Genome-wide copy number variation in sheep : detection and utility as a genetic marker for quantitative traits, with reference to gastrointestinal nematodiasis : thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Palmerston North, New Zealand
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2018
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Massey University
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Abstract
Gastrointestinal nematodes are perhaps the most important parasites of domestic sheep
world-wide. Genetic selection for nematode resistance in domestic sheep is being promoted
in many countries including New Zealand. There are several strategies to identify genetic
markers associated with quantitative traits. Single nucleotide polymorphism (SNP)-based
strategies have been widely used in animal breeding. However, SNP cannot explain all the
genetic variation for a particular trait. A new kind of variation, copy number variation (CNV)
has been identified as contributing to genetic variation in production and disease traits.
Compared with other domestic animals, CNV in sheep is poorly investigated. The primary
objective of this thesis was to explore the utility of genome-wide CNV as a genetic marker
for the analysis of quantitative traits in sheep. Five different studies were undertaken to fulfill
the objective. The first two studies used 50 K SNP BeadChip genotype data and next
generation sequencing (NGS) data to detect CNV. Extensive CNV differences were evident
between breeds as well as detection algorithms. NGS-based detection resulted in better CNV
resolution than that by SNP. Subsequently, a genome-wide association study (with a small
sample size) using CNV detected from a high density (HD) SNP genotype data identified four
CNV regions to be significantly associated with a couple of traits pertaining to
gastrointestinal nematodiasis in Romney sheep, while no significant SNP associations were
found. Somatic mosaicism of CNV, influenced by age (high in foetuses, compared to adults),
individuals, detection algorithm and type of tissue analysed, was also evident in separate
study. The final study detected CNV differences and SNP based selection signatures in two
Romney lines selected for gastrointestinal nematode resistance or resilience. Several
significant SNPs and line-specific CNV regions were identified. However, only one SNP
overlapped to a CNV region, indicating that SNP-based selection signatures and CNV could
represent different aspects of sheep immunogenetics. Overall, CNV could be a potential genetic marker, albeit with methods for detection and validation needing to be refined. The
conclusions from this thesis expand our understanding of CNV in sheep and its potential
application prospects for genetic breeding of sheep in the future.
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Keywords
Sheep, Breeding, Genetics, Romney Marsh sheep, Genetic markers, Identification, Nucleotide sequence, Immunogenetics, Parasites, Nematodes