College of Chemistry and Chemical Engineering, Hunan Normal University
This work was supported by the National Natural Science Foundation of China (Grant No. 32172972), the Science and Technology Innovation Program of Hunan Province (Grant No. 2021RC4028), the National Natural Science Foundation of China (Grant No. U19A2040), the Earmarked Fund for China Agriculture Research System (Grant No. CARS-45), the Hunan Provincial Science and Technology Department (2019RS5001), the Special Funds for Construction of Innovative Provinces in Hunan Province (2021NK1010), Special Science Found of Nansha-South China Agricultural University Fishery Research Institute，Guangzhou.
Autotetraploid Carassius auratus (4nRR, 4n = 200, RRRR) is derived from whole-genome duplication of Carassius auratus red var. (RCC, 2n = 100, RR). Our study demonstrated that chromatophores and pigment changes were direct causes of 4nRR skin coloration and its variation (red coloration in RCC, brownish-yellow coloration in 4nRR). To further explore the molecular mechanisms underlying coloration formation and variation in 4nRR, we performed transcriptome profiling and molecular functional verification in RCC and 4nRR. Our result revealed that scarb1, associated with carotenoid metabolism, underwent significant downregulation in 4nRR. And then, efficiently editing this candidate pigmented gene provided clear evidence that scarb1 plays a significant role in RCC coloration. Subsequently, in 4nRR, we identified four divergent scarb1 homeologs: two original scarb1 homeologs from RCC and two duplicated ones. Notably, three of these homeologs possessed two highly conserved alleles, exhibiting a predominant biased and allele-specific expression in the skin. Remarkably, after the precise editing of both original and duplicated scarb1 homeologs and/or alleles, 4nRR individuals, whether singly or multiply mutated, displayed a transition from brownish-yellow skin to a cyan-grey phenotype. Concurrently, the proportional areas of the cyan-grey regions displayed a gene-dose correlation. These findings illustrate the subfunctionalization of duplicated scarb1, with all scarb1 genes synergistically and equally contributing to the pigmentation of 4nRR. This is the first report concerning the functional differentiation of duplicated homeologs in autopolyploid fish, substantially enriching our understanding of coloration formation and change within this group of organisms.