day model, which was the largest and most complex model used. The new program did well in comparison to other general software. Programs keeping the mixed model equations in random access memory required at least 20 and 435% more time to solve the univariate and multivariate animal models, respectively. Computations of the second best iteration on data took approximately three and five times longer for the animal and test-day models, respectively, than did the new program. Good performance was due to fast computing time per iteration and quick convergence to the final solutions. Use of preconditioned conjugate gradient based methods in solving large breeding value problems is supported by our findings.

Algorithms↗

PubMed2007

Genetic parameters of growth in dairy cattle and associations between growth and health traits.

Body weight (BW) observations on dairy cattle taken on average 35 times between birth and 1,000 d of life were used to estimate daily heritabilities and predict daily breeding values for both pregnancy-adjusted BW (PABW) and growth rate. Daily heritabilities for PABW were moderate to high, ranging from 0.41 (+/-0.027) to 0.82 (+/-0.041). Daily heritabilities for growth rate were high (>0.68 +/- 0.034). The genetic association between various health events, including mastitis and lameness, and weight and growth was investigated by regressing the incidence of health events on breeding values for weight at birth, weaning, calving, and growth rate at 56 d after calving, growth rate at 110 d after calving, and maximum growth rate. Growth at weaning was the only BW measure to significantly affect mastitis (r(g) = 0.24), indicating that cows growing faster at weaning are more prone to mastitis. Increased weight (r(g) = 0.65) and growth rate at weaning (r(g) = 0.38) and increased maximum growth rate (r(g) = 0.71) all contributed to increased feet disorders. The only significant negative genetic association was obtained between reproduction and weight at calving (r(g) = -0.61).

Animals↗

PubMed1992

Sire x herd interactions for weaning weight in beef cattle.

Weaning weight records of 44,357 Australian Angus calves produced by 1,020 sires in 90 herds were used to evaluate the importance of sire x herd interactions. Models fitted fixed effects of contemporary group (herd-year-date of weighing subclass), sex, calf age, and dam age and random effects of sire or of sire and sire x herd interaction using REML. Effects of standardizing the data, including sire relationships and including dam maternal breeding values (MBV) as a covariate were also investigated. Sire x herd interactions were found (P less than .05) in all cases and, in the most complete model, accounted for 3.3% of phenotypic variance. Across-herd heritabilities ranged from .19 to .28. Differential nonrandom mating among herds seemed to occur in the data. Significant sire x herd effects were observed for dam MBV, and adjustment for dam MBV yielded the smallest estimates of interaction variance and across-herd heritability. If sire x herd interactions were due only to genotype x environment interaction, within-herd heritabilities would range from .33 to .49. These estimates are larger than previously reported estimates. Thus, unreported environmental effects common to progeny of individual sires may also be involved in the observed interaction but could not be disentangled from true genotype x environment interaction effects using these data. Results of these analyses suggest that some accommodation of sire x herd interaction effects on weaning weight may be needed in beef cattle genetic evaluations, but a compelling case for development of herd-specific breeding value prediction cannot be made.

Animals↗

PubMed2006

Association of toll-like receptor 4 polymorphisms with somatic cell score and lactation persistency in Holstein bulls.

