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The artificial breeding of carp existed in China 8000 years ago. The breeding of carp played an important role in ancient Chinese history, and it still played a crucial role in modern aquaculture. The output of carp in China is very high, accounting for 8.42 % of the total output of freshwater products in 2023, ranking fifth in the total output of freshwater aquaculture fish. At the same time, carp is also the fish species with the highest number of new varieties bred in China. With the advent of the genomics era, breeding technologies have also made progress. This paper reviews the history and current status of carp farming, the germplasm resources of carp, and the application of fish genetic breeding technology in the germplasm innovation of carp.

Largemouth bass (Micropterus salmoides, LB) is an important aquaculture and fishing species in the world. LB has been introduced into China since 1983, and its aquaculture production has increased year by year. The total yield of LB in China reached 802,486 tons in 2022, ranking seventh in China's freshwater fish aquaculture. However, the LB is facing threats such as degradation of germplasm resources and disease susceptibility due to limitations in the scale of introduction, coupled with the effects of high-density aquaculture, inbreeding, and species hybridization. This paper summarizes the current status of LB germplasm resources, variety genetic improvement, nutrition and fodder, aquaculture mode and diseases, and circulation and processing. This paper also provides recommendations on how to fully explore and utilize the existing germplasm resources of LB; culture new LB germplasm that combines excellent resistance and growth characteristics through innovations in breeding techniques; reduce the morbidity rate and improve the efficiency of cultured LB through the optimization of fodder formulations and innovation of aquaculture modes; and shift the processing of LB toward standardization, efficient nutrition and safety through the integration of high-tech and large-scale production. This paper provides a reference for the sustainable and healthy development of the LB industry.

IntroductionEEG-based emotion recognition has gradually become a new research direction, known as affective Brain-Computer Interface (aBCI), which has huge application potential in human-computer interaction and neuroscience. However, how to extract spatio-temporal fusion features from complex EEG signals and build learning method with high recognition accuracy and strong interpretability is still challenging.MethodsIn this paper, we propose a hybrid attention spatio-temporal feature fusion network for EEG-based emotion recognition. First, we designed a spatial attention feature extractor capable of merging shallow and deep features to extract spatial information and adaptively select crucial features under different emotional states. Then, the temporal feature extractor based on the multi-head attention mechanism is integrated to perform spatio-temporal feature fusion to achieve emotion recognition. Finally, we visualize the extracted spatial attention features using feature maps, further analyzing key channels corresponding to different emotions and subjects.ResultsOur method outperforms the current state-of-the-art methods on two public datasets, SEED and DEAP. The recognition accuracy are 99.12% ± 1.25% (SEED), 98.93% ± 1.45% (DEAP-arousal), and 98.57% ± 2.60% (DEAP-valence). We also conduct ablation experiments, using statistical methods to analyze the impact of each module on the final result. The spatial attention features reveal that emotion-related neural patterns indeed exist, which is consistent with conclusions in the field of neurology.DiscussionThe experimental results show that our method can effectively extract and fuse spatial and temporal information. It has excellent recognition performance, and also possesses strong robustness, performing stably across different datasets and experimental environments for emotion recognition.

The common carp (Cyprinus carpio L., COC, 2n = 100) is one of the most widely consumed and distributed freshwater fish in the world. It ranks fourth in total freshwater aquaculture volume in various regions of China, behind Ctenopharyngodon idella, Hypophthalmichthys molitrix, and Aristichthys nobilis. However, in recent years, environmental degradation, inbreeding, disordered breeding, and other adverse effects have caused problems such as low seed quality and poor disease and stress resistance of the carp. In our laboratory, we developed two types of improved diploid carp the hybrid F1 of common carp (♀) × blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) (♂). To investigate the differences between IDC and IDMC compared to COC, in this study we compared the relevant characteristics of these two types of improved carp with those of COC in terms of muscle nutrient composition, intermuscular bone type, and number. The results showed that among the muscle nutrients, IDC had a higher protein content (18.50%) and lower carbohydrate content (0.70%). In addition, the unsaturated fatty acid content of IDC (3.45%) and IDMC (1.25%) were significantly higher than that of COC (P

