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.

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

“…For growth traits, models with X‐linked effects provided a better fit of the data, in agreement with Noorian et al (2020). Genes on the X chromosome contributed between 9% and 14% to the phenotypic variance of growth traits of Zandi sheep.…”

“…For efficiency‐related traits, Ghafouri‐Kesbi & Abbasi (2019) reported estimates of in Makouei sheep for postweaning KR, EF and RGR as 0.04, 0.07 and 0.06, respectively. In addition, in the Baluchi breed, Noorian et al (2020) estimated for postweaning EF as 0.02. As observed in the current study, inflation of autosomal additive genetic variance was a consequence of ignoring X‐linked effects from the model of genetic evaluation (model I‐ x ).…”

“…As quantitative traits, growth and efficiency‐related traits are determined by a complex interaction between genes and the environment (Noorian et al, 2020). Although genetic variance includes several components, efforts have mainly focused on estimating direct and maternal additive genetic variance, ignoring additional components such as imprinting (parent‐of‐origin) and the X chromosome (see Javanrouh et al, 2021 and references therein).…”

“…In addition, studying the X‐linked genetic effects on growth and efficiency‐related traits in sheep has been limited to recent years (Salemi et al, 2017; Maraveni et al, 2018; Ghafouri‐Kesbi & Abbasi, 2019). Moreover, there is a maternal component that has been often neglected when estimating variance components and heritability for different types of traits in sheep (Mokhtari et al, 2010; Singh et al, 2016; Vatankhah et al, 2016; Salemi et al, 2017; Maraveni et al, 2018; Ghafouri‐Kesbi & Abbasi, 2019; Noorian et al, 2020; Jafaroghli et al, 2021). This component is commonly referred as “litter” (Hagger, 1998), “maternal common environmental” (Fitzmaurice et al, 2022) or “maternal temporary environmental” (Everett‐Hincks et al, 2014).…”

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

“…Genetic evaluation using an animal model in considering the effects of X chromosome inheritance has been proposed [56,73]. Several studies have used this model to estimate the X-linked additive genetic effects using real data (e.g., [74][75][76]), while Meyer [77], with computer simulation, showed the difficulty in accurate estimation of X-linked effects. Wittenburg et al [78] used the statistical model in considering autosomal and gonosomal (X and Y chromosomes) effects to estimate genetic parameters of piglet birth weight.…”