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PubMed2025

Haplotype stacking to improve stability of stripe rust resistance in wheat.

Genotype-by-environment interaction analysis and haplotype-level characterisation provide novel insights into the stability of stripe rust resistance. Breeding selection strategies are proposed to achieve rapid and stable genetic gains across environments. This study investigated stripe/yellow rust (YR) responses in the Vavilov wheat diversity panel evaluated across 11 field experiments conducted in Australia and Ethiopia during 2014-2021. Genotype-by-environment interaction (GEI) was analysed using a factor analytic (FA) model. Genotype-level selection was performed with overall performance (OP) and root-mean-square deviation (RMSD), which reflected average performance and stability of YR resistance across environments, respectively. Genomic estimated breeding values (GEBV) for these traits were calculated and compared with those from a multi-trait GBLUP model with average performance represented by the mean GEBV across environments and stability by the standard deviation of GEBV across environments. The FA-based and multi-trait GBLUP GEBV had high correlations. Haplotypes with large effects on OP and RMSD were identified using the local GEBV method. Favourable haplotypes were then used for stacking in breeding simulations, using the Vavilov collection as a base. Compared to truncation selection, optimal haplotype selection (OHS) using an artificial intelligence (AI)-based algorithm achieved longer-term genetic gains for both OP and RMSD (after many generations) by initially selecting founder parents that maximised favourable haplotypes. Simulations using YR responses from diverse environments that mimicked fluctuating environmental conditions across seasons were conducted to evaluate strategies for selection of YR resistance that is stable across years. Strategies which gave most weight to OP, but some weight to RMSD were optimal in these conditions, and substantially reduced variation of performance across years. This study provides useful information for breeding cultivars with both high YR resistance and high stability of resistance across environments.

Triticum↗

PubMed1992

Divergent selection for immune responsiveness in chickens: estimation of realized heritability with an animal model.

With the aim of improving general disease resistance, chickens were divergently selected for their antibody titers 5 d after immunization with sheep red blood cells for nine generations. Selected and control lines differed significantly for primary and secondary responses after three generations. Heritability of the antibody titer was estimated by REML fitting an animal model using a derivative-free algorithm. The heritability estimate using data on all lines simultaneously was .31. Realized heritability of the antibody titer in the selected lines was estimated by using either the phenotypic cumulative response as the deviation from the control line or the mean breeding values obtained with an animal model. Values from the two methods were consistent, giving a realized heritability of .21 and .25 in the high and low lines, respectively. The genetic trend was not linear and the response to selection tended to accelerate over generations.

Animals↗

PubMed1991

National genetic improvement programs for dairy cattle in the United States.

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)

Animals↗

PubMed2025

Genomic prediction and genome-wide association study for liver abscesses in crossbred beef cattle.

Liver abscesses are a concern in feedlot cattle, and little is known about the role of genetics in their development. This study aimed to estimate genetic parameters and to identify single-nucleotide polymorphisms (SNPs) associated with liver abscesses. Crossbred cattle representing 18 breeds in the U.S. Meat Animal Research Center Germplasm Evaluation Program were phenotyped for liver abscesses at slaughter (n = 9,044). Seventeen percent of cattle had liver abscesses. These cattle had genotypes that were imputed to sequence variant genotypes. After filtering and quality control, 340,723 SNPs were used in the analysis. Liver abscess prevalence was modeled with a single-step genomic best linear unbiased prediction (ssGBLUP) threshold model using a Bayesian framework. The model included contemporary group (sex, treatment group, and slaughter date), additive genomic, and residual effects. Genomic heritability was 0.039 (95% highest posterior density = 0.005, 0.081), which was very small. To assess prediction quality, a 5-fold random cross-validation structure was used. Method Linear Regression was used to assess accuracy, bias, and dispersion by comparing estimated breeding values (EBV) from full and reduced analyses. Cross-validation metrics showed EBV based on genotypes had 0.05 reliability (SD < 0.01) with no bias relative to EBV based on genotypes and phenotypes. For the genome-wide association study, SNP effects were back calculated from the EBV solutions from ssGBLUP. No SNPs were associated with liver abscesses at a Benjamini-Hochberg adjusted 0.05 significance level. Although a large dataset was used, this result was because of the low genomic heritability and imprecise EBV used to calculate SNP effects. Based on these results, environmental factors contribute to most of the variation in liver abscesses. Genetic selection to reduce liver abscesses would be slow because of the low genomic heritability, measurement late in life, and inability to measure breeding animals. A faster approach would be finding additional environmental interventions that maintain animal performance.

