Consequences of paternally inherited effects on the genetic evaluation of maternal effects

Maternal genetic effects throughout the life of the dam in Pirenaica beef cattle. a random regression model approach

In beef cattle, dams play a crucial role in shaping the pre- and postnatal environment for the growth of their offspring. Acknowledging the substantial impact of maternal influence on the early development of calves, researchers utilize maternal animal models. These models take into account both maternal genetic and permanent environmental effects, operating under the assumption that these influences remain constant throughout the productive life of the cow. Nevertheless, it cannot be ruled out that these genetic and environmental effects may evolve throughout the lifespan of the cows. Therefore, this study aims to describe the changes in genetic and environmental maternal effects over the productive lifespan of cows. To accomplish this goal, we utilized random regression models, incorporating the age of the dam effect, maternal genetic effects, and environmental permanent effects using Legendre orthogonal polynomials. Additionally, the analytical model incorporated a covariate to adjust for the calf's age at recording, a two-level sex effect, a random herd-year-season effect, and an additive direct genetic effect associated linked to the calf. The dataset comprised information from dams aged between 2 and 16 years, resulting in a final database that comprised weight records of 58 332 calves from 21 673 dams. The average weight at 90 days was 135.0 ± 39.3 kg, and the mean age of the dam at calving was 7.03 ± 3.41 years. We evaluated models incorporating 2, 3, 4, 5, and 6 orthogonal polynomials alongside the standard maternal animal model. Afterward, we selected the model with five orthogonal polynomials based on the Akaike Information Criteria. The Restricted Maximum Likelihood estimates within this model indicated a direct heritability of around 0.50, and a maternal heritability ranging between 0.15 and 0.25, exhibiting a consistent increase between 4, 5 to 13 years. The genetic correlation estimates between direct and maternal genetic effects remained stable at approximately -0.55 across the lifespan of the cows. Furthermore, maternal genetic correlations between different ages of the dam decreased to around 0.7 for more distant age points. The maternal permanent correlations were notably lower, occasionally even reaching negative values, suggesting variability in environmental influence on maternal effects over the productive lifespan of the cow. Finally, the model enables the prediction of breeding values for the maternal genetic effects of the cow across its lifespan, providing opportunities for innovative selection strategies on the maternal side.

Genetic and genomic analysis of oxygen consumption in mice

We estimated genetic parameters for oxygen consumption (OC), OC per metabolic body weight (OCMBW) and body weight at three through 8 weeks of age in divergently selected mice populations, with an animal model considering maternal genetic, common litter environmental and cytoplasmic inheritance effects. Cytoplasmic inheritance was considered based on maternal lineage information. With respect to OC, estimated direct heritability was moderate (0.32) and the estimated proportion of the variance of cytoplasmic inheritance effects to the phenotypic variance was very low (0.01), implying that causal genes for OC could be located on autosomes. To assess this hypothesis, we attempted to identify possible candidate causal genes through selective signature detection with the results of pooled whole-genome resequencing using pooled DNA samples from high and low OC mice. We made a list of possible candidate causal genes for OC, including those relating to electron transport chain and ATP-binding proteins (Ndufa12, Sdhc, Atp10b, etc.), Prr16 encoding Largen protein, Cry1 encoding a key component of the circadian core oscillator and so on. The results, although careful interpretation must be required, could contribute to elucidate the genetic mechanism of OC, an indicator for maintenance energy requirement, and therefore feed efficiency.

Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed

Simple Summary

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. We have developed a ssGWAS by backsolving the SNP effects after implementing a ssGBLUP. The results showed an apparent heterogeneity of the additive genetic variance across the genome. Some of the genomic regions explaining the most of this additive variance were shared across traits, indicating the presence of pleiotropic effects, which were reflected in their genetic correlations.

Abstract

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: NCK1, MSTN, KCNA3, LCORL, NCAPG, and RIN3.

