Autosomal and X-linked additive genetic effects on body weight, body measurements and efficiency-related traits in sheep

Dissection of X chromosome dosage compensation for quantitative traits in sheep using different statistical models

Since males and females have different number of X chromosome, different mechanisms have evolved to equalize dosage of gene products from the X chromosome between XX females and XY males. The aim of this study was to study X chromosome dosage compensation for growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR) in Zandi sheep. A two steps procedure was adopted to analysis data. In the first step, each trait was analyzed with a series of 6 animal models including different combinations of direct and maternal effects. Using Akanke's Information Criterion (AIC) the best model (Model I) was selected for each trait. In the second step, five additional models were fitted by adding X chromosome effects to the Model I, considering 5 strategies for modeling X chromosome dosage compensation: (1) no global dosage compensation (ngdc), (2) random inactivation in the homogametic sex (hori), (3) doubling of the single shared sex chromosome in the heterogametic sex (hedo), (4) halving expression of both sex chromosomes in the homogametic sex (hoha) or (5) inactivation of the paternal sex chromosome in the homogametic sex (hopi). Predictive ability of models was measured using the mean squared error of prediction (MSE) and Pearson's correlation coefficient between the real and predicted values of records [Formula: see text] Correlations between traits due to autosomal- and X-linked genetic effects were estimated by bi-variate analyses. For GR and KR, models including X-linked effects lead to a much better fit of data, expressed by the strong decrease in the AIC criterion. Models including X-linked effects had also better predictive ability as they provided smaller MSE and higher [Formula: see text] For GR and KR, although all strategies for modeling X chromosome dosage compensation improved general properties of the model, the model "ngdc" fitted the data significantly better than other models. Including X-linked genetic effects in the model led to 10% (GR, KR) decrease in the autosomal additive variance, and 7% (KR) to 19% (GR) decrease in the residual variance. Estimates of autosomal heritability ([Formula: see text]), were 0.15 ± 0.03, 0.13 ± 0.03, 0.9 ± 0.03 and 0.13 ± 0.03 for GR, KR, EF and RGR, respectively. X-linked heritability ([Formula: see text]) was 0.08 ± 0.03 for GR and 0.04 ± 0.03 for KR, respectively. Maternal heritability ([Formula: see text]) were 0.02 ± 0.01, 0.01 ± 0.01, 0.03 ± 0.02 and 0.03 ± 0.02 for GR, KR, EF and RGR, respectively. For GR and KR, the Spearman's correlation between breeding values obtained from the best model and model I deviated from unity, indicating re-ranking of top animals across models. The X-linked additive genetic correlation and autosomal additive genetic correlation were similar in terms of sign and magnitude in a way that they were all positive and high. As considering X-linked genetic effects resulted to an improvement in the general properties of the model and possibility of re-ranking of top animals, including these effects in the model, considering dosage compensation on the X chromosome was recommended.

Autosomal and Z-linked genetic evaluation for body weight in Mazandaran native chicken using different models for dosage compensation on the Z chromosome

The objectives of this study were to assess the autosomal and sex-linked genetic inheritance of growth traits and identify the effective dosage compensation on the Z chromosome in Mazandaran native chickens. The data included body weights at hatching (BW0), 8 weeks (BW8) and 12 weeks (BW12) of age, related to the first 21 generations of selection, were collected from Mazandaran native chicken breeding centre. The fixed effects included sex of birds in two classes, hatch in five classes and generation in 21 classes. The inverse of the sex-linked additive genetic relationship matrix was constructed using nadiv package in R considering different models for dosage compensation on the Z chromosome. The setup inversed matrix was then supplied externally to WOMBAT using the GIN option. Twelve univariate animal models separating participation of autosomal additive genetic, sex-linked additive genetic and maternal effects (both genetic and permanent environment effects) with considering the five different dosage compensation methods for models with sex-linked effects were analysed by WOMBAT software. BW0 was not affected by sex-linked additive genetic effects. For BW8 and BW12 the model which included autosomal, sex-linked direct additive and maternal effects with no global dosage compensation for the Z chromosome was the most appropriate model. Autosomal heritability estimates were 0.05 ± 0.02, 0.10 ± 0.01 and 0.11 ± 0.01, for BW0, BW8 and BW12, respectively. For BW8 and BW12, sex-linked heritability estimates were 0.07 and 0.27, respectively. Spearman rank correlation coefficient between autosomal and sex-linked breeding values were 0.45 and 0.12 for BW8 and BW12, respectively. Spearman rank correlation coefficient between autosomal and sex-linked breeding values were 0.45 and 0.12 for BW8 and BW12, respectively. The autosomal direct additive genetic correlations between all traits were positive. The estimate of direct sex-linked additive genetic correlation between BW8 and BW12 was high (0.88). Also, maternal genetic correlations were 0.53, 0.54 and 0.91 between BW0-BW8, BW0-BW12 and BW8-BW12, respectively. Given the importance of Z-linked genes for BW8 and BW12, it is recommended that Z-linked effects be separated from autosomal effects in order to increase the accuracy of genetic evaluation of birds for these traits.