Mastitis, an inflammatory disease of the mammary gland generally caused by intramammary infections, is the most frequently occurring disease in the North American dairy industry. Reduced milk yield, milk quality, and lactation persistency as well as early culling contribute to the economic losses associated with this disease. During intramammary infections, cells of the innate immune system become activated through pattern recognition receptors that recognize conserved molecular signatures associated with the invading pathogen. The quality, timing, and intensity of the host inflammatory and subsequent immune response determine the fate of this disease. Toll-like receptor 4 (TLR4) is an important pattern recognition receptor that recognizes endotoxins associated with gram-negative bacterial infections. Its role in pathogen recognition and subsequent initiation of the inflammatory and immune response makes it a suitable candidate gene for enhancing disease resistance in Canadian Holsteins. In this study, polymorphisms in the TLR4 gene were identified in the Canadian Holstein bull population. Genotypes and haplotypes were constructed, and their associations with somatic cell score and lactation persistency were determined. Sequencing of selective DNA pools was used to reveal polymorphisms in TLR4. Two DNA pools were constituted based on high and low estimated breeding values for somatic cell scores. A total of 3 single nucleotide polymorphisms (SNP), including 1 SNP in a putative promoter region (P-226) and 2 SNP in exon3 (E3+1656 and E3+2021) of TLR4 were detected. A total of 388 bulls were genotyped for the SNP, haplotypes were reconstructed, and their frequencies were obtained. Polymorphisms in these regions were found to be associated with estimated breeding values for lactation persistency, and somatic cell scores in the Canadian Holstein bull population. The unfavorable alleles at P-226 and E3+1656 were found at a frequency of 40 and 37%, respectively; hence, selection against these alleles is promising in Canadian Holsteins. Selection against the unfavorable allele, T at E3+2021, is limited because of its low frequency (7%). Two frequently occurring haplotypes (GCC and CTC) occurred in 86% of the Canadian Holstein bull population chosen for genotyping. The most frequent haplotype (GCC; 54%) was found to be associated with higher lactation persistency and lower somatic cell scores. The transversion SNP in the putative promoter region (P-226) was in a potential DNA binding site.

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↗

PubMed1987

Breakeven costs for embryo transfer in a commercial dairy herd.

Differences in Estimated Breeding Values expressed in dollars were compared by simulation of two, 100-cow, closed herds. One herd practiced normal intensity of female selection. The other herd generated various herd replacements by embryo transfer by varying 1) selection rate of embryo transfer dams and 2) numbers of daughters per dam from which embryos were transferred, while varying the merit of mates of embryo transfer dams. Estimated Breeding Value dollars were compounded each generation and regressed to remove age adjustments and added feed and health costs. Beginning values in both herds included a standard deviation of 55 Cow Index dollars, herd average of -23 Cow Index dollars, and a 120 Predicted Difference dollars for mates of dams not embryo transferred. Average merit of all sires used increased $12 per year. Herd calving rate (.70), proportion females (.5), calf loss (.15), and heifer survival rate (.83) were used. Breakeven cost per embryo transfer cow entering the milking herd was computed by Net Present Value analysis using a 10% discount rate over 10 and 20 yr. Breakeven cost or the maximum expense that would allow a 10% return on the expenditure ranged from $135 to $510 per surviving cow, $24 to $125 per transfer, $47 to $178 per pregnancy, and $81 to $357 per female calf born. As the number of replacements resulting from embryo transfer increased, breakeven cost per embryo transfer cow decreased due to diminishing return.

Animal Husbandry↗

PubMed2005

Genetic analysis on the direct response to divergent selection for phytate phosphorus bioavailability in a randombred chicken population.

The current study was undertaken to evaluate the direct response to 3 generations of divergent selection for phytate P bioavailability (PBA) in the Athens-Canadian randombred chicken population. Cumulated divergent response (R(C)) was measured as the line difference in PBA at a given generation after adjusting for hatch and sex effects. Results showed a significant response at generation (G)1. The R(C) was unchanged from G1 to G2 and increased (1.62%) from G2 to G3 (P < 0.01) due to the application of best linear unbiased prediction (BLUP) selection in the line selected for high PBA at G2. The average BLUP estimated breeding values were used to estimate the genetic trend for the selected trait across generations. The results showed that the genetic trend was symmetric at G1 and G2 but asymmetric at G3. The application of mixed model methodology was effective in separating the environmental component from phenotypic change. When the data of the high (H) line or the low (L) line in the selected generations (G1 to G3) were combined with the data from the base population (G0), the heritability estimates for PBA were 0.07 +/- 0.02 and 0.09 +/- 0.02, respectively. The line selected for high PBA showed gain, and the line selected for low PBA showed a decrease in estimated breeding values across the generations. The results demonstrated that modest progress could be obtained by incorporating PBA into selection programs. However, other correlated traits of economic importance need to be evaluated before any decision to incorporate selection of PBA into breeding schemes be initiated.

