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PubMed2006

Benefits of cooperation between breeding programs in the presence of genotype by environment interaction.

Dairy cattle breeding programs and dairy farmers are selecting sires and dams across environments. Genotype x environment interaction (G x E) limits the possibilities for cooperation between breeding programs operating in different environments. The objectives of this study were 2-fold: 1) to investigate the effects of heritability, selection intensity, number of progeny per bull, and size of breeding programs on possibilities for cooperation between dairy cattle breeding programs in the short and long term in the presence of G x E, and 2) to quantify the effect of such cooperation on genetic gain. A dairy cattle situation with 2 breeding programs operating in 2 environments was simulated using a deterministic pseudo-BLUP selection index model. Long-term cooperation between the 2 breeding programs was possible in the presence of G x E, when the genetic correlation was higher than 0.80 to 0.90, resulting in up to 15% extra genetic gain. In addition, in the initial generations of selection, the breeding programs could benefit from mutually selecting sires and dams from each other when the genetic correlation was as low as 0.40 to 0.60. With more intense selection, breeding programs were less likely to benefit from cooperation with breeding programs in other environments. Heritability and number of progeny per bull had little effect on possibilities for cooperation, unless the heritabilities and the number of progeny per bull were extremely different in the 2 environments. Small breeding programs benefited more from cooperation than did large breeding programs, and benefits were possible even at lower values (i.e., <0.80) of the genetic correlation. Possibilities for cooperation across environments would affect the optimal design of dairy cattle breeding programs considering genetic gain, inbreeding, and costs.

Animals↗

PubMed2007

Genetic analysis of postpartum measures of luteal activity in dairy cows.

The objective of this study was to estimate genetic parameters for measures of luteal activity during the first 60 d postpartum. Analyses were made with different sampling intervals to investigate the possibility of combining progesterone measurement with routinely performed milk recording. Progesterone level in milk as an indicator of female fertility when selecting sires in a progeny-testing scheme was also examined. Data were collected from 1996 to 1999, and comprised 1,212 lactations from 1,080 British Holstein-Friesian cows at 8 commercial dairy farms in the United Kingdom. Milk samples for progesterone analysis were collected thrice weekly. Mixed linear animal models were used to analyze the data. Heritability for the percentage of samples with luteal activity during the first 60 d postpartum (PLA) was 0.30 and decreased with more infrequent sampling to 0.25, 0.20, and 0.14 for weekly, twice-monthly, and monthly sampling, respectively. Measures of PLA had a high negative genetic correlation with prolonged anovulation (-0.53 for monthly sampling, < -0.87 otherwise) and a moderate positive genetic correlation with persistent corpus luteum in the first estrus cycle (>0.65 if at least twice-monthly sampling). Genetic correlations with interval from calving to commencement of luteal activity were close to -1 for all PLA measurements and the selection index calculations showed that monthly progesterone sampling could be used with high accuracy (0.80 with 50 daughters per bull) to predict breeding values for commencement of luteal activity. Progesterone analysis at the time of regular milk recording could thereby be used to select for an early interval from calving to commencement of luteal activity and, at the same time, a decreased frequency of prolonged anovulation during the postpartum period.

Animals↗

PubMed2006

Genetic associations between clinical mastitis and somatic cell score in early first-lactation cows.

The objectives of this study were to examine genetic associations between clinical mastitis and somatic cell score (SCS) in early first-lactation cows, to estimate genetic correlations between SCS of cows with and without clinical mastitis, and to compare genetic evaluations of sires based on SCS or clinical mastitis. Clinical mastitis records from 15 d before to 30 d after calving and first test-day SCS records (from 6 to 30 d after calving) from 499,878 first-lactation daughters of 2,043 sires were analyzed. Results from a bivariate linear sire model analysis of SCS in cows with and without clinical mastitis suggest that SCS is a heterogeneous trait. Heritability of SCS was 0.03 for mastitic cows and 0.08 for healthy cows, and the genetic correlation between the 2 traits was 0.78. The difference in rank between sire evaluations based on SCS of cows with and without clinical mastitis varied from -994 to 1,125, with mean 0. A bivariate analysis with a threshold-liability model for clinical mastitis and a linear Gaussian model for SCS indicated that heritability of liability to clinical mastitis is at least as large as that of SCS in early lactation. The mean (standard deviation) of the posterior distribution of heritability was 0.085 (0.006) for liability to clinical mastitis and 0.070 (0.003) for SCS. The posterior mean (standard deviation) of the genetic correlation between liability to clinical mastitis and SCS was 0.62 (0.03). A comparison of sire evaluations showed that genetic evaluation based on SCS was not able to identify the best sires for liability to clinical mastitis. The association between sire posterior means for liability to clinical mastitis and sire predicted transmitting ability for SCS was far from perfect.