The kisspeptin system, which involves hypothalamic neuropeptides, plays pivotal roles in the regulation of teleost reproduction. A previous study suggested that the kiss2/kissr2 system in largemouth bass (Micropterus salmoides) was involved in regulating gonadal development through the hypothalamus-pituitary-gonad (HPG) axis. However, whether the kiss2/kiss2r system directly regulates the activity of pituitary gland were not studied. This study aimed to elucidate the detailed mechanism of kisspeptin-induced effects on gonadotropin hormone-producing cells in vivo and in vitro. In situ hybridization analysis revealed very widespread expression of kiss2r mRNA in the optic tectum, hypothalamus and pituitary. In the pituitary, kiss2r-expressing cells were mainly located in the proximal pars distalis and pars intermedia, among which the fshβ- and lhβ-positive cells exhibited expression of kiss2r messengers. Furthermore, primary culture of pituitary cells and peptide administration experiments revealed that the Kiss2-10 peptide stimulates the expression of fshβ and lhβ and the secretion of FSH and LH in 24 h. In addition, histology analysis revealed that three injections of the Kiss2-10 peptide promoted ovary development and increased oocyte size but had little effect on testis development. These results suggested that the intrapituitary kisspeptinergic system, as a hypophysiotropic neuropeptide factor, directly modulates of gonadotroph function. This study will help uncover the reproductive endocrinology network and improve artificial breeding technology for largemouth bass.

The genera Parabramis and Megalobrama are important freshwater aquaculture economic fish, and the excavation and utilization of excellent germplasm resources are pivotal in ensuring the supply of high-quality aquatic protein in China. However, as a consequence of fast domestication, overfishing and water pollution, the germplasm resources of Parabramis and Megalobrama are under threat of recession. These germplasm resources serve as an indispensable material basis for the healthy and sustainable development of the Parabramis and Megalobrama breeding industries. It is of great strategic significance to systematically collect, preserve, identify, evaluate, protect and utilize Parabramis and Megalobrama germplasm resources. This paper reviews the major results of studies on the morphology, cytogenetics, and molecular population genetics of the genera Parabramis and Megalobrama, the progress in their genetic improvement through hybridization, selective breeding and gynogenesis techniques, and the current protection measures for Parabramis and Megalobrama germplasm resources. Then, some suggestions for the protection of these germplasm resources and improved variety creation are provided. It is expected to offer basic resources for the sustainable development of the Parabramis and Megalobrama seed industries.

Distant hybridization is a traditional and effective technology in fish genetic breeding. In this study, we reported a new type of golden pompano (Named as Chenhai No.1) produced by the distant hybridization of (Trachinotus ovatus ♀ ​× ​T. blochii ♂) ♀ ​× ​T. ovatus ♂. The results regarding DNA content, chromosomal number, and morphological traits showed that “Chenhai No.1” was a diploid hybrid with 48 chromosomes, and presented a hybrid appearance compared with those in its parents. Meanwhile, all detected “Chenhai No.1” including males and females showed the normal gonadal structure and could produce offspring by self-crossing at 3 years old. In addition, the growth rate of “Chenhai No.1” was 35.52% faster than T. ovatus. In conclusion, the fertile “Chenhai No.1” with faster growth rate provided a superior germplasm resource, which will further promote the industrial development of golden pompano.

The mitochondria of most organisms follow strict maternal inheritance, and the mechanism of elimination of paternal mitochondria is unclear. Our previous studies showed that the paternal mtDNA presented in the embryo of hybrid Megalobrama Amblycephala (BSB,♀) ​× ​Carassius auratus red var(RCC,♂) (BR) and its reciprocal hybrid (RB), but its expression was quiescent. However, the microinjected mitochondria persisted in the embryo and its mtDNA expressed throughout embryonic development. In addition, the chromosome number of RCC (2n ​= ​100) is much larger than that of BSB (2n ​= ​48). All BR embryos were severely abnormal and ultimately died, while the RB embryos could survive and grow up into adult. It implied that the nuclear-cytoplasm incompatibility may be an important cause of BR abnormality. In this study, exogenous parental mitochondria were microinjected into BR embryos, and it was found that paternal mitochondrial DNA persisted and expressed throughout embryonic development. Meanwhile, the study also found that microinjection of isolated paternal (RCC) mitochondria into BR embryos significantly improved the degree of early embryonic abnormality with some fry swimming normally, comparing to the control embryos. However, injection of maternal (BSB) mitochondria did not improve the development of BR embryos. We safely concluded exogenous mitochondria escape the mechanism of elimination and its DNA persist and express throughout embryonic development. In addition, the expression of paternal mitochondrial genes largely reduces the cyto-nuclear conflict, so that the early BR embryos exhibit less degree of abnormality and enhanced activity.

Abstract Background Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. Results We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. Conclusions Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.

