Microarray evidence for off target effects in tick RNA interference experiments, and the lack of strong correlation between DSRNA and antibody phenotypes in tick In vitro treatments for vaccine candidate screening

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Quantitative Trait Loci Mapping in Merino Sheep and Effect of Accuracy of QTL Parameter Estimation on Marker Assisted Selection

The objectives of this thesis were to perform a genome scan for important production traits in Australian Merino sheep and to investigate issues related to the prediction of marker assisted selection (MAS) response in single and multiple trait selection schemes in animal breeding programs. In the first experimental chapter, a genome scan was performed for 4 growth and 7 fleece traits in Australian Merino sheep. Quantitative trait loci (QTL) parameters were estimated through single QTL interval mapping within and across four paternal half-sib families. The genome scan yielded 21 significant QTL for all traits at the 1% chromosome wise significance threshold level in within family analysis. Across family analysis supported most of the highly significant results from single family analysis but did not show any common significant QTL at the 1% chromosome wise significance threshold level across all families. Because of the relatively small progeny group sizes the power and the precision of the analysis are probably low and the QTL allele substitution effects are overestimated. In the subsequent three chapters some important issues related to the application of QTL information in MAS, including efficient prediction of MAS response and effect of the accuracy of estimated QTL effect in single and multiple trait selection, were investigated

A novel use of high density SNP assays to optimize choice of different crossbred dairy cattle genotypes in smallholder systems in East Africa

We present use of SNP technologies to obtain for the first time, rapid, large-scale, in situ estimates of performance of crossbred cows in smallholder herds. Compared to historical approaches, our approach allowed optimum crossbreed choices to be determined more rapidly and without question about the relevance of the environment. High-density SNP assays were used to estimate breed composition for a monitored population comprising 1292 cows from 610 smallholder farms in Kenya. The achieved milk yields are much lower than generally assumed and lactation curves are very flat out to 400 days. In poor production environments, lower grade crosses (containing <60% exotic dairy alleles) had the same yield as high grade crosses. Allowing for the larger size and maintenance requirements of high grade exotics, lower grade exotics will be the most economically productive animals in these environments

Use of high density SNP genotypes to determine the breed composition of cross bred dairy cattle in smallholder farms: Assessment of reproductive and health performance

Reproductive performance and disease data were recorded for 2 years on 1,824 dairy cows in smallholder farms using participatory approaches and onfarm recording. Most animals experienced one service to conception. Calving intervals were long, ranging between 261 and 761 days, with an average of 451±101days. Herd level of production (HeL) had significant effect on calving interval. However, there was no difference between crossbreds with different levels of exotic breed percentage or in different HeL classes in disease incidence. Most animals had less than 2 treatment events, despite the high disease burden in the study areas. Mortality rates were low, ranging from 2.13% to 2.65%. Even though the crossbred animals had higher performance compared to indigenous animals, the gains obtained were below what would be possible with better management. These results suggest that crosses with low exotic proportions would be the most optimal for the production systems studied

Genome-wide association study of meat quality traits using whole-genome sequence data in a multi-breed sheep population

This is the first study showing GWAS results from whole-genome sequence (WGS) data in sheep. The objective of this study was to fine map previously identified QTL and detect new QTL for meat quality traits in a multi-breed sheep population using WGS data. The traits measured were carcass fat depth, intramuscular fat, post-weaning eye muscle depth, post-weaning body weight and SF5. Corrected phenotypes were available on 13,363 to 26,769 Australian sheep depending on the trait. The GWAS for all five traits for the 50K, HD, and WGS identified 18, 52 and 250 QTL regions, respectively based on a 5% FDR threshold. Together, the largest QTLs explained a substantial part of the additive genetic variance (between 10.6 - 14.3%). Previously identified QTL on chromosomes 6 and 18 were confirmed. Single breed analysis for Merino sheep only, showed a reduced significance of the large QTL, but in similar regions. We were able to identify candidate genes involved in meat quality using functional annotation. We conclude that the WGS data provided more and clearer evidence of QTL regions, potentially resulting in more predictive SNPs and more detailed functional analysis of genes underlying the QTL regions