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。.

To explore the relationship between the mitfa gene and intestinal microbiota, the 16S rRNA gene amplicon sequencing was performed to compare the intestinal microbiota composition of the mitfa knockout zebrafish line (CKO group) and the wild-type zebrafish (WT group) in this study. The results showed that the Fusobacteria and Firmicutes were significantly decreased and the Dependentiae and Patescibacteria were significantly increased in the CKO group at the phylum level. Furthermore, the relative abundance of Citrobacter, Gordonia, Mesorhizobium, Legionella, and Bradyrhizobium were extremely higher in the CKO group, whereas the other four genera Nocardia, Pannonibacter, Shinella, and Cetobacterium were significantly declined in the CKO group at the genus level. Due to these changed intestinal microbiota appear to be related to lipid metabolism and immunity, eight lipid metabolism-related genes and nine inflammation-related genes were detected in the intestinal. The results showed that the expression levels of these genes were significant differences between the CKO and WT group. These results indicated that the deletion of mitfa can affect the expression levels of immune and metabolism-related genes, and causing changes in the composition of the intestinal microbiota.

Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

In zebrafish (Danio rerio), iridophores are specified from neural crest cells and represent a tractable system for examining mechanisms of cell fate and differentiation. Using this system, we have investigated the role of cAMP protein kinase A (PKA) signaling in pigment cell differentiation. Activation of PKA with the adenylyl cyclase activator forskolin reduces the number of differentiated iridophores in wildtype larvae, with insignificant changes to melanophore number. Inhibition of PKA with H89 significantly increases iridophore number, supporting a specific role for PKA during iridophore development. To determine the effects of altering PKA activity on iridophore and melanophore gene expression, we examined expression of iridophore marker pnp4a, melanophore marker mitfa, and the mitfa repressor foxd3. Consistent with our cell counts, forskolin significantly decreased pnp4a expression as detected by in situ hybridization and quantification of pnp4a+ cells. Forskolin had the opposite effect on mitfa and foxd3 gene activity, increasing the area of expression. As mitfa/nacre mutants have extra iridophores as compared to wildtype larvae, we examined the function of mitfa during PKA-sensitive iridophore development. Forskolin treatment of mitfa/nacre mutants did significantly reduce the number of iridophores but to a lesser extent than that observed in treated wildtype larvae. Taken together, our data suggests that PKA inhibits iridophore development in a subset of iridophore precursors, potentially via a foxd3-independent pathway.

Silver_nanoparticles (AgNPs) have been reported to inhibit specification of erythroid cells and to induce spinal cord deformities and cardiac arrhythmia in vertebrates, but have not been implicated in development of neural crest (NC) and pigment cells in an in vivo model yet. In current study, down-regulated expressions of NC genes pax7 and foxd3, melanophore genes mitfa and dct, and xanthophore gene gch2 in AgNPs-exposed embryos were revealed by microarray, qRT-PCR and whole-mount in situ hybridization (WISH). Then, the down-regulated expressions of melanophore genes mitfa and dct but not xanthophore gene gch2 in AgNPs-exposed embryos were found to be recovered by melanogenesis agonists palmitic acid and dibutyryl cyclic AMP (dbcAMP). Finally, Ag+ chelating and AgNPs coating compound l-cysteine was found to neutralize AgNPs-induced hypopigmentation in AgNPs-exposed embryos, and to recover the down-regulated expressions of both dct and gch2 to nearly normal level in embryos, suggesting that AgNPs-releasing Ag+ might mediate their biological effects on zebrafish pigmentation mostly. This study was firstly to unveil that AgNPs might specifically act up-stream of mitfa and pax7 genes to suppress specification and differentiation of melanophore and xanthophore lineages respectively by their releasing Ag+ during vertebrate embryogenesis.

Melanocyte stem cells are a population of immature cells which sustain the self-renewal and replenish the differentiated melanocytes. In this research, a light-colored region (LCR) is observed at the heel of caudal fin in juvenile crucian carp. By cutting off the caudal fin, the operated caudal fin can regenerate in accordance with the original pigment pattern from the retained LCR. As markers of stem cells, Oct4 and Sox2 have been found to be highly expressed in the LCR as well as Mitfa, a label of the melanoblasts. In vitro, Mitfa+ melanoblasts are observed in the cells which are derived from the LCR and transfected with Mitfa-EGFP reporter by using Tol2 transposon system. Furthermore, by real-time qPCR, it is shown that the level of sox2 mRNA is gradually decreased from the LCR to proximal and distal caudal fin, and that of mitfa mRNA in the proximal caudal fin (PCF) is higher than that in the LCR, while it is the lowest in the distal caudal fin. Hence, we propose that the LCR is a pigment progenitor niche, sending melanocytes to the distal of caudal fin, which gradually emerges as caudal fin grow. We reveal that the LCR of caudal fin might be a niche of pigment progenitors, and contribute to pigment-producing stem cells in crucian carp.

Dorso-ventral pigment pattern differences are the most widespread pigmentary adaptations in vertebrates. In mammals, this pattern is controlled by regulating melanin chemistry in melanocytes using a protein, agouti-signalling peptide (ASIP). In fish, studies of pigment patterning have focused on stripe formation, identifying a core striping mechanism dependent upon interactions between different pigment cell types. In contrast, mechanisms driving the dorso-ventral countershading pattern have been overlooked. Here, we demonstrate that, in fact, zebrafish utilize two distinct adult pigment patterning mechanisms - an ancient dorso-ventral patterning mechanism, and a more recent striping mechanism based on cell-cell interactions; remarkably, the dorso-ventral patterning mechanism also utilizes ASIP. These two mechanisms function largely independently, with resultant patterns superimposed to give the full pattern.