Analysis of Variance↗

PubMed2005

Variance components and heritabilities for sow productivity traits estimated from purebred versus crossbred sows.

Genetic parameters were estimated for number of pigs born alive (NBA), adjusted litter weaning weight (ALWT), and the interval from weaning to first service (W2E) using 2002 purebred litter records and 14 583 crossbred litter records from a swine production unit with a defined great-grandparent, grandparent, and parent stock genetic system structure. Estimation of (co)variance components was carried out by REML methods. Heritability estimates from this study for NBA were 0.155, 0.146, 0.145 for the purebred, crossbred, and pooled data, respectively. Heritability estimates for ALWT were 0.162, 0.195, and 0.183 for the purebred, crossbred and pooled data, respectively. Heritability estimates for W2E were 0.205, 0.239 and 0.202 for the purebred, crossbred and pooled data, respectively. Genetic correlations between NBA and ALWT were weak and positive for the three groups. The genetic correlation between W2E and ALWT were -0.158 for the purebred Yorkshires, 0.031 for the crossbreds and 0.051 for the pooled data. The genetic correlation between W2E and NBA was -0.027 for the purebred Yorkshires, 0.310 for the crossbreds and 0.236 for the pooled data. These similarities suggest that pooling of purebred and crossbred data may be considered, which may potentially increase the accuracy of breeding value estimates, which would result in increased genetic progress.

Age Factors↗

PubMed2002

Genetic parameters for level and change of body condition score and body weight in dairy cows.

(Co)variance components for body condition score (BCS), body weight (BW), BCS change, BW change, and milk yield traits were estimated. The data analyzed included 6646 multiparous Holstein-Friesian cows with records for BCS, BW, and(or) milk yield at different stages of lactation from 74 dairy herds throughout Southern Ireland. Heritability estimates for BCS ranged from 0.27 to 0.37, while those for BCS change ranged from 0.02 to 0.10. Heritability estimates for BW records varied from 0.39 to 0.50, while heritabilities for BW change were similar to those observed for BCS change (0.03 to 0.09). The genetic correlations between BCS and BW at the same days in milk deviated little from 0.50, and the genetic correlations between BCS change and BW change over the same period ranged from 0.42 to 0.55. BCS and BW directly postpartum were both phenotypically and genetically negatively correlated with both BW change and BCS change in early lactation. The genetic correlations between BCS and milk yield were negative. The results of the present study show that animals that lose most BCS in early lactation tend to gain most BCS in late lactation, a trend also exhibited by BW.

Animals↗

PubMed2005

Genetic constraints and sexual dimorphism in immune defense.

The absence of continued evolutionary change despite the presence of genetic variation and directional selection is very common. Genetic correlations between traits can reduce the evolvability of traits. One intriguing example might be found in a sexual conflict over sexually dimorphic traits: a common genetic architecture constrains the response to selection on a trait subjected to sexually asymmetric selection pressures. Here we show that males and females of the mealworm beetle Tenebrio molitor differ in the quantitative genetic architecture of four traits related to immune defense and condition. Moreover, high genetic correlations between the sexes constitute a genetic constraint to the evolution of sexual dimorphism in immune defense. Our results suggest a general mechanism by which sexual conflict can promote evolutionary stasis. We furthermore show negative genetic correlations, strong indications of trade-offs, between immune traits for two pairs of traits in females.

Analysis of Variance↗

PubMed2001

Usefulness of subjective ovine milk scores: II. Genetic parameter estimates.

