Genetic analysis reveals candidate genes for activity QTL in the blind Mexican tetra,Astyanax mexicanus

Abstract

Animal models provide useful tools for exploring the genetic basis of morphological, physiological and behavioral phenotypes. Cave-adapted species are particularly powerful models for a broad array of phenotypic changes with evolutionary, developmental and clinical relevance. Here, we explored the genetic underpinnings of previously characterized differences in locomotor activity patterns between the surface-dwelling and Pachón cave-dwelling populations of Astyanax mexicanus. We identified multiple novel QTL underlying patterns in overall levels of activity (velocity), as well as spatial tank use (time spent near the top or bottom of the tank). Further, we demonstrated that different regions of the genome mediate distinct patterns in velocity and tank usage. We interrogated eight genomic intervals underlying these activity QTL distributed across six linkage groups. In addition, we employed transcriptomic data and draft genomic resources to generate and evaluate a list of 36 potential candidate genes. Interestingly, our data support the candidacy of a number of genes, but do not suggest that differences in the patterns of behavior observed here are the result of alterations to certain candidate genes described in other species (e.g., teleost multiple tissue opsins, melanopsins or members of the core circadian clockwork). This study expands our knowledge of the genetic architecture underlying activity differences in surface and cavefish. Future studies will help define the role of specific genes in shaping complex behavioral phenotypes in Astyanax and other vertebrate taxa.

Expression of extraocular opsin genes and light-dependent basal activity of blind cavefish

“…The expression of cavefish rgr opsins suggests two possibilities: (i) rgr expression is not deleterious so that it remains as an evolutionary residual, or (ii) rgr opsins have an unknown physiological function that has been retained in the absence of light. It is noteworthy that Carlson et al (2018) showed that rgra was upregulated 2-2.5 fold in cavefish embryos compared with surface fish at the same stage (10-24 h post fertilization). However, there were no detectable differences in rgra expression between cave and surface fish in this study.…”

“…Second, in adult Mexican cavefish (e.g., Pachón cavefish) there is no circadian locomotor activity during 24 h dark conditions following a 12:12 h light-dark training period (Beale et al, 2013; Moran, Softley & Warrant, 2014). In other independently arisen cave populations (e.g., Tinaja cave population), a weakly trainable circadian clock appears to have been retained, i.e., light-dark cycles make expression levels of circadian clock genes oscillate and these oscillations continue briefly after the removal of the light-dark cycle (∼1 day) (Caballero-Hernández et al, 2015; Carlson & Gross, 2018; Carlson et al, 2018). However, the majority of light-dependent basal locomotor activity seems to be regulated by “masking”, where the ambient light overwrites 24 h-rhythmic circadian behaviors (Rietveld, Minors & Waterhouse, 1993; Caballero-Hernández et al, 2015).…”

A chromosome level genome ofAstyanax mexicanussurface fish for comparing population-specific genetic differences contributing to trait evolution

“…It is also worth noting that comparing cavefish to surface fish reveals substantial differences in many traits of possible relevance to human disease, including sleep duration, circadian rhythmicity, anxiety, aggression, heart regeneration, eye and retina development, craniofacial structure, insulin resistance, appetite, and obesity 7–17 . Further, generation of fertile surface-cave hybrids in a laboratory setting has allowed for genetic mapping in these fish 10, 18–25 . Clear phenotypic differences, combined with availability of genetic tools, positions A. mexicanus as a natural model system for identifying the genetic basis of ecologically and evolutionary relevant phenotypes 17, 26, 27 .…”

“…In addition to the compiled database of older QTL studies, a number of genomic intervals associated with previously described locomotor activity difference between cavefish and surface fish 25 were also re-screened using the surface-anchored locations of markers from the high-density linkage map 30 . Within this Pachón/surface QTL map we confirmed the presence of 20 previously reported candidate genes, and identified 96 additional genes with relevant GO terms, including rx3 , further demonstrating the power and utility of this new genomic resource (Supplementary Table 4).…”

Raising the Mexican Tetra <em>Astyanax mexicanus</em> for Analysis of Post-larval Phenotypes and Whole-mount Immunohistochemistry

“…The Mexican tetra, Astyanax mexicanus, is a single species of fish that exists as river-dwelling populations (surface fish) and a number of cave-dwelling populations (cavefish) named for the caves they inhabit ( i.e., Tinaja, Molino, Pachón). A growing number of researchers are using A. mexicanus to investigate the genetic and developmental bases of behavioral 1,2,3,4 , metabolic 5,6,7,8 , and morphological evolution 9,10,11 . Available resources for studies of A. mexicanus include a sequenced and annotated genome 12 ; transcriptome 13 ; developmental staging table 14 ; and methods for breeding 15,16,17 , creating transgenics 18 , and editing genes 19 .…”