Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish

Abstract

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole genome sequencing, QTL mapping, genome-wide association studies and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double tail mutant was suggested to be caused by a deletion in a zic1/zic4 co-enhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish

“…S2A). The whole pedigree of this population from parental (P) to F 2 generations were raised under normal laboratory conditions and had been previously used for mapping fin and pigmentation related traits [ 23 ]. The F 1 population showed a sex ratio of F: M ≈ 1:5 while the overall sex ratio across these two F 2 families was F: M ≈ 1:2.8 (Additional file 1 : Fig.…”

The genetic architecture of phenotypic diversity in the betta fish (Betta splendens)

“…Wang et al [10] investigated the same phenotype using F ST scan and located a 1.3Mb region on chromosome 16 (chromosome 9 in their assembly) that contains our GWAS peak. They suggested, based on gene expression analyses, that the causal gene could be kcnh8 [10]. However, this gene resides outside of the associated locus on chromosome 16 identified in this study (Fig.…”

“…B. splendens is easy to breed and maintain, and provides a useful resource for exploration of the genetic basis of behavior and morphology in vertebrates, due to the high degree of intraspecific variability and the vast number of characterized phenotypes. Although researchers have examined the inheritance of body color, fin length and sex in classic crosses in the 1930s to 1940s [3][4][5][6][7][8][9], relatively little was known until a recent study investigated the double tail, elephant ear, albino and fin spot phenotypes [10]. Here we report a high-quality chromosomal-level genome assembly of a female B. splendens, resequencing data of 727 domesticated individuals, and resequencing data of 59 individuals from six other species in the B. splendens complex.…”

Genome editing and its applications in genetic improvement in aquaculture

“…6,28 In over 20 aquaculture species, CRISPR/Cas9 system has been used in studies on gene functions and breeding (Table 1). These species include Nile tilapia (O. niloticus), 23,79 Atlantic salmon (Salmo salar), 26,80,81 Atlantic killifish (Fundulus heteroclitus), 25 oriental prawn (Exopalaemon carinicauda), 82 Labeo rohita, a farmed carp (known as rohu), 83 common carp (Cyprinus carpio), 76,84 The Burton's mouth-brooder (Astatotilapia burtoni), 61 Chinese tongue sole (Cynoglossus semilaevis), 85 Red sea bream (Pagrus major), [86][87][88] channel catfish (Ictalurus punctatus), [89][90][91] grass carp (Ctenopharyngodon idella), 92 sterlet (Acipenser ruthenus), 93 olive flounder (Paralichthys olivaceus), 27,94,95 Pacific oyster (Crassostrea gigas), 96 blunt snout bream (Megalobrama amblycephala), 97 white prawn (Exopalaemon carinicauda), 82 fighting fish (Betta 98 and other species. 12 Studies on genome editing in aquaculture species confirmed that the CRISPR/Cas system is highly efficient, has lower off-target tendencies, and is able to generate long fragment deletions.…”