Using Functional Genomics to Refine Our Understanding of the Equine Retina

In order to better understand the equine retina, we examined the RNA-seq transcriptome data of retina tissue generated from two horses, one unaffected and one affected with Congenital Stationary Night blindness (CSNB). An analysis of 40.7 million 81-bp paired end reads allowed us to segregate out genes having high transcript abundance (top 10% of transcripts by RPKM – 1486/14,858 CTRL transcripts, RPKM range 32-8077; 1473/14,725 CSNB transcripts; RPKM range 37-8179) when mapped to the equCab2 equine genome. This identified 1653 genes unique genes within the upper 10% of expression. Analysis of the gene ontology of these genes demonstrated functional annotation clusters of enrichment for vision, pigmentation, sensory processes, and metabolism. From these RNA-seq data, further analysis of coverage to confirm gene structure is underway for improvement of genes expressed within equine retinal tissue. The RNA-seq data were applied to the CLC Bio Genomics Workbench 8.0 Large Gap Read Mapping tool; we detected ~45,000 transcripts representing ~27,600 genes within the retina transcriptome. Comparison to de novo assembly of transcriptome sequences is ongoing. In addition, in comparing the transcriptomes of the affected and unaffected individuals, we generated a list of candidate genes for follow-up investigation to better define ocular phenotypic differences in Appaloosa horses.