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EGS-ABG : European Graduate School in Animal Breeding and Genetics


Identification of causal factors for recessive genetic defects for embryonic lethality in dairy cattle combining whole exome and genome sequencing

Nr : 4-AU-APT

Topic :
Identification of causal factors for recessive genetic defects for embryonic lethality in dairy cattle combining whole exome and genome sequencing

Host Institutions :
Aarhus University (Denmark)
AgroParisTech (France)

Summary :
Fertility has gradually decreased in dairy cows over the last decades and low heritability makes it difficult to improve. Genomic information provides new opportunities. The recent discoveries of bovine haplotypes with negative effects on fertility in the French and Nordic Holstein cattle populations illustrate the power of these designs. Very large reference populations with phenotypic and genomic information provide unique resources for QTL characterization and causal mutations discovery. Whole genome sequence (WGS) can then be used to identify the causative mutations. However WGS is still expensive and cannot be generalized to large populations. An alternative is to sequence exome. This cheap method can be extended to a large number of animals, allowing studying rare variants. Reduced fertility is primarily due to increased embryonic mortality. A fraction of this mortality is likely due to polymorphisms in the coding sequence that might disrupt normal gene function resulting embryonic mortality, making exome sequencing an attractive approach. So far exome sequencing has been a very successful technique in rare diseases in human. The objectives of the PhD study are to 1) identify causal factor underlying fertility QTL or recessive lethal haplotypes in French and Nordic Holstein cattle, 2) validate candidate sequence variants through genotyping and, when possible, functional validation for lethality, 3) study the distribution of functional variants within exome regions.


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