Animals↗

PubMed1998

Maximizing the response of selection with a predefined rate of inbreeding: overlapping generations.

In a breeding scheme, the aim is high rates of genetic gain with limited inbreeding. A dynamic selection rule is developed that maximizes selection response in populations with overlapping generations. The rule maximizes the genetic merit of selected animals while limiting the average relationship of the population after the current round of selection. The latter is shown to limit the contribution of the current population to the future inbreeding. The rule accounts for the selection of some candidates during previous selection rounds and for the expected future contributions of the selection candidates. Inputs for the rule are the BLUP breeding values and ages of selection candidates, the relationship matrix of all animals, and contributions of animals during previous selection rounds. Output is the optimal number of offspring for each candidate. Computer simulations of dairy cattle nucleus schemes showed that predefined rates of inbreeding were actually achieved, without compromising long-term selection response, at least up to 20 yr of selection. At the same rates of inbreeding, the dynamic selection rule obtained up to 44% more genetic gain than direct selection for BLUP breeding values. The advantage of the dynamic rule over BLUP selection decreased with increasing population sizes and with greater predefined rates of inbreeding. Consequently, the dynamic rule should be especially useful in small selection schemes in which relatively low rates of inbreeding are desired.

Age Factors↗

PubMed2005

Genetics of parity-dependant production increase and its relationship with health, fertility, longevity, and conformation in swiss holsteins.

Genetic analysis of production increase (ProdI), defined as an increase in production from early to later lactations, was conducted using data from the Holstein Association of Switzerland. This production increase describes the maturity rate of the cow. The data set contained 42,807 cows with a ProdI value. All cows had completed the first 3 lactations. Different formulas were derived for the computation of ProdI using 1) milk yields or energy-corrected milk yields and 2) yields from all 3 lactations or only 2 of them (first and second, first and third, second and third). Heritabilities of ProdI and genetic and phenotypic correlations of ProdI with somatic cell score, days to first service, nonreturn rate, longevity, and 27 conformation traits were estimated by univariate and bivariate sire models that included relationship among sires. Heritabilities for ProdI were low (0.06 to 0.08), but genetic variation among sires existed. For nonreturn rate and longevity, regressions on the sire estimated breeding values were estimated. Additive genetic correlations of ProdI were moderately favorable with somatic cell score (-0.22 to -0.33) and chest width (0.21 to 0.30), i.e., with traits often associated with long-lasting cows. Unfavorable correlations were found with angularity (-0.18 to -0.26). Regression coefficients from regressing ProdI on sire estimated breeding values for longevity tend to show favorable relationships between these 2 traits (0.10 to 0.20). Results show that animals can be selected for ProdI, as there is good genetic variation between bulls. ProdI is a potential trait to be included in selection indices, as it has favorable genetic relationships with economically important functional traits such as health, conformation, and longevity.

Aging↗

PubMed2004

Sparse inverse of covariance matrix of QTL effects with incomplete marker data.

Gametic models for fitting breeding values at QTL as random effects in outbred populations have become popular because they require few assumptions about the number and distribution of QTL alleles segregating. The covariance matrix of the gametic effects has an inverse that is sparse and can be constructed rapidly by a simple algorithm, provided that all individuals have marker data, but not otherwise. An equivalent model, in which the joint distribution of QTL breeding values and marker genotypes is considered, was shown to generate a covariance matrix with a sparse inverse that can be constructed rapidly with a simple algorithm. This result makes more feasible including QTL as random effects in analyses of large pedigrees for QTL detection and marker assisted selection. Such analyses often use algorithms that rely upon sparseness of the mixed model equations and require the inverse of the covariance matrix, but not the covariance matrix itself. With the proposed model, each individual has two random effects for each possible unordered marker genotype for that individual. Therefore, individuals with marker data have two random effects, just as with the gametic model. To keep the notation and the derivation simple, the method is derived under the assumptions of a single linked marker and that the pedigree does not contain loops. The algorithm could be applied, as an approximate method, to pedigrees that contain loops.