Animals↗

PubMed2005

Animal breeding and disease.

Single-locus disorders in domesticated animals were among the first Mendelian traits to be documented after the rediscovery of Mendelism, and to be included in early linkage maps. The use of linkage maps and (increasingly) comparative genomics has been central to the identification of the causative gene for single-locus disorders of considerable practical importance. The 'score-card' in domestic animals is now more than 100 disorders for which the molecular lesion has been identified and hence for which a DNA test is available. Because of the limited lifespan of any such test, a cost-effective and hence popular means of protecting the intellectual property inherent in a DNA test is not to publish the discovery. While understandable, this practice creates a disconcerting precedent. For multifactorial disorders that are scored on an all-or-none basis or into many classes, the effectiveness of control schemes could be greatly enhanced by selection on estimated breeding values for liability. Genetic variation for resistance to pathogens and parasites is ubiquitous. Selection for resistance can therefore be successful. Because of the technical and welfare challenges inherent in the requirement to expose animals to pathogens or parasites in order to be able to select for resistance, there is a very active search for DNA markers for resistance. The first practical fruits of this research were seen in 2002, with the launch of a national scrapie control programme in the UK.

Animal Diseases↗

PubMed2026

Transition from Conventional to Genomic Selection (ssGBLUP) led to improve in accuracy gains and selection decisions in Sahiwal Cattle.

By using genome-wide markers to predict an individual's genetic potential, the introduction of Genomic Selection (GS) has transformed animal breeding. This greatly accelerated selection for complex traits by lowering reliance on drawn-out field trials, allowing for faster genetic gains in livestock. However, there is little research on the effects of genomic selection on Sahiwal cattle in India, and comparing it to the current culling or selection process is even more uncommon, particularly in nations with fewer genotyped animals. This study is an initial effort to address the aforementioned gaps in knowledge. Genomic selection was implemented in Sahiwal cattle for the 305 days milk yield using univariate animal model and the single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) method. The Effective Population size (Ne) of the Sahiwal herd was calculated using genomic data and was reported for the previous generation to be 71.927. The heritability of 305 days milk yield was estimated as 0.177 ± 0.068. Genomic estimated breeding values (GEBVs) were predicted for each individual using ssGBLUP, yielding a mean prediction accuracy of 43.11%, compared with 40.88% obtained using conventional pedigree-based BLUP. Cross-validation further demonstrated superior predictive performance of ssGBLUP, with accuracies of 76.82% and 70.50% for ssGBLUP and PBLUP, respectively. To further check the effectiveness of the genomic selection methodology, we also compared the GEBVs obtained and compared it with the Expected Progeny Difference (EPD) which is being applied in our farm for culling decisions. It was seen that GEBVs obtained from ssGBLUP methodology were also in line with the conventionally used method of EPD. The use of genomic selection enables genetic studies with limited pedigree information. Additionally, the ssGBLUP methodology allows to check for pedigree errors, where family relationships are incorrectly recorded. The EPD and GEBVs were consistent with one another, indicating that genomic selection may also be utilised to support culling and selection decisions in a farm. Thus, in a conventional animal breeding program with constraint resources and an incomplete pedigree, we recommend employing the ssGBLUP model for regular genomic assessment and identification of suitable candidates to effectively carry out a genomic selection program.

Animals↗

PubMed1991

Threshold models applied to Holstein conformation traits.

Threshold animal models were applied to five conformation traits of Canadian Holsteins. The estimated breeding values for sires from the threshold model allowed the calculation of predicted percentages of daughters in the desirable categories. Results were compared with those from a linear animal model in terms of their ability to predict future percentages of daughters in the desirable categories using an independent set of data. There was no advantage in a threshold model compared with a conventional linear animal model in its ability to predict future daughter performance. This was likely due to the 18 categories used in the classification of major type traits in Canada and the nearly normal distribution of observations across categories.

Animals↗

PubMedDate not supplied

Estimation of genotypic and environmental variation in plants.

The frequency of genotypes with the desired degree of expression of economically important quantitative characters within a hybrid or mutant population is usually very low. Therefore, the early identification and selection of such genotypes involves the analysis of very large populations. Because the breeding values of individuals in a population are masked by environmental, competitional, and ontogenic noises, special quantitative--genetic methods of analysis have to be used in order to eliminate their disturbing effects. The present chapter deals with a new approach to such an analysis by using either a simple background character or a background index obtained as a linear function of two, or more than two, background characters. It is believed that the use of this approach would greatly increase the efficiency of selection and shorten the time needed to produce improved new crop cultivars. As the analyses require the handling of large amounts of measurement data, plant breeders must use computer facilities.

