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Sheep Shearing and Epigenetic Change

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Sheep Shearing and Epigenetic Change Project No. 18-025 Contract No. ON-00593 AWI Project Manager: Dr Carolina Diaz Contractor Name: The University of Queensland Prepared by: Dr Edward Narayan, Mr Gregory Sawyer, Mr Dylan Fox and Prof. Alan Tilbrook Publication date: June 2020 Sheep Shearing and Epigenetic Change Published by Australian Wool Innovation Limited, Level 6, 68 Harrington Street, THE ROCKS, NSW, 2000 This publication should only be used as a general aid and is not a substitute for specific advice. To the extent permitted by law, we exclude all liability for loss or damage arising from the use of the information in this publication. AWI invests in research, development, innovation and marketing activities along the global supply chain for Australian wool. AWI is grateful for its funding which is primarily provided by Australian woolgrowers through a wool levy and by the Australian Government which provides a matching contribution for eligible R&D activities © 2019 Australian Wool Innovation Limited. All rights reserved. Contents Executive Summary 1. Introduction 2. Literature Review 3. Project Objectives 4. Success in Achieving Objectives 5. Methodology 6. Results 7. Discussion 8. Impact of Wool Industry – Now & in 5 years’ time 9. Conclusions and Recommendations 10. Bibliography 11. List of abbreviations and/or glossary 12. Appendices a. Appendix 1 – AWI Communication Report Template (see attached) b. Appendix 2 – List of Milestones & Dates submitted c. Appendix 3 – Remaining Assets d. Appendix 4 – Any Project Intellectual Property e. Appendix 5 – Storage of Primary Research Data (Paper based and electronic) f. Appendix 6 – Animal Ethics Approval (if any) 2 | Page PROJECT FINAL REPORT Executive Summary The primary objective of this research was to test the influence of shearing frequency (twice shorn versus single shorn) on the epigenetic DNA methylation patterns in a Merino sheep flock over a period of 1 generation. To keep the trial commercially relevant the selected flock was genetically derived from a variety of bloodlines and of mixed aged Merino ewes. Within the results of this research, the frequency of shearing pattern did not provide an evidence of significant epigenetic changes within the ewes and lambs. This report also presents data and discussion on the trait variation in ewe sheep body condition, physiological (stress hormonal) parameters and wool quality indicators between once and twice shorn ewe groups. It is concluded: Smart tags sensor based technology provides a reliable way to track sheep activity. Merino ewes and lambs (first generation) show diverse molecular epigenetic signatures that are not significantly influenced by shearing frequency. This study provided foundation knowledge on the molecular epigenetic signatures in Merino sheep under exposure to natural environmental and management factors. The high quality molecular data obtained through this research project included DNA methylation profiles of over 30,000 genes that are directly associated with cellular and molecular processes that regulate whole-animal physiology, development and growth. Thus, the baseline molecular data can provide a useful resource for future research in many key areas such as animal welfare, diseases and climatic resilience that will benefit Merino sheep and wool production. Page | 3 1 Introduction In the past decade, there has been an increase in scientific reporting into the effects of adversity in early life on the participants DNA profile within both human and animal studies (Bock et al., 2015; Lutz and Turecki, 2014). This emerging research area continues to be driven by scientists globally to better understand a wide range of effects caused by a variety of intrinsic and extrinsic influences on the DNA profile of ongoing generations within observed genotypes. From within the cell of the early stage developing embryo, transcriptional and epigenetic changes to the cell are occurring via remodelling and reprogramming within the cell nucleus. What is still unclear is how does the ram and ewe sheep interaction within their external and internal environments alter DNA, and at what phases of the embryo’s development and within its activation of the embryonic genome. This science is what is known as Epigenetics (Suzuki and Bird, 2008). The term epigenetics since its inception in 1942 has evolved with increasingly varying terms of what is epigenetics. Generally, epigenetics represents the genome-wide study of the distribution of methylated and unmethylated nucleoside residues within the genome (Thompson et al., 2020). Whereas Daxinger and Whitelaw (2012) concluded that epigenetics refers to effects on phenotype (or on patterns of gene expression) that are passed from one generation to the next by molecules in the germ cells and that cannot be explained by Mendelian genetics (or by changes to the primary DNA sequence). More recent studies have further expanded on this description to now include that epigenetics includes heritable states of gene expression that are not dependent on alterations in the DNA sequence (Ibeagha-Awemu