Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp ( Cyprinus carpio wuyuanensis )

• Published in: Dōngwùxué yánjiū Vol. 44; no. 2; pp. 276 - 16A
• Main Authors: Li, Bi-Jun, Chen, Lin, Yan, Meng-Zhen, Zou, Xiao-Qing, Bai, Yu-Lin, Xue, Ya-Guo, Jiang, Zhou, Chen, Bao-Hua, Li, Cheng-Yu, He, Qian, Feng, Jian-Xin, Zhou, Tao, Xu, Peng
• Format: Journal Article
• Language: English
• Published: China Kunming Institute of Zoology, The Chinese Academy of Sciences 18.03.2023
• Subjects: Alleles; Animals; Breeding; Carp; Carps - genetics; Chromosomes; Color; Colour; Cyprinus carpio; Domestication; Fish; Fish skin; Freshwater fishes; Gene duplication; Gene mapping; Genes; Genetic research; Genome; Genomes; Genotype & phenotype; Genotypes; Laboratory animals; Mutation; Phenotypes; Phenotypic variation; Phenotypic variations; Phylogenetics; Population dynamics; Population studies; Population-based studies; Positive selection; Proteins; Skin; Skin pigmentation; Skin Pigmentation - genetics; Transcriptomes; China; Yellow River; Structural variant; Artificial selection; mitfa; Cyprinus carpio; Coloration
• ISSN: 2095-8137; 0254-5853
• DOI: 10.24272/j.issn.2095-8137.2022.388

Common carp are among the oldest domesticated fish in the world. As such, there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection. Hebao red carp (HB, ), an indigenous strain in China, is renowned for its unique body morphology and reddish skin. To reveal the genetic basis underlying the distinct skin color of HB, we constructed an improved high-fidelity (HiFi) HB genome with good contiguity, completeness, and correctness. Genome structure comparison was conducted between HB and a representative wild strain, Yellow River carp (YR, ), to identify structural variants and genes under positive selection. Signatures of artificial selection during domestication were identified in HB and YR populations, while phenotype mapping was performed in a segregating population generated by HB×YR crosses. Body color in HB was associated with regions with fixed mutations. The simultaneous mutation and superposition of a pair of homologous genes ( ) in chromosomes A06 and B06 conferred the reddish color in domesticated HB. Transcriptome analysis of common carp with different alleles of the mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids. This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp.