From QTL to QTN: Identification of a Quantitative Trait Nucleotide Influencing Muscle Development and Fat Deposition in Pig

Most traits of economical importance in animal production are quantitative i.e. they are
characterized by a continuous variation of phenotypic values. Examples for such traits
are carcass weight, milk production and lean meat content. The phenotype of an animal
for a quantitative trait depends on its genotype at several loci (called quantitative trait
loci, QTL) as well as on environmental factors. Up to date, a large number of QTLs have
been identified in farm animals by segregation analysis either within commercial
populations or in crossbreed populations. Animal geneticists face now the challenge to
identify the causative mutations lying behind these QTLs.
In this thesis, we report the identification of the causative mutation for a major QTL
influencing muscle development, fat deposition and heart size in pig. Previous studies
have mapped this locus to the distal end of pig chromosome 2p. Furthermore, they
have hypothesized that the causative mutation(s) may lie in an element regulating the
expression of insulin-like growth factor 2 (IGF2). Firstly, we sequenced the IGF2
region in the pig and made comparative sequence analysis with available human and
mouse sequences. We then used an identity-by-descent approach and managed to
pinpoint the causative mutation to a GA transition located in an evolutionary
conserved CpG island in IGF2 intron 3 (IGF2-intron3-G3070A). Subsequently, we used
electrophoretic mobility shift assay and transient transfection experiments and showed
that the QTN (quantitative trait nucleotide) abrogates the binding of a putative
repressor. We completed our study by determining the core binding site of this transacting
factor and by performing DNase I footprinting of the CpG island containing the
QTN. In addition, we identified an IGF2 antisense transcript (IGF2-AS) and showed that
its expression was also influenced by the QTN.
The discovery of mutations causing QTLs in farm animals opens great future prospects.
Besides evident practical breeding interests there are also major scientific interests, as
understanding the mechanism causing the QTL effects will broaden our general
knowledge on how the genome operates.