Investigating the genetic basis of pork tenderness: genomic analysis of porcine CAST

A quantitative trait locus (QTL) affecting pork tenderness was recently detected within the Illinois Meat Quality Pedigree (IMQP) and fine-mapped to the region of porcine chromosome 2 (SSC2) harbouring the functional candidate gene calpastatin (CAST). To identify molecular variation that may underlie the observed differences in tenderness phenotypes, we characterized the porcine CAST gene and analysed allelic variation within the F(1) boars of the IMQP. The complete genomic sequence of porcine CAST has been determined, and was found to contain 35 exons spanning nearly 123 kb. Using the rapid amplification of cDNA ends (RACE) method, calpastatin transcript types I-III, as well as a putative novel transcript type, were detected within porcine skeletal muscle. Variability in transcription initiation and termination sites was observed, and alternative splicing of exons 1y and 3 was evident. Nearly 77.6% of the CAST gene, including all exons, was re-sequenced from each of six IMQP F(1) boars, and almost 900 polymorphisms were identified. The heterozygosity of nearly 400 polymorphisms appeared to be concordant with the previous QTL data, and the location of this variation within the CAST gene suggests that a causative mutation is likely to be regulatory. Functional characterization of CAST variation should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. The effectiveness of CAST polymorphisms for marker-assisted selection of pork tenderness can now be assessed.