Environment↗

PubMed2026

Adaptive evolution of polyploid crops.

Crop evolution represents a fundamental biological process through which plants respond to selection in different environments. This encompasses mechanisms operating at multiple scales of biological organization, including genetic and epigenetic regulation and higher-order interactions among molecular complexes. This Review synthesizes how polyploidy shapes crop evolution by generating duplicated genes, driving genome reorganization, altering dosage relationships and promoting regulatory divergence, which together influence crop metabolism, physiology, development and environmental responses. We focus mainly on the mechanisms underlying adaptation in polyploid crops, including the consequences of gene and genome duplication, genome reorganization and subfunctionalization. We also examine how hybridization, phenotypic plasticity and crop-microbiome interactions intersect with polyploidy to expand or constrain adaptive potential. Together, these processes affect crop survival, fitness and breeding value under changing environments. We suggest that future research connect polyploid genome architecture with experimentally validated signatures of selection and field performance to make better use of polyploidy-derived variation in crop improvement.

Polyploidy↗

PubMed1991

Multistage selection for genetic gain by orthogonal transformation.

An exact transformed culling method for any number of traits or stages of selection with explicit solution for multistage selection is described in this paper. This procedure does not need numerical integration and is suitable for obtaining either desired genetic gains for a variable proportion selected or optimum aggregate breeding value for a fixed total proportion selected. The procedure has similar properties to multistage selection index and, as such, genetic gains from use of the procedure may exceed ordinary independent culling level selection. The relative efficiencies of transformed to conventional independent culling ranged from 87% to over 300%. These results suggest that for most situations one can chose a multistage selection scheme, either conventional or transformed culling, which will have an efficiency close to that of selection index. After considering cost savings associated with multistage selection, there are many situations in which economic returns from use of independent culling, either conventional or transformed, will exceed that of selection index.

Animals↗

PubMed1992

Selection for postweaning growth in inbred Hereford cattle: the Fort Keogh, Montana line 1 example.

Demographic characteristics and genetic trends in birth weight and pre- and postweaning ADG were examined in a population of Hereford cattle (Line 1). Line 1 was founded largely from two paternal half-sib sires and has been selected for postweaning growth. There were pedigree records on 951 members of the base population that predated 1935, when data collection began. Numbers of records analyzed using mixed-model methodology were 4,716 birth weight, 4,427 preweaning ADG, and 3,579 postweaning ADG. Birth weight and preweaning ADG were considered to have direct and maternal genetic components. Inbreeding accumulated rapidly from 1935 to 1960 and more slowly (.22%/yr) thereafter. Any reduction in additive genetic variance due to inbreeding and selection may have been offset by a concurrent reduction in generation interval that was observed as time progressed. Expected selection differential for 365-d weight, averaged over sexes, was 31.2 kg per generation. For birth weight, annual genetic trends in direct and maternal effects were 42 +/- 3 g and 15 +/- 3 g, respectively. Annual direct and maternal genetic trends for preweaning ADG were .70 +/- .06 g/d and .63 +/- .06 g/d, respectively. Direct response in postweaning ADG was linear and equal to 5.3 +/- .6 g.d-1.yr-1. As a result, estimated breeding values of birth weight, 200-d weight, and 365-d weight increased by 3.2 kg, 14.5 kg, and 62.4 kg, respectively, from 1935 to 1989. Selection within Line 1 was effective in increasing genetic potential for growth over 13 generations. No selection plateau was observed in any of the traits examined.

Age Factors↗

PubMed2026

Effects of replacing sulfate with hydroxychloride sources of trace minerals on mineral status and production performance in dairy cows.