and Zhao, 2015). Early biomedical studies into animals’ epigenetic behaviour have been focussed on mice due to their ability to reproduce quickly and for researchers to gain fast results with multiple offspring from the same female. Due to the nature of sheep growth and time to reach puberty, a predominant single offspring and the lack of funding for epigenetic research into the sheep there has been very limited research into this field (see Gonzalez-Recio et al., 2015; Goddard and WhiteLaw, 2014-MLA Report B.BSC.0114). However, due to foresight by early researchers there have been substantial advances in current genomic technologies to allow for development of genome analysis and sequencing in livestock (Ross and Sampaio, 2018). This Australian Wool Innovation funded study (18-025) will continue to grow this body of evidence to assist further research into environmentally induced effects on the sheep DNA as caused via epigenetics. Similar to bovine embryo research, the sheep is also better suited mammalian model than mice to study human 4 | Page PROJECT FINAL REPORT embryo development. A clear example of this interaction is the cloning of “Dolly” the sheep and her ability to create greater human scientific understanding of genetics and their interaction with the environment. This explanation of epigenetics within the extensive studies of sheep globally has shown no known literature about the benefits of epigenetic and transgenerational epigenetic effect on the DNA caused by shearing patterns. This was until unpublished research outcomes into sheep physiology and wool quality within an artificial insemination and embryo transfer program were discovered within an earlier (2015 – 2017) research trial undertaken by Dr Edward Narayan and Gregory Sawyer (Narayan et al., 2018; Sawyer and Narayan, 2019a). This research discovered that the embryos from the same sire and dam that were placed into surrogates and raised under the same environmental and management regimes had significant varying wool quality trait outcomes (Fig. 1.) This data led researchers to conceptualize under the current project that epigenetic influences on embryos life-time productivity are influenced by nature and nurture of the offspring by the ewe, ewe’s exposure to various external stressors while gestating including but not limited to shearing pattern. This research selected shearing patterns as the external stressor to investigate epigenetic changes in the DNA profile of merino ewes and lambs of twice versus once shorn ewes. Sire Dam name Dam body temp (oC) at AI Yearling Weight Yearling Micron 1 14 39.4 82 16.5 1 14 39.4 83 15.8 1 14 39.4 80 16.5 1 14 39.4 62.5 17.9 2 9 39.3 72 16.8 2 9 39.3 68 17.4 2 9 39.3 59.5 18.1 3 27 38.9 73.5 15.6 3 27 38.9 67 16.7 Figure 1.0 Production traits (Yearling Weight and Yearling Fibre Diameter-Microns) of merino lambs from donor ewes placed into same recipient ewe during AI/ET trial). Bold numbers for yearling weight and yearling microns represent variation across dam and lambs. Page | 5 2 Literature Review The accepted common science application of evolution is based on Mendelian theories of which there are three in total. Of significance to this research is the first law, that being the Law of Dominance and Uniformity. The Law of Dominance and Uniformity express that within a cross between a homozygous dominant and a homozygous recessive organism yields a heterozygous organism whose phenotype displays only the dominant trait. The offspring in the first generation (F1) are equal to the examined characteristic in the genotype and phenotype showing the dominant trait. Varriale (2019) expanded on this law to conclude that accepted inheritance on the F1 generation does not depend on the exclusivity of the transmission of genetic material from both parents to the offspring – but is a combination of various responses to environmental stimuli (ES) that are delivered through variations in epigenetic marks on DNA sequence. A vast array of ES (nutrition, pathogens, warming or cooling climate and other environmental factors) modify epigenetic marks in the DNA and leads to varying effects on production traits (phenotype) in livestock species (Ibeagha-Awemu and Zhao, 2015). The influence of ES on the phenotype of an animal is not only a function of its underlying DNA sequence but also of its current and past environment (Singh et al., 2010). It is therefore the science of epigenetics that challenges the previously accepted Mendelian theories with the divergence of traits that are not reliant on differences in the primary sequence of the DNA (Vogt, 2017). Many previous authors of epigenetics and transgenerational epigenetic change have further suggested that environmentally induced epigenetic change promotes DNA changes, which can be selected for and maintained as preserved environmentally induced traits in many generations (Varriale, 2019). This phenomena within science is known as transgenerational epigenetic change. Furthermore, Charles Darwin, “Original of Species” highlighted that the changing conditions throughout the lifetime of the sheep is of the highest importance in causing variability throughout the phenotype.
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