DOI: 10.6084/m9.figshare.29456534
title: <b>Metabolic Investigation into Dairy Cow Longevity</b> - <i>Thesis Supplementary Documents and Data</i>

description: Supplementary data for a thesis submitted in fulfilment of the requirements of the Degree of Doctor of Philosphy.<br><br>Dairy cow longevity is a multifactorial outcome determined by a combination of health, reproduction, production, management practices, and chance events. Optimising longevity can reduce the demand for replacement heifers, enable diversification into beef production, reduce lifetime emission per litre of milk produced, improve feed efficiency, and enhance the social license of the dairy industry. Increasing age and parity are associated with increased risk of adverse health events, reproductive inefficiency, culling and mortality, and prevent optimal herd longevity. Despite knowing that these poor outcomes increase with age, the underlying metabolic changes that occur with aging have received little attention. Identifying the physiological changes that occur with age and how these modulate cow health and survival may reveal opportunities to improve herd longevity and optimise production. This thesis explored physiological aspects of cow longevity through three primary investigations: 1) body tissue reserves and association with dairy housing systems of pasture-based production and confinement-based production, parity and blood metabolites; 2) association between age, housing system, reproduction and health events; and 3) lipidomic and metabolite profile associations with cow age, housing systems, and survival. The study design enabled multiple lines of inquiry from a single set of biological samples. Thirty farms (15 pasture-based, 15 total mixed ration, confinement farms) contributed 29 randomly selected, parity stratified cows to both a dry-cow and peak-milk cow cohort, totalling approximately 1,700 samples. Liquid chromatography – mass spectrometry targeted lipidomics identified 185 lipids species in plasma, and colorimetric analysis measured 15 other metabolites in serum. Novel statistical approaches that included machine learning, cluster analysis, and variable stability selection were used to address each chapter’s objectives, and to present interpretable and actionable results. The first chapter of the thesis reviewed the role of blood glycerophospholipids, specifically the subclasses of phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylserine, in dairy cattle health and longevity and provided rationale for a lipidomic approach to investigate aging and survival. Chapters 2 and 3 examined the association between measures of body tissue reserves, including a novel metric that combined body condition score and body weight, with parity, housing systems, and a standard panel of serum metabolites. Higher parity cows had greater BW but lower BCS compared to lower parity cows. Albumin was consistently associated with all metrics, suggesting protein metabolism efficiency is an important determinant of body tissue reserves. Chapter 4 explored the relationship between parity, housing systems and the important longevity-related outcomes of reproduction, mastitis, and lameness. This chapter introduced the Dairy UP database, which integrates multiple data sources that include different herd management software, pasture information, milk production and quality, and weather. Increasing parity was associated with reduced reproductive efficiency, and increased hazards of mastitis and lameness. Housing system did not differ for reproductive or lameness risk, but confinement-based farms had increased mastitis risk compared to pasture-based farms across all parity groups. The final three chapters explored lipidomic associations with 1) age and parity, 2) housing systems, and 3) survival. Glycerophospholipids containing omega-3 fatty acids had reduced plasma concentrations in older cattle compared to younger cattle, had lower concentrations in confinement-based housing systems compared to pasture-based systems, and lower concentrations were associated with increased hazards of culling. Collectively, these findings suggest omega 3 fatty acid pathways may be altered with age and could partially explain the increased risk of adverse outcomes in older cattle. We speculated that diet was the major differentiating factor between housing system lipid profiles, with the corn-silage based total mixed rations provided in confinement-based farms containing greater amounts of omega-6 fatty acids and less omega-3 fatty acids compared to pasture-based diets. This body of work represents the first application of lipidomics to characterise aging and survival in dairy cattle, identified the influence of housing systems of blood metabolite profiles, and introduced novel statistical approaches to high-dimensional agricultural data. The thesis provides new targets for interventional studies and practice to help optimise cow longevity.