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

Bi-Jun Li; Lin Chen; Meng-Zhen Yan; Xiao-Qing Zou; Yu-Lin Bai; Ya-Guo Xue; Zhou Jiang; Bao-Hua Chen; Cheng-Yu Li; Qian He; Jian-Xin Feng; Tao Zhou; Peng Xu

doi:10.24272/j.issn.2095-8137.2022.388

Volume 44 Issue 2

Mar. 2023

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Article Navigation > Zoological Research > 2023 > 44(2): 276-286

Bi-Jun Li, Lin Chen, Meng-Zhen Yan, Xiao-Qing Zou, Yu-Lin Bai, Ya-Guo Xue, Zhou Jiang, Bao-Hua Chen, Cheng-Yu Li, Qian He, Jian-Xin Feng, Tao Zhou, Peng Xu. Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp (Cyprinus carpio wuyuanensis). Zoological Research, 2023, 44(2): 276-286. doi: 10.24272/j.issn.2095-8137.2022.388

Citation:

Bi-Jun Li, Lin Chen, Meng-Zhen Yan, Xiao-Qing Zou, Yu-Lin Bai, Ya-Guo Xue, Zhou Jiang, Bao-Hua Chen, Cheng-Yu Li, Qian He, Jian-Xin Feng, Tao Zhou, Peng Xu. Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp (Cyprinus carpio wuyuanensis). Zoological Research, 2023, 44(2): 276-286. doi: 10.24272/j.issn.2095-8137.2022.388

Citation:

Bi-Jun Li, Lin Chen, Meng-Zhen Yan, Xiao-Qing Zou, Yu-Lin Bai, Ya-Guo Xue, Zhou Jiang, Bao-Hua Chen, Cheng-Yu Li, Qian He, Jian-Xin Feng, Tao Zhou, Peng Xu. Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp (Cyprinus carpio wuyuanensis). Zoological Research, 2023, 44(2): 276-286. doi: 10.24272/j.issn.2095-8137.2022.388

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

doi: 10.24272/j.issn.2095-8137.2022.388

Bi-Jun Li^{1, 2},
Lin Chen^{1, 2},
Meng-Zhen Yan^{1, 2},
Xiao-Qing Zou^{1, 2},
Yu-Lin Bai^{1, 2},
Ya-Guo Xue³,
Zhou Jiang^{1, 3},
Bao-Hua Chen^{1, 2},
Cheng-Yu Li^{1, 2},
Qian He^{1, 2},
Jian-Xin Feng⁴,
Tao Zhou^{1, 2},
Peng Xu^{1, 2
,
,}

1.
State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
2.
Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
3.
College of Fisheries, Henan Normal University, Xinxiang, Henan 453007, China
4.
Henan Academy of Fishery Science, Zhengzhou, Henan 450039, China

All sequencing data generated in this study were deposited at the Sequence Read Archive (https://ncbi.nlm.nih.gov/sra) under BioProjectID PRJNA510861, PRJNA824207, PRJNA853462, and PRJNA853504, Genome Sequence Archive (GSA) database of the National Genomics Data Center (NGDC) under accession number CRA009294, and Science Data Bank (doi: 10.57760/sciencedb.j00139.00045).
Supplementary data to this article can be found online.

Funds: This work was supported by the National Key R&D Program of China (2019YFE0119000), National Natural Science Foundation of China (31872561), National Science Fund for Distinguished Young Scholars (32225049), and Alliance of International Science Organizations (ANSO-CR-PP-2021-03)

More Information

Corresponding author: E-mail: xupeng77@xmu.edu.cn
Received Date: 2022-12-11
Accepted Date: 2023-02-10

Published Online: 2023-02-11

Publish Date: 2023-03-18

Abstract

Abstract

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, Cyprinus carpio wuyuanensis), 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, C. carpio haematopterus), 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 (mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB. Transcriptome analysis of common carp with different alleles of the mitfa 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.
- Cyprinus carpio,
- Artificial selection,
- Coloration,
- mitfa,
- Structural variant

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References(73)

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