Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

Abstract

The optimal phenotypes to survive and reproduce in given evolutionary settings are often in conflict, which manifest as trade-offs in life history traits. Genome-wide association studies have been successful in uncovering genome regions controlling for life history trade-offs in a range of species [1][2][3][4][5][6][7][8] . However, lack of functional studies of the discovered genotype-phenotype associations restrains our understanding how alternative life history traits evolved and are mediated at the molecular level. Here we establish a molecular mechanism by which allelespecific expression differences of the transcription co-factor vgll3 mediate variation in age at maturity in male Atlantic salmon (Salmo salar). By way of a common-garden experiment and temporal sampling of vgll3 expression, we show that vgll3 genotype and expression control male puberty timing in one-year old salmon. Vgll3 expression was high in immature testicular tissue and males entering puberty reduced their vgll3 expression by 66% compared to immature males. Testicular expression of the early maturation associated allele in immature males was constitutively lower compared to the late maturation allele, shifting the liability of early allele carriers towards earlier maturation. These results reveal how gene regulatory differences can be a central mechanism for the evolution of life history variation. Main textSurvival and reproduction often require trade-offs because size and age at maturity are at odds with the risk of dying before reproduction. The molecular basis of variation in life history traits and such trade-offs have thus far remained elusive. In Atlantic salmon, age at maturity is a key life history trait that is evolving under a trade-off of survival and fecundity 2,[9][10][11] . Genetic variation in a single genome region including the transcription co-factor gene vestigial-like 3 (vgll3) was recently found to explain nearly 40% of variation in sea-age at maturity across 57 Northern-European salmon populations 2 . The functional basis of this genotype-phenotype association remains unknown. Seeing that the strongest association in natural populations maps to a single nucleotide polymorphism (SNP) in a non-coding region adjacent to vgll3 2 , we hypothesized that genetic variation in linked cis-regulatory sequences (e.g. enhancers) underlie the functional differences among salmon vgll3 genotypes by changing their expression level or pattern.To uncover the functional genetic basis of age at maturity variation in Atlantic salmon, we first validated that the genotype at the vgll3 locus on chromosome 25 (termed "E" for early sea-age at maturity and "L" for late sea-age at maturity after previous association study 2 ) is associated with age at maturity in controlled conditions by rearing 656 individuals with known vgll3 genotypes from 32 families in common garden conditions (Extended Data Fig. 1). Vgll3*EE males had a significantly higher probability of maturing during their first year compared to males with vgll3*LL genotypes (probit ...

Strong regulatory effects of vgll3 genotype on reproductive axis gene expression in immature male Atlantic salmon

“…In Atlantic salmon, the vestigial-like family member 3 gene ( vgll3 ) is strongly associated with maturation timing in the wild in both sexes but also exhibits sex-specific maturation effects (Barson et al, 2015; Czorlich et al, 2018). This association between vgll3 and maturation probability has been subsequently validated in one year-old males in common garden settings (Debes et al, 2021; Sinclair-Waters et al, 2021; Verta et al, 2020). This makes vgll3 a potential candidate regulating reproductive axis genes in place of the absent gnrh1 , however, the molecular details of the action of vgll3 on reproductive axis genes has remained unexplored.…”

“…This makes vgll3 a potential candidate regulating reproductive axis genes in place of the absent gnrh1 , however, the molecular details of the action of vgll3 on reproductive axis genes has remained unexplored. It has already been suggested that vgll3 might affect gametogenesis by regulating cell fate commitment genes (Kjærner-Semb et al, 2018; Kurko et al, 2020), and its repression in salmon testis has been associated with induced onset of puberty (Kjærner-Semb et al, 2018; Verta et al, 2020). A recent study demonstrated that expression of alternative isoforms of vgll3 associates with variation in age at maturity in one-year-old salmon males (Verta et al, 2020).…”

“…It has already been suggested that vgll3 might affect gametogenesis by regulating cell fate commitment genes (Kjærner-Semb et al, 2018; Kurko et al, 2020), and its repression in salmon testis has been associated with induced onset of puberty (Kjærner-Semb et al, 2018; Verta et al, 2020). A recent study demonstrated that expression of alternative isoforms of vgll3 associates with variation in age at maturity in one-year-old salmon males (Verta et al, 2020). The vgll3 alleles previously associated with later and earlier maturation, vgll3* L and vgll3*E, respectively, display cis-regulatory expression differences and vgll3* L allele expresses a rare transcript isoform in the testis at the pre-pubertal stage.…”

Refining the genomic location of SNP variation affecting Atlantic salmon maturation timing at a key large-effect locus

“…Additionally, we cannot rule out the possibility that the causal variation driving the vgll3 genotype effect alters the functioning of a different gene, however given the tight genetic linkage of the vgll3-SNPs and vgll3, vgll3 variation is nevertheless strongly associated with maturation timing. Recent functional research also supports this notion -2 vgll3 expression in immature testes of Atlantic salmon differs between vgll3 genotypes, EE and LL (Verta et al 2020), which suggests that SNP variation linked with vgll3 also associates with altered vgll3 function. Further, we cannot exclude the possibility that the causal variation may regulate both vgll3 and akap11 given their close proximity.…”

Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon

“…We collected immature male gonads from five 11-12-month-old male Atlantic salmon raised in common-garden conditions (see details in (Verta et al 2020). Fish were euthanized using an overdose of MS-222, followed by decapitation.…”