Genomic consequences of domestication of the Siamese fighting fish

Abstract

Siamese fighting (betta) fish are among the most popular and morphologically diverse pet fish, but the genetic bases of their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced 98 individuals across five closely related species. We find evidence of bidirectional hybridization between domesticated ornamental betta and other wild Betta species. We discover dmrt1 as the main sex determination gene in ornamental betta and that it has lower penetrance in wild B. splendens . Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body or on the shape of individual fins and that most are unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication and launch betta as a powerful new system for evolutionary genetics.

Something Fishy about Siamese Fighting Fish (Betta splendens) Sex: Polygenic Sex Determination or a Newly Emerged Sex-Determining Region?

“…The primary genetic mechanisms of SDS in Siamese fighting fish remain poorly understood. Recent studies revealed that Siamese fighting fish in one commercial stock have an XX/XY SDS [ 13 ], while the dmrt1 gene might be a candidate for sex determination [ 13 , 14 ]. To extend our understanding of the SDS of Siamese fighting fish, we genotyped 75 offspring from five commercial populations at 23,509 loci (without filtering) derived from genome-wide SNPs distributed throughout the genome—on average, one every 18.79 kb.…”

“…Similar cases were also observed in Atlantic salmon ( Salmo salar Linnaeus, 1758 [ 85 ]) [ 86 ] and Nile tilapia ( Oreochromis niloticus Linnaeus, 1758 [ 87 ]) chromosomes [ 88 ] where sex-specific and sex-linked loci were distributed on the sex chromosomes. The highest repeat area richness of the Siamese fighting fish genome is BSP9, having more than twice the number of repeats than that of the other chromosomes [ 13 ]. Repetitive elements can mediate chromosomal rearrangements that further induce sex chromosome differentiation and heterochromatin propagation [ 3 , 89 , 90 , 91 ].…”

“…Recent population genetic analyses show that captive populations from farms show remarkable differences from the wild forms [ 13 ]. This might reflect the result of breeding plans that collected all dominant traits from different species by backcrossing or hybridization.…”

“…Inheritance tests, genome scanning, whole-genome sequencing, expression analyses, and gene knockout studies suggest that Siamese fighting fish likely exhibit an XX/XY SDS with homomorphic sex chromosomes [ 3 , 11 , 12 , 13 , 14 ]. The sex locus was found to be located in a very narrow region on chromosome 9 [ 13 , 14 ].…”

“…Inheritance tests, genome scanning, whole-genome sequencing, expression analyses, and gene knockout studies suggest that Siamese fighting fish likely exhibit an XX/XY SDS with homomorphic sex chromosomes [ 3 , 11 , 12 , 13 , 14 ]. The sex locus was found to be located in a very narrow region on chromosome 9 [ 13 , 14 ]. The functional dmrt1 gene showed male-biased expression before gonad differentiation, with a high level of epigenetic markers in the genome but not for the X chromosome.…”