Quantitative Genetic Analysis of Retinal Degeneration in the Blind Cavefish Astyanax mexicanus

Abstract

The retina is the light-sensitive tissue of the eye that facilitates vision. Mutations within genes affecting eye development and retinal function cause a host of degenerative visual diseases, including retinitis pigmentosa and anophthalmia/microphthalmia. The characin fish Astyanax mexicanus includes both eyed (surface fish) and eyeless (cavefish) morphs that initially develop eyes with normal retina; however, early in development, the eyes of cavefish degenerate. Since both surface and cave morphs are members of the same species, they serve as excellent evolutionary mutant models with which to identify genes causing retinal degeneration. In this study, we crossed the eyed and eyeless forms of A. mexicanus and quantified the thickness of individual retinal layers among 115 F2 hybrid progeny. We used next generation sequencing (RAD-seq) and microsatellite mapping to construct a dense genetic map of the Astyanax genome, scan for quantitative trait loci (QTL) affecting retinal thickness, and identify candidate genes within these QTL regions. The map we constructed for Astyanax includes nearly 700 markers assembled into 25 linkage groups. Based on our scans with this map, we identified four QTL, one each associated with the thickness of the ganglion, inner nuclear, outer plexiform, and outer nuclear layers of the retina. For all but one QTL, cavefish alleles resulted in a clear reduction in the thickness of the affected layer. Comparative mapping of genetic markers within each QTL revealed that each QTL corresponds to an approximately 35 Mb region of the zebrafish genome. Within each region, we identified several candidate genes associated with the function of each affected retinal layer. Our study is the first to examine Astyanax retinal degeneration in the context of QTL mapping. The regions we identify serve as a starting point for future studies on the genetics of retinal degeneration and eye disease using the evolutionary mutant model Astyanax.

Complex Craniofacial Changes in Blind Cave-Dwelling Fish Are Mediated by Genetically Symmetric and Asymmetric Loci

“…This integrated map represents a comprehensive analysis of multiple cave 3 surface fish crosses and therefore is a proxy for the genomic positions of several markers . Three analyses have identified numerous syntenic blocks shared between Astyanax and D. rerio O'Quin et al 2013). These blocks were identified through sequence similarity (BLAST hit) queries of noncoding sequences flanking polymorphic microsatellites or SNP markers used in RAD-seq studies.…”

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

“…RADseq is being increasingly used for the construction of HD genetic maps in fish comprising thousands of markers (e.g. Refs 14–19 ). These maps have allowed the identification of genomic regions associated with productive traits 20 , 21 or with adaptation to specific environments 14 , 16 .…”

“…Refs 14–19 ). These maps have allowed the identification of genomic regions associated with productive traits 20 , 21 or with adaptation to specific environments 14 , 16 . The pattern of samples and families used in fish for map construction has been quite similar, and only very recently, the number of families has increased 19 , 22 .…”

The cavefish genome reveals candidate genes for eye loss

“…In this work, we present the first de novo genome assembly for A. mexicanus cavefish to allow for more precise identification of candidate genes underlying QTL than was previously possible with syntenic comparisons to zebrafish1516. We demonstrate the effectiveness of this approach by identifying candidate genes for eye development and other cave-derived traits.…”