Transcriptomic regulation of seasonal coat color change in hares.

Mafalda S Ferreira,Colin M Callahan,José Melo-Ferreira,Klaus Hackländer,Jeffrey M Good,L Scott Mills,Iwona Giska,Liliana Farelo,Paulo C Alves,Hannes Jenny

doi:10.1002/ece3.5956

Abstract

Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year‐round in environments with seasonal snow. Despite the eco‐evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression—“brown” (early molt), “intermediate,” and “white” (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.

Highlights

Seasonal environments impose numerous challenges to organismal survival
Given an aberrant expression pattern estimated for one individual, which did not result in the individualization of molting stages (Figure S1) expected from our sampling strategy (Ferreira et al, 2017), we evaluated the biological coefficient of variation (BCV) and estimated the expected power to detect gene expression changes in the 4 versus 3-individual dataset using RNASeqPower (Hart, Therneau, Zhang, Poland, & Kocher, 2013)
Genes EN1, SPARC, EDAR, and MEF2C are annotated to the Gene Ontology term “pigmentation” and the child term “melanosome differentiation,” being all upregulated in “brown.” one gene, MC3R, annotated to child terms of “circadian rhythm” (“circadian regulation of gene expression” and “locomotor rhythm”), showed higher expression in “white” and “intermediate.” KTR71 was the only candidate gene found differentially expressed both here and in Ferreira et al, (2017), though its late molt upregulation contrasts with the higher expression early in the molt in the snowshoe hare (Figure 3b)

Summary

| INTRODUCTION

Seasonal environments impose numerous challenges to organismal survival. To track seasonality, individuals cycle important biological processes, known as phenologies (e.g., reproduction, migration, hibernation, or molt), allowing a better phenotypic match with seasonal selective pressures (Helm et al, 2013; Visser, Caro, Oers, Schaper, & Helm, 2010). Pathways and genes involved in the perception of the photoperiodic signal, such as the circadian clock and melatonin production and reception, hair growth cycle, and melanogenesis, are expected to be involved in the regulation of seasonal coat color changing molts (Allain & Rougeot, 1980; Balsalobre, 2002; Duncan & Goldman, 1984; Ferreira et al, 2017; Lin et al, 2009; Lincoln et al, 2006; Slominski, Tobin, Shibahara, & Wortsman, 2004). Cis-regulatory variation at ASIP has been linked to polymorphism in winter coat color in snowshoe hares (Lepus americanus) (Jones et al, 2018) and mountain hares (L. timidus) (Giska et al, 2019) It remains unclear how generalizable these results are across species. By integrating results across both species, we expand the model of genic regulation during both autumn and spring seasonal coat color change in hares and provide a context to understand the functional mechanisms controlling this crucial seasonal adaptation

| MATERIALS AND METHODS

Findings

| DISCUSSION

| CONCLUSIONS AND SIGNIFICANCE