RNA-Seq results of six Chinese Sutai piglets from ear tissue based on Illumina HiSeq 2000 platform

Purpose: The paired-end sequencing strategy of RNA-Seq improves sequencing efficiency and extends short read lengths for better understanding pig transcriptome. The goals of this study are to identify whether alternative splicing sites or alternative 3' gene boundary caused by a CNV located in 3' region of MSRB3 gene and find differential expression genes in ear tissue between QQ and qq genotype piglets for QTL of ear size Methods: Ear tissue mRNA profiles of 6 piglets including 3 QQ and 3 qq genotypes responsible for QTL of ear size were generated by deep sequencing, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 93.6-95.3 million 2 x 90 bp paired-end clean reads per sample to the pig genome (Sscrofa 10.2) and identify 19,819-20,136 annotated genes in each sample. Our ranking analysis identified a list of 281 differentially expressed genes with a >1 fold change at a false discovery rate lower than 0.001. But we found no alternative transcripts and differential expression of MSRB3 gene. Conclusions: In our study, the expression levels of MSRB3 gene had no significant difference in the ear tissue between QQ and qq individuals, and no alternative splicing was found for MSRB3 gene between QQ and qq individuals. Overall design: Ear tissue mRNA profiles of 3 QQ and 3 qq genotype piglets were generated by deep sequencing, using Illumina HiSeq 2000.