Genetic parameters for a subjective milk score given to ewes within 24 h of parturition were estimated to determine the usefulness of milk score as a selection trait to improve milk production, which influences total litter weight weaned. Heritability of milk score and the genetic correlation of milk score with litter weight weaned were estimated by REML separately for four sheep breeds, Rambouillet (n = 1,731), Targhee (n = 1,638), Columbia (n = 1,731), and Polypay (n = 1,129). Litter weight weaned was the total weight of lambs weaned at approximately 120 d of age under a western range production system. Observed heritability estimates for milk score at first parity were moderate and similar among breeds, ranging from 0.18 to 0.32. Heritability estimates adjusted for a binomial distribution of milk scores at first parity were high (Columbia, 0.43; Polypay, 0.35; Rambouillet, 0.50; Targhee, 0.84). Estimates of observed heritability for second-parity milk score were moderate to high, ranging from 0.23 to 0.46. Milk score at first or second parity was genetically correlated with milk score records at maturity (third parity and greater), with estimates ranging from 0.69 to 1.00. Milk score and litter weight weaned were genetically correlated at first or second parity in Rambouillet (r(g) = 1.00) and Targhee breeds (r(g) = 1.00 and 0.61, respectively), but not in the Columbia and Polypay breeds. Estimates of heritability for lifetime records for milk score ranged from 0.16 to 0.26 across breeds. Estimates of genetic correlations of annual lifetime milk score records with litter weight weaned were high (Columbia, 1.00; Polypay, 0.81; Rambouillet, 1.00; and Targhee, 0.77). Repeatability estimates for milk score were similar across breeds, 0.23 for Columbia, Rambouillet, and Targhee ewes and 0.28 for Polypay ewes. Milk score measured at first or second parity may be a good predictor of future potential milking ability. Further, milk score can be used as a selection trait to improve maternal ability for increasing litter weight weaned. The need for increasing ewe milking performance and lamb growth rate at first parity in commercial range sheep production systems may be addressed by selection for milk score at first parity.

Animals↗

PubMedDate not supplied

Estimation of genetic parameters for test day records of dairy traits in the first three lactations.

Application of test-day models for the genetic evaluation of dairy populations requires the solution of large mixed model equations. The size of the (co)variance matrices required with such models can be reduced through the use of its first eigenvectors. Here, the first two eigenvectors of (co)variance matrices estimated for dairy traits in first lactation were used as covariables to jointly estimate genetic parameters of the first three lactations. These eigenvectors appear to be similar across traits and have a biological interpretation, one being related to the level of production and the other to persistency. Furthermore, they explain more than 95% of the total genetic variation. Variances and heritabilities obtained with this model were consistent with previous studies. High correlations were found among production levels in different lactations. Persistency measures were less correlated. Genetic correlations between second and third lactations were close to one, indicating that these can be considered as the same trait. Genetic correlations within lactation were high except between extreme parts of the lactation. This study shows that the use of eigenvectors can reduce the rank of (co)variance matrices for the test-day model and can provide consistent genetic parameters.

Animals↗

PubMed2003

Evolutionary ecology of egg size and number in a seed beetle: genetic trade-off differs between environments.

In many organisms, large offspring have improved fitness over small offspring, and thus their size is under strong selection. However, due to a trade-off between offspring size and number, females producing larger offspring necessarily must produce fewer unless the total amount of reproductive effort is unlimited. Because differential gene expression among environments may affect genetic covariances among traits, it is important to consider environmental effects on the genetic relationships among traits. We compared the genetic relationships among egg size, lifetime fecundity, and female adult body mass (a trait linked to reproductive effort) in the seed beetle, Stator limbatus, between two environments (host-plant species Acacia greggii and Cercidium floridum). Genetic correlations among these traits were estimated through half-sib analysis, followed with artificial selection on egg size to observe the correlated responses of lifetime fecundity and female body mass. We found that the magnitude of the genetic trade-off between egg size and lifetime fecundity differed between environments--a strong trade-off was estimated when females laid eggs on C. floridum seeds, yet this trade-off was weak when females laid eggs on A. greggii seeds. Also differing between environments was the genetic correlation between egg size and female body mass-these traits were positively genetically correlated for egg size on A. greggii seeds, yet uncorrelated on C. floridum seeds. On A. greggii seeds, the evolution of egg size and traits linked to reproductive effort (such as female body mass) are not independent from each other as commonly assumed in life-history theory.

