Fashions change all the time, and food is no exception. What's `in' one year is `out' another. Fifty years ago, a nice piece of pork came with a rich coating of fat. But in the 21st century, fat is out of favour, and now pigs are bred for pork muscle rather than lard. Muscle mass is an example of a measurable physical characteristic that varies significantly between individuals: it is a `quantitative trait'. Quantitative traits are produced by intricate interactions between environmental factors and regions in genes,known as `quantitative trait loci'. In the case of muscle mass, it seems that a single quantitative trait locus in the insulin growth factor 2 (IGF2) gene accounts for a significant proportion of muscle mass and back-fat variations amongst pigs. Nonetheless, a major question remained: what are the differences in DNA sequence in this quantitative gene locus that could explain the change in muscle mass between pigs? Puzzled by the problem, AnneSophie Van Laere and colleagues decided to track down the elusive mutations and found that a single nucleotide mutation in the IGF2 gene is responsible for making porky pigs!
Identifying the mutations underlying quantitative trait loci is not a trivial task, since each locus is usually only responsible for a fractional change in the quantitative trait. Knowing that IGF2 stimulates myogenesis, the authors started by sequencing the genomic region corresponding to the IGF2 quantitative trait locus. Working with crossbred piglets from wild-type and muscly parents, the team analysed the parents' and youngsters' DNA sequence polymorphisms and found that the muscly pigs had a guanine base where less well built pigs had an adenine. The team had found a needle in the haystack:this single mutation is the quantitative trait nucleotide that contributes to a 3–4% increase in muscle mass.
When the team took a closer look at the position of the mutation in the gene, they noticed that the causative mutation does not affect the IGF2 protein sequence; instead, it is in a non-coding region of the gene that might control its expression. Whilst the wild-type allele with the adenine base was able to bind a nuclear protein that repressed IGF2 transcription, the muscly pig's guanine mutation inhibits this interaction, which might affect the expression of IGF2. The team went on to investigate the effect of the causative mutation in the regulation of IGF2 expression. They monitored the levels of IGF2 transcripts from pigs at different growth stages and found that the paternally inherited mutant allele induced a three-fold increase of post-natal IGF2 expression in skeletal muscle, without affecting its expression in the liver. These results confirm that this non-coding region has an important regulatory role in IGF2 expression in muscle. And when the team mapped the mutant allele's distribution in farmed animal populations, they found high frequencies of the mutation in leaner breeds, matching the modern preference for lean cuts. Artificial selection pressure imposed on commercial pig populations has caused the mutant allele to spread between breeds.
In general terms, this outstanding work establishes a direct relationship between a single nucleotide substitution in a non-coding region and the expression of quantitative trait in a domestic animal. It is yet another example of the importance of introns and untranslated regions in regulation of gene expression, and it also shows that farm animals can help us to unveil the molecular basis of complex traits.