Transcriptome mapping and assembly of the DLK1-DIO3 domain in callipyge lambs

The callipyge trait is caused by a single nucleotide polymorphism in the imprinted DLK1-DIO3 gene cluster of ovine chromosome 18. The predominant phenotype is postnatal muscle hypertrophy in the loin and hind limbs. The trait has a polar overdominant inheritance pattern and the phenotype only occurs in heterozygous lambs with a paternal callipyge allele. The mutation has occurred in a long-range control element that results in the up regulation of paternal allele-specific DLK1 and RTL1 expression in the paternal heterozygous lambs. Maternal inheritance of the callipyge allele results in up-regulation of several maternal allele-specific long non-coding RNA and associated C/D snoRNA and microRNA. Semimembranosus muscle poly A+ RNA as well as ribosomal RNA depleted total RNA from the four possible genotype combinations were used for RNA-seq. The cDNA sequence reads were mapped to the bovine UMD 3.1 genome assembly and analyzed by Tophat-Cufflinks as well as transcriptome assembly by Trinity to identify differentially expressed genes contributing to muscle hypertrophy.  The reads were mapped to sheep genome sequence from the callipyge region for analysis of maternal and paternal cis-effects of the mutation on transcription from the imprinted DLK1-DIO3 region.