The objectives were to determine the effects of replacing sulfate with hydroxychloride sources of Cu, Mn, and Zn on mineral status and production performance in dairy cows. One hundred forty-one Holstein cows were stratified by parity group prepartum as nulliparous (lactation 0) or parous cows (lactation >0) and, within parity, cows were blocked by genomic breeding value for ECM yield (nulliparous cows) or recently completed lactation 305-d ECM (parous cows) and then randomly assigned to 1 of 2 treatments. Treatments were supplemental sources of Cu, Mn, and Zn as sulfate trace minerals (STM) or hydroxychloride trace minerals (HTM). Diets were formulated to contain approximately 16, 60, and 60 mg/kg of Cu, Mn, and Zn, respectively, and treatments were fed from 246 d of gestation to 105 d of lactation. Cows were weighed twice weekly prepartum and intake of DM, milk yield, and postpartum BW were measured daily, and composition of milk was analyzed twice weekly. Blood was sampled pre- and postpartum and hepatic tissue collected at 10 (50 STM and 52 HTM cows) and at 50 d postpartum (17 STM and 18 HTM cows) and analyzed for concentrations of minerals. Treatment did not affect intake or measures of energy balance prepartum. Numerical results between parentheses are presented following the sequence of STM and HTM. Concentrations of trace minerals in serum differed between treatments only prepartum and those of Cu (1.291 vs. 1.183 ± 0.031 mg/L) and Zn (1.307 vs. 1.211 ± 0.031 mg/L) were greater for cows fed STM compared with cows fed HTM; however, the opposite response was observed for serum Mn (1.628 vs. 1.754 ± 0.038 µg/L). Treatment did not affect liver Mn or Zn concentration, but for Cu, cows fed STM had greater concentration in the liver on d 10 postpartum compared with cows fed HTM (310 vs. 296 ± 7 mg/kg DM); however, the opposite response was observed on d 50 and cows fed STM had smaller concentration of Cu in liver than those fed HTM (287 vs. 318 ± 9 mg/kg DM). Cows fed HTM produced an additional 1.0 kg colostrum than STM cows (5.21 vs. 6.22 ± 0.63 kg), thus resulting in increased yield of colostrum solids. Treatment did not affect the content or yield of IgG in colostrum. Cows fed HTM produced 1.3 kg/d more milk (41.7 vs. 43.0 ± 0.5 kg/d) and 1.5 kg/d more energy-corrected milk (42.5 vs. 44.0 ± 0.6 kg/d) in the first 15 wk of lactation compared with cows fed STM. The estimated NEL content of the postpartum diet consumed by cows, after accounting for the different energy sinks and DMI, was 3.4% greater for HTM than STM (1.68 vs. 1.74 ± 0.02 Mcal/kg). Replacing sulfate with hydroxychloride sources of Cu, Mn, and Zn had small effects on the concentrations of those minerals in tissues and improved production performance in the first 15 wk of lactation.

Animals↗

PubMed1991

Method and effect of adjustment for heterogeneous variance.

Lactation records were standardized for differing genetic and error variances across herds and over time based on phenotypic variance for each herd-year-parity group. Each herd-year-parity phenotypic variance estimate was combined with those of adjacent years and regressed toward a region-year-parity variance. Heritability was assumed to be .25 at mean variance within year and to range from .2 for herds with smallest phenotypic SD to .3 for herds with largest phenotypic SD. Lactation deviations from management group mean were adjusted by ratio of base genetic SD to genetic SD estimated from heritability and phenotypic SD. The base was defined as 1987 calvings for first parity and 1988 calvings for later parities. Records were weighted according to heritability by multiplying lactation length weight by herd error weight defined as ratio of base error variance to error variance in the adjusted record. Estimated genetic trend for milk increased by nearly 5 kg/yr for Holsteins with this adjustment, which caused predicted breeding values of oldest animals to be lower by about 100 kg. Most correlations of parent and progeny information were slightly higher with adjusted data. Cows in high variance herds were most likely to have large reductions in their evaluations. Adjustment for heterogeneous variance was implemented in July 1991 for national evaluations for yield traits.

Animals↗

PubMed1992

Analysis of levels of inbreeding and inbreeding depression in Jersey cattle.

A pedigree file of 157,015 male and female Jersey cattle (born after 1955) from the Canadian herdbooks was investigated for the occurrence of inbreeding. A large proportion of Jersey bulls and cows were inbred (32.4 and 36.3% for bulls and cows, respectively). However, average inbreeding coefficients of these inbred cows and of all cows were low. First lactation milk, fat, and fat percentage records for 53,592 Jersey cows were analyzed. Inbreeding was included in the animal model as a linear covariate. The regression coefficients of milk, fat, and fat percentage on inbreeding were -9.84 kg, -.55 kg, and -.0011% per 1% increase of inbreeding. Inbreeding depression was not enough to cause large reductions of milk and fat yield of a cow with average inbreeding. However, when the inbreeding coefficient was greater than 12.5%, the inbreeding depression was significantly higher than expected and such that intentional inbreeding is not justified unless the mating is to an animal with exceptionally high breeding value.