Analysis of Variance↗

PubMed2000

Genetic parameters among weight, prolificacy, and wool traits of Columbia, Polypay, Rambouillet, and Targhee sheep.

Genetic parameters for Columbia, Polypay, Rambouillet, and Targhee sheep were estimated using REML with animal models for prolificacy, weight, and wool traits. All bivariate analyses included a covariance between additive genetic effects for the two traits plus appropriate additional covariances. Number of observations by breed ranged from 5,140 to 7,095 for prolificacy traits, from 7,750 to 9,530 for weight traits, and from 4,603 to 34,746 for wool traits. Heritability estimates ranged from .03 to .11 for prolificacy traits (litter size at birth and litter size at weaning), from .09 to .26 for weight traits (birth weight and average daily gain), and from .25 to .53 for wool traits (fleece weight, fleece grade and staple length). Estimates of direct genetic correlations among prolificacy and among weight traits were positive and ranged from .58 to 1.00 and .18 to 1.00, respectively. Estimates of direct genetic correlation between fleece weight and staple length were positive (.50 to .70) but were negative between fleece weight and fleece grade (-.60 to -.34) and between staple length and fleece grade (-.72 and -.40). Prolificacy and wool traits were essentially uncorrelated. Weight and prolificacy traits were slightly positively correlated. Weight traits had a moderate positive direct genetic correlation with fleece weight and staple length, but were uncorrelated with fleece grade. These estimates of genetic parameters between prolificacy, weight, and wool traits can be used to construct multiple-trait selection indexes for dual-purpose sheep.

Age Factors↗

PubMed2025

Exploring the shared genetic basis of attention-deficit/hyperactivity disorder and obstructive sleep apnea: A multi-omics analysis.

BACKGROUND: Observational studies have suggested an association between attention-deficit/hyperactivity disorder (ADHD) and obstructive sleep apnea (OSA), but these findings are often inconsistent due to potential biases from medication use, and varying diagnostic criteria. Genetic analyses can help mitigate these confounding factors, providing additional evidence. METHODS: This study evaluated the genetic correlations between ADHD and OSA using Genome-wide association study (GWAS) summary data, applying linkage disequilibrium score regression (LDSC) and SUPER GeNetic cOVariance Analyzer (SUPERGNOVA). Cross-trait association and colocalization analysis identify potential pleiotropic loci. Tissue enrichment analysis and gene-level analysis of shared genes between OSA and ADHD was conducted. Additionally, bidirectional Mendelian randomization was used to assess potential causal relationships. RESULTS: We found significant genetic correlations between ADHD and OSA (rg = 0.309, p = 3.252E-27), and identified 8 novel pleiotropic loci through cross-trait association analysis. Tissue enrichment analysis showed that these shared genes were primarily concentrated in brain tissues, particularly in deep gray matter regions, and were associated with immune and inflammatory pathways. Forward Mendelian Randomization analysis showed that ADHD was significantly associated with the risk of OSA (OR 1.070, 95 % CI 1.013-1.130, p = 0.016), and reverse analysis showed that OSA was significantly associated with the risk of ADHD (OR 1.240, 95 % CI 1.106-1.390, p = 2.213E-4). CONCLUSION: The findings of this study show a significant positive genetic correlation between ADHD and OSA and each is a risk factor for the other. Inflammation in specific brain regions may be the underlying mechanism for their comorbidity.

Humans↗

PubMedDate not supplied

Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture.