Journal Article↗

PubMed1990

Plasma somatotropin and prolactin concentrations in young dairy sires before and after a 24-hour fast.

To examine the efficacy of plasma concentrations of bST or prolactin as predictors of expected daughter performance, blood samples were collected from young Holstein sires. Blood samples were collected at 15-min intervals via jugular cannulas from 1000 until 1600 h (d 1), beginning 4 h after morning hay feeding. Bulls were not fed again until after collection of blood samples on d 2. Samples were collected at 15-min intervals from 1000 until 1300 h on d 2. Peak values and frequency of hormonal secretory patterns of each bull were characterized by an iterative process in which values greater than 2 SD from the mean were flagged as peaks and excluded from the subsequent calculation of SD and mean. The process continued until an iteration in which no new peaks were flagged. Imposition of a 24-h fast did not alter mean basal bST or prolactin concentrations, but reduced mean peak and overall concentrations of both hormones. The number of bST peaks on d 1 was inversely related to both USDA and Northeast Artificial Insemination Sire Comparison Pedigree Index for milk yield and both USDA and Northeast Artificial Insemination Sire Comparison sire PD for milk yield, but was positively correlated on d 2 with USDA Pedigree Index for milk yield. Mean peak bST on d 2 was correlated with Northeast Artificial Insemination Sire Comparison Estimated Breeding Value for fat yield and sire USDA PD for fat yield. Prolactin peak frequency on d 1 was negatively related to Northeast Artificial Insemination Sire Comparison Pedigree Index for milk yield and sire PD for fat yield. Difference between mean prolactin on d 1 and 2 was negatively related to Northeast Artificial Insemination Sire Comparison Pedigree Index for milk yield and Estimated Breeding Value for fat yield. Endocrine parameters in young sires may be related to genetic merit for production parameters.

Animals↗

PubMed1994

Genetic variation of residual feed consumption in a selected Finnish egg-layer population.

The purpose of the study was to estimate the heritability of residual feed consumption (RFC) and the genetic correlations between RFC and economically important traits. The genetic progress after four generations of selection for RFC and the changes in economically important traits were also investigated. A selection experiment for RFC was carried out from 1983 to 1987. The total data consisted of 3,750 birds and 2,661 records. The (co)variance components were calculated using derivative-free bivariate animal model restricted maximum likelihood (REML). Breeding values were estimated for calculating genetic progress in RFC and correlated responses in the other traits. The heritability of RFC calculated from the whole recorded period (16 to 42 wk) and using all 2,661 records was .46 (+/- .04). The genetic correlations between RFC and egg mass, number of eggs, egg weight, and body weight were not significant. The genetic correlation between RFC and feed consumption was .50 (+/- .04). The breeding value estimates indicated a moderate genetic progress in RFC due to selection. Feed consumption was decreased and body weight gain showed reduction in the last two generations. No change could be found in egg mass, number of eggs, egg weight, age at first egg, or body weight.

Animals↗

PubMed2000

Genetic change in milk, fat, days open, and body weight after calving based on three methods of sire selection.

Three Holstein lines, were compared, based on different methods of sire selection, for genetic change in 3.7% FCM, fat yield, days open, and predicted body weight after calving. The three lines were 1) evaluated sires selected only for 3.7% FCM (milk line), 2) evaluated sires selected on an index that included 3.7% FCM and type traits (index line), and 3) young bulls selected on pedigree for 3.7% FCM (young line). Cows from these lines were born in 1971 through 1993 in five experimental herds owned by the State Farm Division of North Carolina Department of Agriculture. Breeding values of cows in each line computed with a repeatability model were averaged by and regressed on birth year to estimate genetic change. Genetic gains in 3.7% FCM were 81 kg/yr for the milk line, 61 kg/yr for the line selected on index, and 68 kg/yr for the young sire line. Estimates of genetic gain in fat yield were 2.99, 2.16, and 2.54 kg/ yr in the three lines, respectively. Genetic gains in 3.7% FCM and fat yield in the milk line were significantly different from the index and young sire lines, but the index and young sire lines were not significantly different. Estimates of genetic change in days open were 0.71, 0.57, and 0.63 d/yr in the milk, index, and young sire lines, respectively. These estimates were not significantly different. Average breeding values for body weight decreased for births from 1971 to 1981 then rapidly increased for later births in all lines.

