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>)
Bijun Li, 厦门大学海洋与地球学院近海海洋环境科学国家重点实验室, 福建 厦门361102, 中国, Lin Chen, Mengzhen Yan, Xiaoqing Zou, Yulin Bai, Yaguo Xue, Zhou Jiang, Baohua Chen, Chengyu Li, Qian He, Jianxin Feng, Tao Zhou, Peng Xu, 厦门大学海洋与地球学院福建省海洋经济生物遗传育种重点实验室, 福建 厦门361102, 中国, 河南师范大学水产学院, 河南 新乡453007, 中国, 河南省水产科学研究院, 河南 郑州 450039, 中国
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, <i>Cyprinus carpio wuyuanensis</i>), 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, <i>C. carpio</i> <i>haematopterus</i>), 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 (<i>mitfa</i>) in chromosomes A06 and B06 conferred the reddish color in domesticated HB. Transcriptome analysis of common carp with different alleles of the <i>mitfa</i> 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.