Genomic consequences of domestication of the Siamese fighting fish

Abstract

Siamese fighting fish, commonly known as betta, are among the world's most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics.

Sex Reversal in Siamese Fighting Fish Larvae by Thermal Management

“…In bettas, recently, two papers (Kwon et al, 2021;Zhang et al, 2021) showed that the most of heterozygous individuals are male, which supports that in such specie, the male phenotype could be formed by heterogametic sexual chromosomes (XY/XX). However, even when XX vs XX cross was performed, 10% of offspring were male, confirming an incomplete genotypic sex determination in betta (Kwon et al, 2021).…”

“…In bettas, recently, two papers (Kwon et al, 2021;Zhang et al, 2021) showed that the most of heterozygous individuals are male, which supports that in such specie, the male phenotype could be formed by heterogametic sexual chromosomes (XY/XX). However, even when XX vs XX cross was performed, 10% of offspring were male, confirming an incomplete genotypic sex determination in betta (Kwon et al, 2021). Zhang et al (2021) also find in minor proportions homogametic males in their study, which, according with authors, suggest the influence of environmental factors in sex determination in this species.…”

“…The thermal treatment lasted up to 15 days post-hatch (DPH), according with the ontogenetic period corresponding to the beginning of sexual differentiation and the appearance of the gonadal tissue in B. splendens (Pattiasina et al, 2021;Kwon et al, 2021). Throughout the experimental period, the temperatures were monitored four times daily using a digital multiparameter device.…”

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

“…This increased complexity is produced through a combination of structural colors, melanin pigments, and non-melanin pigments, and it relies on multiple types of specialized color-producing cells in the skin [11][12][13][14][15]. Color cell development has been characterized to some extent in fish [16][17][18], and genes controlling the use of non-melanin pigments have been identified in a few species of fish and birds [19][20][21][22][23][24][25]. The genetics and development of non-mammalian color patterns are less well understood in other vertebrates, particularly in reptiles [although see [26][27][28][29].…”

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

“…This increased complexity is produced through a combination of structural colors, melanin pigments, and non-melanin pigments, and it relies on multiple types of specialized color-producing cells in the skin [11][12][13][14][15]. Color cell development has been characterized to some extent in fish [16][17][18], and genes controlling the use of non-melanin pigments have been identified in a few species of fish and birds [19][20][21][22][23][24][25]. The genetics and development of non-mammalian color patterns are less well understood in other vertebrates, particularly in reptiles [although see [26][27][28][29].…”