Animals↗

PubMed2005

The evolution of genetic architecture. I. Diversification of genetic backgrounds by genetic drift.

The genetic architecture of a phenotype plays a critical role in determining phenotypic evolution through its effects on patterns of genetic variation. Genetic architecture is often considered to be constant in evolutionary quantitative genetic models. However, genetic architecture may be variable and itself evolve when there are dominance and epistatic interactions among alleles at the same and different loci, respectively. The evolution of genetic architecture by genetic drift is examined here by testing the breeding value of four standard inbred mouse strains mated across a set of 26 related recombinant quasi-inbred (RqI) lines generated from the intercross of the Large (LG/J) and Small (SM/J) inbred mouse strains. Phenotypes of interest include age-specific body weights, growth, and adult body composition. If the genetic architecture of these traits has differentiated by genetic drift during the production of the RqI strains, we should observe interactions between tester strain and RqI strain. The breeding values of the tester strains will change relative to one another depending on which RqI strain they are crossed to. The study included an average of 15.1 offspring per cross, over a total of 100 different crosses. Multivariate and univariate analyses of variance indicate that there is strongly significant interaction for all traits. Interaction is more pronounced in males than in females and accounted for an average of about 40% of the explained variation in males and 30% in females. These results indicate that the genetic architecture of these traits has differentiated by genetic drift in the RqI strains since their isolation from a common founder population. Further analysis indicates that this differentiation results in changes in the order of tester strain effects so that common patterns of selection in these differentiated populations could result in the fixation of different alleles.

Animals↗

PubMed2006

Prediction of genetic gain from quadratic optimisation with constrained rates of inbreeding.

There are selection methods available that allow the optimisation of genetic contributions of selection candidates for maximising the rate of genetic gain while restricting the rate of inbreeding. These methods imply selection on quadratic indices as the selection merit of a particular individual is a quadratic function of its estimated breeding value. This study provides deterministic predictions of genetic gain from selection on quadratic indices for a given set of resources (the number of candidates), heritability, and target rate of inbreeding. The rate of gain was obtained as a function of the accuracy of the Mendelian sampling term at the time of convergence of long-term contributions of selected candidates and the theoretical ideal rate of gain for a given rate of inbreeding after an exact allocation of long-term contributions to Mendelian sampling terms. The expected benefits from quadratic indices over traditional linear indices (i.e. truncation selection), both using BLUP breeding values, were quantified. The results clearly indicate higher gains from quadratic optimisation than from truncation selection. With constant rate of inbreeding and number of candidates, the benefits were generally largest for intermediate heritabilities but evident over the entire range. The advantage of quadratic indices was not highly sensitive to the rate of inbreeding for the constraints considered.

Animals↗

PubMed1999

Prediction of genetic contributions and generation intervals in populations with overlapping generations under selection.

A method to predict long-term genetic contributions of ancestors to future generations is studied in detail for a population with overlapping generations under mass or sib index selection. An existing method provides insight into the mechanisms determining the flow of genes through selected populations, and takes account of selection by modeling the long-term genetic contribution as a linear regression on breeding value. Total genetic contributions of age classes are modeled using a modified gene flow approach and long-term predictions are obtained assuming equilibrium genetic parameters. Generation interval was defined as the time in which genetic contributions sum to unity, which is equal to the turnover time of genes. Accurate predictions of long-term genetic contributions of individual animals, as well as total contributions of age classes were obtained. Due to selection, offspring of young parents had an above-average breeding value. Long-term genetic contributions of youngest age classes were therefore higher than expected from the age class distribution of parents, and generation interval was shorter than the average age of parents at birth of their offspring. Due to an increased selective advantage of offspring of young parents, generation interval decreased with increasing heritability and selection intensity. The method was compared to conventional gene flow and showed more accurate predictions of long-term genetic contributions.

Animals↗