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.
鲤鱼是世界上人工养殖最早的鱼类之一。由于长期的自然选择和人工选择，形成了多种食用和观赏用的鲤鱼品系，具有丰富的表型差异。荷包红鲤是中国本土的一个鲤鱼品种，因其独特的外型和红色皮肤而得名。为了揭示荷包红鲤独特体色背后的遗传学机制，我们组装了荷包红鲤新版本HiFi基因组，该基因组具有良好的连续性、完整性和准确性。通过对荷包红鲤与黄河鲤的基因组结构比较，鉴定基因组中的结构变异和受到正选择的基因。荷包红鲤与黄河鲤的群体遗传学分析，鉴定到基因组上的人工选择信号。对荷包红鲤与黄河鲤的杂交子代进行体色性状的GWAS定位，发现鉴定到的候选区段与选择信号重合。A06和B06号染色体上 mitfa基因的两个拷贝同时突变并叠加，导致了荷包红鲤的红色体色。选取具有不同突变类型的杂交子代进行皮肤转录组分析，进一步证实了异源四倍体中基因的加倍能够缓冲基因突变带来的有害效应。该研究为异源四倍体物种的表型-基因型关联提供了新见解，为鲤鱼未来的选育奠定基础。.

Genome-wide association studies based on SNP have been completed for multiple traits in dairy cattle; however, copy number variants (CNV) could add genomic information that has yet to be harnessed. The objectives of this study were to identify CNV in genotyped Holstein animals and assess their association with hoof health traits using deregressed estimated breeding values as pseudophenotypes. A total of 23,256 CNV comprising 1,645 genomic regions were identified in 5,845 animals. Fourteen genomic regions harboring structural variations, including 9 deletions and 5 duplications, were associated with at least 1 of the studied hoof health traits. This group of traits included digital dermatitis, interdigital dermatitis, heel horn erosion, sole ulcer, white line lesion, sole hemorrhage, and interdigital hyperplasia; no regions were associated with toe ulcer. Twenty candidate genes overlapped with the regions associated with these traits including SCART1, NRXN2, KIF26A, GPHN, and OR7A17. In this study, an effect on infectious hoof lesions could be attributed to the PRAME (Preferentially Expressed Antigen in Melanoma) gene. Almost all genes detected in association with noninfectious hoof lesions could be linked to known metabolic disorders. The knowledge obtained considering information of associated CNV to the traits of interest in this study could improve the accuracy of estimated breeding values. This may further increase the genetic gain for these traits in the Canadian Holstein population, thus reducing the involuntary animal losses due to lameness.