Analysis of X chromosome and autosomal genetic effects on growth and efficiency-related traits in sheep
Milad Noorian
A , Sahereh Joezy-Shekalgorabi B C and Nasser Emam Jomeh Kashan A
A Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran.
B Department of Animal Science, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran.
C Corresponding author. Email: joezy5949@gmail.com
Animal Production Science - https://doi.org/10.1071/AN20233
Submitted: 12 April 2020 Accepted: 9 October 2020 Published online: 8 December 2020
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.
Keywords: animal models, heritability, maternal effects, REML, X-linked loci.
References
Akaike H (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19, 716–723.| A new look at the statistical model identification.Crossref | GoogleScholarGoogle Scholar |
Bahreini-Behzadi MR, Aslaminejad AA, Sharifi AR, Simianer H (2014) Comparison of mathematical models for describing the growth of Baluchi sheep. Journal of Agriculture Science and Technology 14, 57–68.
Eskandarinasab M, Ghafouri-Kesbi F, Abbasi MA (2010) Different models for evaluation of growth traits and Kleiber ratio in an experimental flock of Iranian fat-tailed Afshari sheep. Journal of Animal Breeding and Genetics 127, 26–33.
| Different models for evaluation of growth traits and Kleiber ratio in an experimental flock of Iranian fat-tailed Afshari sheep.Crossref | GoogleScholarGoogle Scholar | 20074184PubMed |
Fernando RL, Grossman M (1990) Genetic evaluation with autosomal and X-chromosomal inheritance. Theoretical and Applied Genetics 80, 75–80.
| Genetic evaluation with autosomal and X-chromosomal inheritance.Crossref | GoogleScholarGoogle Scholar | 24220813PubMed |
Fitzhugh HA, Taylor CS (1971) Genetic analysis of degree of maturity. Journal of Animal Science 33, 717–725.
| Genetic analysis of degree of maturity.Crossref | GoogleScholarGoogle Scholar | 5092769PubMed |
Ghafouri-Kesbi F, Abbasi MA (2019) Autosomal and X-linked additive genetic effects on body weight, body measurements and efficiency-related traits in sheep. Small Ruminant Research 180, 21–26.
| Autosomal and X-linked additive genetic effects on body weight, body measurements and efficiency-related traits in sheep.Crossref | GoogleScholarGoogle Scholar |
Ghafouri-Kesbi F, Baneh H (2012) Genetic parameters for direct and maternal effects on growth traits of sheep. Archiv fur Tierzucht 55, 603–611.
| Genetic parameters for direct and maternal effects on growth traits of sheep.Crossref | GoogleScholarGoogle Scholar |
Ghafouri-Kesbi F, Baneh H (2018) Genetic aspects of sexual size dimorphism in a synthesized breed of sheep. Meta Gene 17, 177–183.
Ghafouri-Kesbi F, Rafiei-Tari A (2015) Relative growth rate in sheep: heritability and relationship with absolute growth rate and body weight. Songklanakarin Journal of Science and Technology 37, 21–27.
Gholizadeh M, Ghafouri-Kesbi F (2015) Estimation of genetic parameters for growth-related traits and evaluating the results of a 27-year selection program in Baluchi sheep. Small Ruminant Research 130, 8–14.
| Estimation of genetic parameters for growth-related traits and evaluating the results of a 27-year selection program in Baluchi sheep.Crossref | GoogleScholarGoogle Scholar |
Grossman M, Eisen EJ (1989) Inbreeding, coancestry and covariance between relatives for X-chromosomal loci. The Journal of Heredity 80, 137–142.
| Inbreeding, coancestry and covariance between relatives for X-chromosomal loci.Crossref | GoogleScholarGoogle Scholar | 2926116PubMed |
Rance K, Heath SC, Keightley PD (1997) Mapping quantitative trait loci for body weight on the X chromosome in mice. II. Analysis of congenic backcrosses. Genetical Research 70, 125–133.
| Mapping quantitative trait loci for body weight on the X chromosome in mice. II. Analysis of congenic backcrosses.Crossref | GoogleScholarGoogle Scholar | 9449189PubMed |
Kariuki CM, Ilatsia ED, Kosgey IS, Kahi AK (2010) Direct and maternal (co)variance components, genetic parameters and annual trends for growth traits of Dorper sheep in semi-arid Kenya. Tropical Animal Health and Production 42, 473–481.
| Direct and maternal (co)variance components, genetic parameters and annual trends for growth traits of Dorper sheep in semi-arid Kenya.Crossref | GoogleScholarGoogle Scholar | 19763868PubMed |
Kirkpatrick M, Hall DW (2004) Male-biased mutation, sex linkage, and the rate of adaptive evolution. Evolution 58, 437–440.
| Male-biased mutation, sex linkage, and the rate of adaptive evolution.Crossref | GoogleScholarGoogle Scholar | 15068360PubMed |
Kleiber M (1947) Body size and metabolic rate. Physiological Reviews 27, 511–541.