Growth rate and efficiency-related traits in Kermani lambs: estimations of (co)variance components and genetic parameters

Using Kermani sheep, the current study estimated (co)variance components and genetic parameters for average daily gain, Kleiber's ratio, growth efficiency, and relative growth rate. Data were analyzed by the average information restricted maximum likelihood (AI-REML) method using six animal models with different combinations of direct and maternal effects. The best-fitting model was determined after testing for improvement in log-likelihood values. The estimates of h² for average daily gain (ADG), Klieber's ratio (KR), growth efficiency (GE), and relative growth rate (RGR) in pre- and post-weaning phases were 0.13 ± 0.6 and 0.17 ± 0.02, 0.12 ± 0.04, and 0.16 ± 0.03; 0.05 ± 0.05 and 0.07 ± 0.03 and 0.06 ± 0.02 and 0.07 ± 0.01, respectively. Maternal heritabilities (m²) ranged from 0.03 ± 0.01 for relative growth rate in pre-weaning phase to 0.11 ± 0.04 for average daily gain in post-weaning period. The maternal permanent environmental component (Pe²) accounted for 3 to 13% to the phenotypic variance for all the studied traits. Estimated values of additive coefficient of variations (CV_A) ranged from 2.79% for relative growth rate at 6 months of age to 23.74% for growth efficiency at yearling age. Genetic and phenotypic correlations among traits were ranged from -0.687 to 0.946 and -0.648 to 0.918, respectively. The result indicated that selection for growth rate and efficiency-related traits would also be less effective in achieving genetic change, because there was little additive genetic variation among Kermani lambs.

Relative contribution of Imprinting, X chromosome and Litter effects to phenotypic variation in economic traits of sheep

Data on Zandi sheep were analysed to quantify maternal and paternal imprinting, X chromosome and litter effects' contribution to phenotypic variation in birth weight (BW), weaning weight (WW), growth rate (GR), Kleiber ratio (KR), efficiency of growth (EF) and relative growth rate (RGR). To this end, a two-step approach was adopted. In the first step, each trait was analysed with a series of 16 animal models, which were identical for fixed and autosomal additive genetic effects but differed for combinations of maternal permanent environmental, maternal genetic, X chromosome and litter effects. For each trait, the best model was selected by the Akaike information criterion (AIC) and likelihood ratio tests (LRTs). In the second step, three additional models were fitted by adding maternal imprinting, paternal imprinting or both (models 17, 18 and 19) to the best model selected in the first step. Estimators of bias, dispersion and accuracy of breeding values estimated within 19 models with whole, and partial data were used to evaluate how well were the 19 models in estimating breeding values for the animals when their records were masked. For all traits studied, fitting the litter effect led to a better data fit. Also, it resulted in noticeable decreases in residual variance and other maternal variances. For growth traits, models containing the X-linked effects fitted the data substantially better than corresponding models without the X-linked effects. For BW, WW and GR, estimates of X-linked heritability ( h s 2 $$ {h}_s^2 $$ ) ranged between 0.09 (GR) and 0.14 (BW). Ignoring X-linked effects from the genetic evaluation model resulted in significant inflated autosomal additive genetic variance. For BW, WW, EF and RGR, models containing the imprinting effects provided a better fit of the data than otherwise identical models. Imprinting effects contributed significantly to the phenotypic variation of these traits in a range between 5% (RGR) and 8% (BW, WW). A sharp decline was observed in autosomal additive genetic variance following including imprinting effects in the model (27% to 40% depending on the trait). The least bias and dispersion, as well as greater accuracies for breeding values of focal animals, were for a model which included imprinting, X-linked and litter effects. It was concluded that imprinting, X-linked and litter effects need to be included in the genetic evaluation models for growth and efficiency-related traits of Zandi lambs.

Analysis of X chromosome and autosomal genetic effects on growth and efficiency-related traits in sheep

Abstract Context It is believed that the X chromosome plays an important role in influencing quantitative traits. Despite this, until recently, X-linked genetic effects have not been considered in models to estimate genetic parameters for economically important traits of livestock. Aims A large dataset was analysed to quantify autosomal additive genetic, X-linked additive genetic and maternal effects on growth and efficiency-related traits in Baluchi sheep. Methods Traits included bodyweight at birth, weaning (WW), 6 months (W6), 9 months and yearling age, pre- and post-weaning average daily gain, pre- and post-weaning Kleiber ratio, pre- and post-weaning efficiency of growth (EFb), and pre- and post-weaning relative growth rate. Each trait was analysed using the REML procedure fitting a series of eight univariate animal models. For each trait, the most appropriate model was selected by the Akaike information criterion and Bayesian information criterion. Key results The X-linked genetic effect was significant only in models fitted to EFb, where the estimate of X-linked heritability was 0.02 ± 0.01 from the best model. Other traits were not affected significantly by X-linked genetic effects. Estimates of autosomal heritability () for growth traits were between 0.06 ± 0.02 (post-weaning average daily gain, pre-weaning relative growth rate) and 0.22 ± 0.04 (bodyweight at yearling age), and ranged between 0.02 ± 0.01 (EFb) and 0.08 ± 0.02 (pre-weaning Kleiber ratio) for efficiency-related traits. Maternal effects significantly contributed to phenotypic variation of most traits, with larger effects on traits measured early in life. For EFb, the Spearman’s correlation between breeding values including and excluding X-linked effects was 0.95. It was 1.00 for traits that were not affected by X-linked genetic effects. Conclusions Although the proportion of phenotypic variance attributed to X-linked loci for most traits was zero, the importance of X-linked genetic effects should be at least tested in models when estimating variance components for growth and efficiency traits of Baluchi sheep. Implications As estimates of genetic parameters are breed-specific, we recommend for growth and efficiency traits of sheep that the importance of X-linked genetic effects should be evaluated to assess if these effects should be included in models used in genetic evaluation.