Summary Morphological variation within organisms is integrated and often modular in nature. That is to say, the size and shape of traits tend to vary in a coordinated and structured manner across sets of organs or parts of an organism. The genetic basis of this morphological integration is largely unknown. Here, we report on quantitative trait loci (QTL) analysis of leaf and floral organ size in Arabidopsis thaliana. We evaluate patterns of genetic correlations among traits and perform whole-genome scans using QTL mapping methods. We detected significant genetic variation for the size and shape of each floral and leaf trait in our study. Moreover, we found large positive genetic correlations among sets of either flower or leaf traits, but low and generally nonsignificant genetic correlations between flower and leaf traits. These results support the hypothesis of independent floral and vegetative modules. We consider co-localization of QTL for different traits as support for a pleiotropic basis of morphological integration and modularity. A total of eight QTL affecting flower and three QTL affecting leaf traits were identified. Most QTL affected either floral or leaf traits, providing a general explanation for high correlations within and low correlations between modules. Only two genomic locations affected both flower and leaf growth. These results are discussed in the context of the evolution of modules, pleiotropy, and the putative homologous relationship between leaves and flowers.

Arabidopsis↗

PubMed2006

Variance components for live weight, body measurements and reproductive traits of pair-mated ostrich females.

Estimates of genetic parameters for reproductive traits, live weight and body measurements were obtained using data from a pair-mated ostrich flock at Oudtshoorn in South Africa. Reproductive traits included total egg and chick production, along with hatchability percentage. Live weight, chest circumference and tail circumferences were recorded at the commencement and cessation of breeding. Heritability estimates (h(2)) were 0.23 for egg production, 0.20 for chick production, 0.10 for hatchability, 0.20 to 0.34 for live weight, 0.12 for chest circumference and 0.30 to 0.38 for tail circumference. Female permanent environmental effects (c(2)) amounted to 0.18 for egg production, 0.18 for chick production, 0.21 for hatchability, 0.32 to 0.36 for live weight and 0.23 to 0.32 for chest circumference. Service sire exerted significant effects only on hatchability (0.22) and subsequently chick production (0.09). Genetic correlations of reproductive traits with live weight were low to moderate, variable in sign, and did not differ significantly from zero. Correlations between live weight recorded at the beginning and end of the breeding season were unity for additive genetic and permanent environmental effects. Egg and chick production were highly correlated genetically and phenotypically, with the genetic correlation exceeding the theoretical limit. In unconstrained analyses, hatchability was positively related to chick production, including at the service sire level. Selection gains in the current flock and future generations are likely. No significant adverse relationships were found between live weight, body measurements and reproductive traits.

Animals↗

PubMed2025

Evaluating the causal effect of mitochondrial dysfunction on Alzheimer's and Parkinson's disease using Polygenic Risk Scores and Mendelian Randomization.

INTRODUCTION: Mitochondrial DNA copy number (mtDNAcn), a measure of mitochondrial genomes per nucleated cell, has an unclear causal relationship with AD and PD. We integrate genetic correlation, Polygenic Risk Scores (PRS), and Mendelian Randomization (MR) to assess whether mtDNAcn influences the risk of AD and PD, and evaluate how study-specific factors in mtDNAcn genome-wide association studies (GWAS) may distort these causal estimates. METHODS: Using GWAS of four mtDNAcn measures, AD, AD/dementia, and PD, we evaluated genetic correlations, generated ancestry-normalized PRS in the AD Genetics Consortium (N=27,383), and applied MR methods including Latent Heritable Confounder MR (LHC-MR). RESULTS: Across the four mtDNAcn GWAS, only one was consistently associated with AD/dementia and PD, with genetic correlations and PRS analysis showing negative correlations and MR indicating that higher mtDNAcn reduced AD/dementia and PD risk. DISCUSSION: Higher blood-based mtDNAcn was causally associated with reduced risk of AD/dementia and PD, with limited evidence to suggest a bidirectional effect.

Alzheimer’s disease↗

PubMed1996

Genetic parameters of longevity traits of an upgrading population of dairy cattle.