| Body size and metabolic rate.Crossref | GoogleScholarGoogle Scholar | 20267758PubMed |
Larsen CT, Holand AM, Jensen H, Steinsland I, Roulin A (2014) On estimation and identifiability issues of sex- linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba). Ecology and Evolution 4, 1555–1566.
| On estimation and identifiability issues of sex- linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba).Crossref | GoogleScholarGoogle Scholar | 24967075PubMed |
Mandal A, Karunakaran M, Sharma DK, Baneh H, Rout PK (2015) Variance components and genetic parameters of growth traits and Kleiber ratio in Muzaffarnagari sheep. Small Ruminant Research 132, 79–85.
| Variance components and genetic parameters of growth traits and Kleiber ratio in Muzaffarnagari sheep.Crossref | GoogleScholarGoogle Scholar |
Maraveni M, Vatnkhah M, Eydivandi S (2018) Phenotypic and genetic analysis of Lori‐Bakhtiari lamb’s weight at different ages for autosomal and sex‐linked genetic effects. Iranian Journal of Applied Animal Science 8, 67–75.
Meyer K (2007) WOMBAT: a program for mixed model analyses by restricted maximum likelihood. User notes.
Miraei-Ashtiani SR, Seyedalian SAR, Moradi Shahrbabak M (2007) Variance components and heritabilities for body weight traits in Sangsari sheep, using univariate and multivariate animal models. Small Ruminant Research 73, 109–114.
| Variance components and heritabilities for body weight traits in Sangsari sheep, using univariate and multivariate animal models.Crossref | GoogleScholarGoogle Scholar |
Mohammadi Y, Rashidi A, Mokhtari MS, Esmailizadeh AK (2010) Quantitative genetic analysis of growth traits and Kleiber ratios in Sanjabi sheep. Small Ruminant Research 93, 88–93.
| Quantitative genetic analysis of growth traits and Kleiber ratios in Sanjabi sheep.Crossref | GoogleScholarGoogle Scholar |
Mohammadi H, Moradi-Shahrebabak M, Vatankhah M, Moradi-Shahrebabak H (2012) Direct and maternal (co)variance components, genetic parameters, and annual trends for growth traits of Makooei sheep in Iran. Tropical Animal Health and Production 45, 185–191.
| Direct and maternal (co)variance components, genetic parameters, and annual trends for growth traits of Makooei sheep in Iran.Crossref | GoogleScholarGoogle Scholar | 22648206PubMed |
Morey C, Avner P (2011) Genetics and epigenetics of the X chromosome. Annals of the New York Academy of Sciences 12, 18–33.
Panning B (2008) X-chromosome inactivation: the molecular basis of silencing. Journal of Biology 7, 30
| X-chromosome inactivation: the molecular basis of silencing.Crossref | GoogleScholarGoogle Scholar | 18983701PubMed |
Rance KA, Hastings IM, Hill WG, Keightley PD (1994). Mapping of putative QTL for body weight on the X chromosome of mice. In ‘Proceedings of the 5th World Congress on Genetics Applied to Livestock Production’, August 7–12, University of Guelph, Guelph, Ontario, Canada. (Ed Smith et al.) vol. 21, pp. 268–269.
Safari E, Fogarty NM, Gilmour AR (2005) A review of genetic parameter estimates for wool, growth, meat and reproduction traits in sheep. Livestock Production Science 92, 271–289.
| A review of genetic parameter estimates for wool, growth, meat and reproduction traits in sheep.Crossref | GoogleScholarGoogle Scholar |
Salemi A, Vatankhah M, Asadi B (2017) Phenotypic and genetic analysis of Lori‐Bakhtiari lamb’s longevity up to yearling age for autosomal and sex‐linked chromosomes. Iranian Journal of Applied Animal Science 7, 37–44.
Singh H, Pannu U, Narula HK, Chopra A, Naharwara V, Bhakar SK (2016) Estimates od (co)variance components and genetic parameters of growth traits in Marwari sheep. Journal of Applied Animal Research 44, 27–35.
| Estimates od (co)variance components and genetic parameters of growth traits in Marwari sheep.Crossref | GoogleScholarGoogle Scholar |
SAS (2004) ‘SAS users’ guide.’ version 9.1. (SAS Institute: Cary, NC)
VanRaden PM (1987) Evaluations of sires based on sons and on maternal grandsons. Journal of Dairy Science 70, 185
Vatankhah M, Talebi A, Blair H (2016) Genetic analysis of Lori-Bakhtiari lamb survival rate up to yearling age for autosomal and sex-linked. Small Ruminant Research 136, 121–126.
| Genetic analysis of Lori-Bakhtiari lamb survival rate up to yearling age for autosomal and sex-linked.Crossref | GoogleScholarGoogle Scholar |
Wolfinger RD (1993) Covariance structure in general mixed models. Communications in Statistics 22, 1079–1106.
| Covariance structure in general mixed models.Crossref | GoogleScholarGoogle Scholar |