Algorithms↗

PubMed1992

Estimation of heterogeneous within-herd variance components using empirical Bayes methods: a simulation study.

Genetic evaluation using BLUP can accommodate heterogeneous variances if the necessary variance components are known; this may require estimation of variance components within each heterogeneous subclass. Properties of sire and residual variance estimates obtained by an empirical Bayes approach, which combines within-herd and prior estimates, were examined via simulation. Prior estimates were obtained using REML across herds, as if variances were homogeneous. Convergence was improved by incorporation of prior information such that variance component estimates could be obtained in within-herd situations for which a REML algorithm failed to converge. Accuracy of sire variance estimates was greatest when both within-herd and prior information were used, but improvement in accuracy of residual variance estimates associated with incorporation of prior information was minimal. Correlations between sires' standardized true transmitting abilities and PTA that used empirical Bayes variance estimates were larger than those obtained when heterogeneity was ignored. Proportions of sires selected, based on standardized PTA, from environments with differing genetic and residual variances became more uniform as the relative weight placed on within-herd data in variance estimation increased. Thus, useful variance component estimates can be obtained within individual herds by using empirical Bayes methods with across-herd estimates as prior information; this may allow prediction of breeding values that are less influenced by heterogeneous variances.

Algorithms↗

PubMed2026

Validation of a national genetic evaluation for methane emission in Holstein cattle.

Lactanet Canada launched a genomic evaluation for methane efficiency for Holsteins in April 2023, utilizing milk mid-infrared-predicted methane (CH4) emissions (CH4MIR) as a proxy. This study validated the methane efficiency genomic evaluation using genotyped cows with CH4MIR and CH4 records from GreenFeed systems (CH4GF), along with relative breeding values (RBV) for methane production and methane efficiency from the April 2023 evaluation. In Lactanet's methane efficiency evaluation, a higher RBV indicates more desirable, lower-emitting animals. For the validation, RBV were categorized into quintiles for the CH4MIR dataset and tertiles for the CH4GF dataset to evaluate trends across the RBV distribution. Mean CH4MIR decreased progressively across RBV quintiles for both traits, with all pairwise comparisons among quintiles significantly different. Similarly, CH4GF emissions declined across RBV tertiles, with significant differences observed between the lowest and highest tertiles. Additional analyses using RBV threshold categories confirmed that cows with the highest RBV consistently exhibited lower methane emissions. Linear regression analyses further demonstrated a negative relationship between RBV and methane emissions, supporting the predictive ability of the genomic evaluation. These findings confirm that Canada's genomic evaluation for methane efficiency effectively differentiates cows by methane emission potential, reinforcing its potential as a tool for genetic selection to reduce methane emissions in dairy cattle.

Journal Article↗

PubMed1978

Age and milk production data of cattle culled from a dairy herd with paratuberculosis.

Statistical assessment of age and milk production data revealed a significantly shorter life expectancy and reduced milk production of Mycobacterium paratuberculosis-infected dairy cows, when compared with non-infected herdmates. High producing cows were frequently culled after their 1st or 2nd gestation, contributing to an undetermined economic loss with regard to their potential breeding value. Cows with subclinical infection frequently had problems of infertility and of mastitis.

Age Factors↗

PubMed1992

Potential improvements in rate of genetic gain from marker-assisted selection in dairy cattle breeding schemes.

The value of marker-assisted selection in dairy cattle breeding schemes is predicted by a deterministic model. In these schemes, associations between markers and milk production were assessed from production records of daughters of a grandsire by a multiple regression model with random marker effects. By tracing markers from the grandsire to grandoffspring, deviations of grandoffspring from their full-sib family mean were predicted. Predictions of the within-family variance of the grandoffspring accounted for by markers amounted to up to 13.3%. This figure decreased when the number of daughters of the grandsire analyzed decreased and, less markedly, when the distance between flanking markers increased. Prediction of within-family deviations hardly improved rates of genetic gain in conventional progeny testing schemes; equal numbers of young bulls were born annually. Genetic gain and improvement of genetic gain because of prediction of within-family deviations were much higher in nucleus schemes. In these shemes, with short optimized generation intervals, conventional selection was mainly for pedigree information and did not use the within-family variance. Analysis of highly polymorphic markers in daughters of both grandsires accounted for 4.1 to 13.3% of the within-family variance, which increased rates of gain by 9.5 to 25.8% and 7.7 to 22.4% in open and closed nucleus schemes, respectively. Risk of breeding schemes, measured by the variance of the selection response, was not increased by the use of markers.

Animals↗