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    Value added wheat through applied genomic prediction : a genomic approach for breeding low gluten epitope wheat : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Breeding and Genetics at Massey University, Palmerston North, New Zealand. EMBARGOED until 24 July 2026.
    (Massey University, 2023) Macalister, Jamie
    Gluten epitopes are known to trigger coeliac disease (CD) in affected consumers and are believed to be linked to some cases of gluten intolerance. Research suggests that if consumers were exposed to wheat with reduced concentrations of gluten epitopes, the incidence of CD and gluten intolerance may be reduced. Methods have recently been developed allowing researchers to measure gluten epitope concentrations in wheat. This offers wheat breeders the potential to select towards varieties with lower epitope concentrations than existing cultivars. However, the methods for measuring epitope concentrations remain costly and time consuming. Therefore, it is proposed that a genomic based approach for breeding low epitope wheat lines is a more practical method than traditional phenotype-based selections. The genetic factors associated with epitope concentrations remain poorly understood. In this thesis, heritability estimates of between 0.37-0.93 are reported for concentrations of 6 distinct gluten epitopes. The associations between epitope concentrations and baking quality are also assessed and are shown to range from being near zero for some epitopes to strong positive correlations between other epitopes and particular baking quality characteristics. A Genome Wide Association Study and a model for genomic prediction are employed to determine the genetic factors associated with epitope concentrations. In these analyses, 3 significant genomic windows are identified as being associated with concentrations of 3 particular epitopes. Empirical prediction accuracies of between 0.16-0.53 are observed for predictions of epitope concentrations in a breeding population. Additionally, accuracies of between 0.37-0.67 are achieved by adjusting the population structure to represent the ideal circumstances that breeders would aim to achieve in their training and target populations. These results demonstrate that genomic selection (GS) will be an effective method for breeding low gluten epitope wheat. The outcome of this thesis will allow implementation of GS in the New Zealand Institute for Plant & Food Research wheat breeding program where epitope concentrations will be established as a new breeding target. This is expected to lead to the release of niche, low epitope cultivars with a value-add component that benefits growers, industry and consumers.
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    An empirical analysis of the cost of rearing dairy heifers from birth to first calving and the time taken to repay these costs
    (Cambridge University Press, 8/02/2017) Boulton AC; Rushton J; Wathes DC
    Rearing quality dairy heifers is essential to maintain herds by replacing culled cows. Information on the key factors influencing the cost of rearing under different management systems is, however, limited and many farmers are unaware of their true costs. This study determined the cost of rearing heifers from birth to first calving in Great Britain including the cost of mortality, investigated the main factors influencing these costs across differing farming systems and estimated how long it took heifers to repay the cost of rearing on individual farms. Primary data on heifer management from birth to calving was collected through a survey of 101 dairy farms during 2013. Univariate followed by multivariable linear regression was used to analyse the influence of farm factors and key rearing events on costs. An Excel spreadsheet model was developed to determine the time it took for heifers to repay the rearing cost. The mean±SD ages at weaning, conception and calving were 62±13, 509±60 and 784±60 days. The mean total cost of rearing was £1819±387/heifer with a mean daily cost of £2.31±0.41. This included the opportunity cost of the heifer and the mean cost of mortality, which ranged from £103.49 to £146.19/surviving heifer. The multivariable model predicted an increase in mean cost of rearing of £2.87 for each extra day of age at first calving and a decrease in mean cost of £6.06 for each percentile increase in time spent at grass. The model also predicted a decrease in the mean cost of rearing in autumn and spring calving herds of £273.20 and £288.56, respectively, compared with that in all-year-round calving herds. Farms with herd sizes⩾100 had lower mean costs of between £301.75 and £407.83 compared with farms with <100 milking cows. The mean gross margin per heifer was £441.66±304.56 (range £367.63 to £1120.08), with 11 farms experiencing negative gross margins. Most farms repaid the cost of heifer rearing in the first two lactations (range 1 to 6 lactations) with a mean time from first calving until breaking even of 530±293 days. The results of the economic analysis suggest that management decisions on key reproduction events and grazing policy significantly influence the cost of rearing and the time it takes for heifers to start making a profit for the farm.