Hybrid bream (BBTB) is a high-quality bream derived from a hybrid lineage of blunt snout bream (Megalobrama amblycephala, 2n ​= ​48, BSB, ♀) ​× ​topmouth culter (Culter alburnus, 2n ​= ​48, TC, ♂). In this study, to explore the laws of artificial propagation of BBTB in a brackish water environment, 150 pairs of BBTB with an average weight of 1000 ​g were selected as brood fish, and a successful artificial propagation experiment was carried out at the Freshwater Fish Nansha (Nanfan) Breeding Center (2‰–5‰ brackish water). The fertilization and hatching rate was 86% and 78%, respectively, and a total of 1 ​800 ​000 larvae were obtained. After 26 days of cultivation, 400 ​000 larvae survived, showing a survival rate of 22%. This study is of great significance regarding the basic theories and applications of fish genetics.

The surprising variation in the number of Hox clusters and genome structure in ray-finned fish lineages reflects the history of duplications and subsequent lineage-specific gene loss. However, there are few studies on whether Hox clusters in the early generations of hybrid lineages show more significant variation due to the continuous genomic oscillation caused by distant hybridization. We sequenced and analyzed Hox gene clusters from a crucian carp-like homodiploid fish (NCRC) lineage (a new hybrid lineage derived from common carp (Cyprinus carpio) (♀) ​× ​blunt snout bream (Megalobrama amblycephala) (♂)). In the NCRC lineage, we reconstructed seven Hox clusters consisting of 48 Hox genes, ten of which were pseudogenes. The number of putative Hox clusters generated in NCRC-F1 was increased greatly by distant hybridization to an average number almost twice that in the maternal parent. This increasing trend continued in the subsequent self-mating generations of NCRC-F1. In contrast, the number of Hox cluster fragments inherited from the original parents gradually decreased as the number of NCRC lineage generations increased. This pattern was also found in the inheritance of recombinant Hox clusters. In terms of base composition, some genetic rules for the inheritance of these Hox clusters between different generations of the NCRC lineage were identified. Furthermore, the newly derived mutated Hox clusters in the NCRC lineage showed phylogenetic relationships that were closer to either crucian carp or silver crucian carp, revealing a clear evolutionary path. This study deepens our understanding of the evolution of Hox genes in the ray-finned fish clade.

Fisheries is a social production sector that captures and farms fish and other aquatic animals and plants for aquatic products. In a broad sense, fisheries also include upstream departments (e.g., manufacturing, maintenance and supply of fishing gear, fishing boats, fishery machinery, fishery instruments and other means of production), downstream departments (e.g., storage, processing, comprehensive utilization, transportation and sales of aquatic products), and auxiliary departments (e.g., the construction of fishing ports). As an important constituent part of the national economy in China, fisheries not only provide a large amount of food sources for humans but also provide many industrial raw materials for national construction. In this paper, the development of fisheries in China is reviewed, including the development history of fisheries, the current situations of the aquatic seed industry, aquaculture industry, capture industry, aquatic product processing industry, aquatic animal nutrition and feed industry, and leisure fishery; additionally, the contribution of Chinese fisheries in the global fisheries is assessed, as are the current fisheries development problems and development strategies in China. This paper has important guiding significance for the development of fisheries in China.

Abstract Background Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, the establishment of two bisexual fertile carp lineages, including the improved diploid common carp (IDC) lineage and the improved diploid scattered mirror carp (IDMC) lineage, from the interspecific hybridization of common carp (Cyprinus carpio, 2n = 100) (♀) × blunt snout bream (Megalobrama amblycephala, 2n = 48) (♂), provided a good platform to investigate the genetic relationship between the parents and their hybrid progenies. Result In this study, we investigated the genetic variation of 12 Hox genes in the two types of improved carp lineages derived from common carp (♀) × blunt snout bream (♂). Hox gene clusters were abundant in the first generation of IDC, but most were not stably inherited in the second generation. In contrast, we did not find obvious mutations in Hox genes in the first generation of IDMC, and almost all the Hox gene clusters were stably inherited from the first generation to the second generation of IDMC. Interestingly, we found obvious recombinant clusters of Hox genes in both improved carp lineages, and partially recombinant clusters of Hox genes were stably inherited from the first generation to the second generation in both types of improved carp lineages. On the other hand, some Hox genes were gradually becoming pseudogenes, and some genes were completely pseudogenised in IDC or IDMC. Conclusions Our results provided important evidence that distant hybridization produces rapid genomic DNA changes that may or may not be stably inherited, providing novel insights into the function of hybridization in the establishment of improved lineages used as new fish resources for aquaculture.