Longevity reflects the ability of a cow to avoid being culled for low production, low fertility, or illness. Longevity could be used in breeding programs if genetic parameters were known. Various measures are used for longevity. In this study, lifetime measures including number of lactations, total milk production, number of days in lactation, herd life, and length of productive life were analyzed. Also analyzed were stayability measures (dead or alive) to 36, 48, 60, or 72 mo of age and to 12, 24, 36, or 48 mo of productive life. Measures of longevity were also analyzed after correction for milk production during first lactation (functional longevity traits). Data on 1,72,988 cows were used to calculate means for longevity traits per year of birth. All cows were known to have been culled. Longevity decreased from 1978 through 1984 and increased in 1985. Possible causes for the decrease of longevity were implementation of the quota system and introduction of Holstein genes. heritabilities of longevity traits were estimated for cows born in 1985 (38,957 records), 1982 (166,324 records), and 1978 (94,935 records) after data were edited to require at least 25 daughters per sire and 10 cows per herd. Phenotypic and genetic correlations were estimated for the 1985 data. Heritability estimates differed between years of birth, and estimates of functional traits were lower than those of uncorrected longevity traits. Genetic correlations between uncorrected longevity traits were high (0.733 to 1.000); phenotypic correlations were lower (0.131 to 0.980). Genetic correlations between uncorrected and functional longevity traits were high (0.577 to 0.975).

Aging↗

PubMed1993

[Estimation of the sampling variance of co-heritability].

Formulae for the sampling variances of co-heritability and co-environment are developed from the one-fold and two-fold nested genetic analyses of variance and covariance with balanced and unbalanced data. Some potential roles of the co-heritability in breeding programs and the relationship with genetic correlation have also been investigated. The co-heritability has dual characteristics of both heritability and genetic correlation. Heritability is a special case of co-heritability with co-heritability an extended form of heritability. The use of co-heritability to express the genetic covariation between two characters will give smaller sampling errors than those of the genetic correlation (gamma A).

Analysis of Variance↗

PubMed2005

Genotype x environment interaction effects on carcass traits in Japanese Black cattle.

The importance of genotype x environment (region or management system) interactions for carcass traits in Japanese Black cattle was investigated using both univariate and multivariate animal models. The univariate approach was used mainly to test the significance of interaction effects. The multivariate approach was used to estimate genetic correlations, which indicated the magnitude of genotype x environment (GE) interactions. The more a genetic correlation deviates from 1, the larger the interaction. From the univariate approach, the addition of genotype x environment (region or management system) interaction (co)variance components resulted in an improved fit of the model for all traits in both cases (P < 0.001). However, estimates of genetic correlation between regions obtained from the multivariate approach for hot carcass weight, LM area, rib thickness, s.c. fat thickness, and marbling score were 0.97, 0.95, 0.93, 0.97, and 0.93, respectively. The corresponding estimates between management systems were 0.84, 0.92, 0.84, 0.90, and 0.97, respectively. These results indicate that GE interaction effects on carcass traits of Japanese Black cattle may be biologically unimportant. Therefore, breeding values obtained using the multivariate method would rank sires similarly in all environments. Consequently, carcass traits measured in these two different regions or management systems can be treated as the same traits.

Animal Husbandry↗

PubMed2005

Estimates of genetic parameters for Canadian Holstein female reproduction traits.

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 related to reproductive performance of dairy cows. Other frequently used fertility characteristics, like days open or calving intervals, could easily be derived from the analyzed traits. Data included 94,250 records in parities 1 to 6 on 53,158 cows from Ontario and Quebec, born in the years 1997 to 2002. Reproductive characteristics of heifers and cows were treated as different but genetically correlated traits that gave 16 total traits in the analysis. Repeated records for later parities were modeled with permanent environmental effects. Direct and maternal genetic effects were included in linear models for traits related to calving performance. Bayesian methods with Gibbs sampling were used to estimate covariance components of the model and respective genetic parameters. Estimates of heritabilities for fertility traits were low, from 3% for nonreturn rate in heifers to 13% for age at first service. Interval traits had higher heritabilities than binary or categorical traits. Service sire, sire of calf, and artificial insemination technician were important (relative to additive genetic) sources of variation for nonreturn rate and traits related to calving performance. Fertility traits in heifers and older cows were not the same genetically (genetic correlations in general were smaller than 0.9). Genetic correlations (both direct and maternal) among traits indicated that different traits measured different aspects of reproductive performance of a dairy cow. These traits could be used jointly in a fertility index to allow for selection for better fertility of dairy cattle.

Animals↗