Department of Genetics

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Browsing Department of Genetics by Subject "Abalone -- Genetics"

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    Critical assessment of the “internal reference” method to eliminate non-genetic effects within a Combined Family Selection program on the abalone species (Haliotis midae)
    (Stellenbosch : Stellenbosch University, 2013-12) Difford, Gareth Frank; Brink, Danie; Stellenbosch University. Faculty of Agricultural Science. Dept. of Genetics, division of aquaculture.
    ENGLISH ABSTRACT: The aim of this study was to critically assess the implementation of the internal reference method within the most recent 173 full-sibling growth trial of the Innovation Fund Abalone Breeding Project. The trial was conducted over two locations for a period of five years, with minimal replication for the majority of test families and a single full-sibling family was entered into each experimental unit (basket) as an internal reference group. The primary focus was firstly, to validate the performance of the internal reference group as a control for comparisons and correction of environmental variation in test family performances. Secondly, to identify areas of weakness and either make recommendations to remedy areas of weakness or justify devoting resources to alternative methods of reducing extraneous environmental variance with limitations on replication. The efficiency and statistical power associated with utilising internal reference information as a covariate and for manual correction respectively were examined for the 6 full-sibling test families that were replicated. This study reports on the evaluation of factors which are potential sources of bias in the internal reference method, the first of which, tag loss, was found to be significant after 6- 12 months. However, it was not found to bias internal reference group performances as the factors which contribute to tag loss were found to act randomly. Variability in size ratio of internal reference to test family at co-stocking proved a significant source of bias, as reference groups smaller than their test family counterparts had reduced performances. Testing for genotype by environment interactions was precluded due to the inherent lack of replication and the subsequent confounding of genotype effects with inter-rearing structure effects at one of the locations. However, significant differences were detected for both traits of interest of the internal reference group over the two locations. Significant antagonistic interactions were detected and identified as a source of bias for average daily weight gain of replicate test families. The evaluation of average daily length gain for the efficiency of adjustment when the internal reference is a covariate and the change in statistical power when the internal reference is used for a manual correction, yielded conflicting results. The latter shows a decrease in statistical power and the former shows an increase in efficiency, both resulting in poor goodness of fit in the respective models. There was however evidence that when no antagonistic interactions occurred “between replicate variance” decreased and therefore the internal reference method has statistical merit provided all critical success factors are satisfied. Recommendations were made for future implementation of the internal reference method to facilitate adequate statistical testing for sources of bias and the prevention thereof. Additionally, an alternative method which may have merit in decreasing environmental variance and the need for replication, is discussed.