Genomic imprinting variances of beef carcass traits and physiochemical characteristics in Japanese Black cattle

The objective of this study was to estimate variance components related to imprinting for carcass traits and physiochemical characteristics in Japanese Black cattle. The carcass records obtained from 4,220 Japanese Black feedlot cattle included carcass weight (CW), rib eye area (REA), rib thickness, subcutaneous fat thickness, and beef marbling score (BMS), and the physiochemical characteristics were fat, moisture, glycogen per proportion of moisture content, oleic acid, and monounsaturated fatty acids (MUFA). To detect gametic effects, an imprinting model was fitted. High additive heritabilities were estimated for all traits (from 0.516 for glycogen to 0.853 for fat) and were reduced in Mendelian heritability. The range of the differences was from 0.002 (CW) to 0.331 (fat and moisture), and the reductions were due to their imprinting variances. The ratio of the imprinting variance to the total additive genetic variance for REA (0.374), BMS (0.291), fat (0.387), moisture (0.388), and MUFA (0.337) were large (p < 0.05). These imprinting variances were due to the maternal contribution and suggested the existence of maternally expressed genomic imprinting effects on the traits in Japanese Black cattle. Therefore, maternal gametic effects should be considered in breeding programs for Japanese Black cattle.

Effects of parent-of-origin models with different pedigree information on beef carcass traits and fatty acid composition in Japanese Black cattle

Genomic imprinting should be considered in animal breeding systems to avoid lead in bias in genetic parameter estimation. The objective of this study was to clarify the effects of pedigree information on imprinting variances for carcass traits and fatty acid composition in Japanese Black cattle. Carcass records [carcass weight, rib eye area, rib thickness (RT), subcutaneous fat thickness and beef marbling score (BMS)] and fatty acid composition were obtained for 11,855 Japanese Black feedlot cattle. To estimate and compare the imprinting variances for the traits, two imprinting models with different pedigree information [the sire-dam gametic relationship matrix (Model 1) and the sire-maternal grandsire (MGS) numerator relationship matrix (Model 2)] were fitted. The ratio of the imprinting variance to the total additive genetic variance for RT (6.33%) and BMS (19.00%) was significant in Model 1, but only that for BMS (21.09%) was significant in Model 2. This study revealed that fitting the sire-MGS model could be useful in estimating imprinting variance under certain conditions, such as when restricted pedigree information is available. Furthermore, the present result suggested that the maternal gametic effects on BMS should be included in breeding programmes for Japanese Black cattle to avoid selection bias caused by imprinting effects.

Parent-of-origin effects on carcass traits in Japanese Black cattle

Variances caused by the differential expression of paternally and maternally imprinted genes controlling carcass traits in Japanese Black cattle were estimated in this study. Data on marbling score (BMS), carcass weight, rib thickness, rib-eye area (REA) and subcutaneous fat thickness (SFT) were collected from a total of 13,115 feedlot steers and heifers in a commercial population. A sire-maternal grandsire model was used to analyse the data, and then, imprinting parameters were derived by replacing the genetic effect of the dam with the effect of the maternal grandsire in the imprinting model to calculate the genetic parameter estimates. The proportions of the total genetic variance attributable to imprinted genes ranged from 8.7% (SFT) to 35.2% (BMS). The remarkably large imprinting variance of BMS was mainly contributed by maternally expressed inheritance because the maternal contribution of the trait was much larger than that of the paternal trait. The parent-of-origin effect originating from maternal gene expression was also observed for REA. The results suggested the existence of genomic imprinting effects on the traits of the Japanese Black cattle. Hence, the parent-of-origin effect should be considered for the genetic evaluation of Japanese Black cattle in breeding programmes.

A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data

Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial). Imprinting effects (or more generally: parent-of-origin effects (POE)) are determined by taking the difference between the two genetic effects in each animal. However, the computation of their prediction error variance (PEV) is laborious; thus, we propose a new model that is equivalent to the aforementioned imprinting model, which facilitates the direct estimation of imprinting effects instead of taking the differences and the PEV is readily obtained. We applied the new model to slaughterhouse data for Brown Swiss cattle, among which imprinting has never been investigated previously. Data were available for up to 173 051 fattening bulls, where the pedigrees contained up to 428 710 animals representing the entire Brown Swiss population of Austria and Germany. The traits analysed comprised the net BW gain, fat score, EUROP class and killing out percentage. The analysis demonstrated that the net BW gain, fat score and EUROP class were influenced significantly by POE. After estimating the POE, the new model yielded estimates with reliabilities ranging between 0.4 and 0.9. On average, the imprinting variances accounted for 9.6% of the total genetic variance, where the maternal gamete was the main contributor. Moreover, our results agreed well with those obtained using linear models when the EUROP class and fat score were treated as categorical traits by applying a GLMM with a logit link function.