Tryptophan (Trp) has received increasing attention in the maintenance of intestinal function. In this study, improved triploid crucian carp (ITCC) fed diets containing 6.35 g kg−1 Trp had higher average daily gain (ADG) and improved villus height (VH) and crypt depth (CD) in the intestine compared to the control group. To elucidate the potential mechanisms, we used RNA sequencing (RNA-seq) to investigate changes in the intestinal transcriptome and 16S rRNA gene sequencing to measure the intestinal microbiota in response to 6.35 g kg−1 Trp feeding in ITCC. Dietary Trp altered intestinal gene expression involved in nutrient transport and metabolism. Differentially expressed transcripts (DETs) were highly enriched in key pathways containing protein digestion and absorption and the AMPK signaling pathway. 16S rRNA sequencing showed that 6.35 g kg−1 Trp significantly increased the abundance of the genus Cetobacterium, and the Firmicutes/Bacteroidetes ratio at the phylum level (P < 0.05). In addition, bacterial richness indices (Simpson index) significantly increased (P < 0.05) community evenness in response to 6.35 g kg−1 Trp. In conclusion, appropriate dietary Trp improves the growth performance, and influences the intestinal flora of ITCC. This study might be helpful to guide the supply of dietary exogenous Trp in ITCC breeding.

Abstract Background Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates. Results We successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 108 (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids. Conclusions Our results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution.

Abstract It is commonly believed that hybridization might lead to the formation of new polyploidy species, but it is unclear whether hybridization can produce a new homodiploid species. Here, we report the spontaneous occurrence of a new crucian carp-like homodiploid fish (2n = 100) that originated from the interspecific hybridization of female common carp (Cyprinus carpio, Cyprininae, 2n = 100) × male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n = 48). The phenotype and reproductive traits of this new crucian carp-like homodiploid fish were found to be very similar to those of the existing diploid species (diploid crucian carp; Carassius auratus). FISH and 5S rDNA analyses revealed that the genotype of the crucian carp-like homodiploid fish differs from those of its parents but is closely related to that of diploid crucian carp. The results provide evidence of the existence of a possible route through which the distant hybridization of this cross can generate crucian carp. The new type of homodiploid fish is of great value in fish genetic breeding and for studying the early evolutionary process.

Based on the formation of an autotetraploid fish line (4nAUT, 4n = 200; F2–F11) derived from the distant hybridization of female Carassius auratus red var. (RCC, 2n = 100) × male Megalobrama amblycephala (BSB, 2n = 48), we produced autotriploid hybrids (3nAUT) by crossing females of RCC with males of 4nAUT and allotriploid hybrids (3nALT) by crossing females of Cyprinus carpio (CC, 2n = 100) with males of 4nAUT. The aim of this study was to comparatively investigate the reproductive characteristics of 3nALT and 3nAUT. We investigated morphological traits, chromosomal numbers, DNA content and gonadal development in 3nAUT and 3nALT. The results indicated both 3nAUT and 3nALT possessed 150 chromosomes and were triploid hybrids. The females and males of 3nALT and males of 3nAUT had abnormal gonadal development and could not generate mature eggs or sperm, but the females of 3nAUT had normal gonadal development and generated mature eggs at 2 years old. The females of 3nAUT generated different sizes of eggs, which fertilized with haploid sperm from RCC and formed viable diploid, triploid, and tetraploid offspring. The formation of these two kinds of triploid hybrids provides an ideal model for studying the reproductive traits of triploid hybrids, which is of great value in animal genetics and reproductive biology.

Gut microbiota play critical roles in host nutrition and metabolism. However, little is known about the genetic effects on the gut microbiota assemblages because a suitable model for investigation is lacking. In the present study, we established the reciprocal hybrid fish lineages derived from the parents with different feeding habits, namely, herbivorous blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) and carnivorous topmouth culter (Culter alburnus, TC, 2n = 48). We investigated the genetic effects on gut microbiota assemblages by using 16S rRNA gene sequencing. The results showed that the gut characteristics (structure, relative gut length, relative gut mass, and Zihler’s index) differed between the two types of hybrids and the two parents. In particular, a strong correlation between genotype and gut microbial assemblages indicated that host genetic (subgenome) significantly altered the gut microbial communities. In addition, the microbial structures (composition and abundance) in the two types of hybrids were more similar to those in BSB parent (P > 0.05) than to those in TC parent (P < 0.05), and the cellulase contents in the gut (produced by gut microbes) also showed the similar results. The results suggested that the host genomic interaction (mainly subgenome domination) had a sizeable effect on shaping the gut microbiota assemblages in reciprocal hybrid fish. This study enriches our understanding of the relationship between host genetic and gut microbiota assemblages, and provides insight into gut microbiota and metabonomics.