1 Introduction

The genus Channa or snakehead fishes comprises a species complex of predatory freshwater fishes that are extensively distributed in Asia, from Iran eastwards to South and Southeast Asia, via China and Russian Far East. About 50 species of this genus have been found, and most of them were endemic to the Mekong River basin, Indian subcontinent, and Southeast Asia. Channa spp. are adapted to low-oxygen environments through their labyrinth organ, allowing facultative air respiration. Some species are terrestrial-locomoting in reality, allowing them to survive seasonal or oxygen-sparse situations. Their food adaptability and wide physiological tolerance make them well-adapted to aquaculture under a range of conditions (Dong et al., 2022; Fernández-González et al., 2024).

Channa spp., blotched snakehead (Channa maculata) and northern snakehead (Channa argus), are two of the most valued cultured fish with high market prices in China and Southeast Asia. They exhibit notable sexual dimorphism, and males generally exhibit improved growth performance. Due to the firmer texture of their flesh, high protein content, and medicinal values in traditional Chinese medicine, Channa products are highly sought after by consumers. Increased aquaculture activity has been observed in recent years with support from improved hatchery technology and availability of seeds year-round. Still, more than reliance on wild or low-diversity broodstock is a concern. More emphasis has been laid on the speeding up of breeding efficiency and improvement of characteristics through genomic aid in the form of marker-assisted selection (MAS) and genomic selection (GS) (Cui et al., 2024; Tang et al., 2024).

Artificial methods of breeding-phenotypic selection, family selection, hybridization, and sex control-have been piling up traits in aquaculture species for hundreds of centuries. Older methods are beset by inefficiency, long generation intervals, and cannot cope with polygenic traits. Environmental variation and genotype-environment interaction add to the complexity of selection responses. Genomic selection (GS) provides a better alternative through the prediction of breeding values as a function of high-density genome-wide SNP markers. This provides for early and high-accuracy selection for complex traits, with enhanced genetic gain with fewer generations. Recent studies in Channa have demonstrated the efficacy of GS with 50K SNP chips, with reasonably satisfactory heritability estimates (0.29-0.31) of body weight and length, and identification of putative QTLs and candidate regions through GWAS analysis. The use of GS in artificial breeding programs offers the potential for precision breeding and sustainable genetic improvement in Channa aquaculture.

2 Genetic Resources and Breeding Basis of Channa

2.1 Current status of germplasm resources and evaluation of genetic diversity in Channa

Channa species have high genetic diversity within species and populations. Mitochondrial DNA and AFLP marker-related studies have demonstrated high polymorphism and genetic differentiation among Channa populations and species, and low genetic diversity and compact genetic distances among some populations ('white' type Channa argus), and these are of concern from inbreeding and genetic resource conservation points of view (Wang et al., 2018; Butet et al., 2021; Su et al., 2022; Liu et al., 2023). New species were found and large DNA barcoding projects further advanced knowledge of Channa diversity and provided useful tools for diversity estimates and species identification (Figure 1) (Laskar et al., 2025).

2.2 Breeding objectives and key traits of Channa

Channa breeding schemes strive to enhance economically valuable traits such as growth rate, hypoxia tolerance, and tolerance of culture conditions. Genome and transcriptome sequencing in Channa asiatica, for example, have been employed for the purpose of discovering gene families involved in oxygen binding and stress response and that play a key role in breeding hypoxia-tolerant strains (Liu et al., 2024). Some of the other primary objectives include improving reproductive capacity, disease immunity, and genetic variability to produce input for sustainable aquaculture as well as conservation (Liu et al., 2020; Nayak, 2020; Su et al., 2022).

2.3 Established genetic populations and pedigree management systems

Genetic population patterns in Channa for development and management are the design of SNP markers and DNA barcoding information that can be employed to undertake population genetic analysis, selective breeding, and pedigree control (Liu et al., 2023; Laskar et al., 2025). Captive breeding tools such as hormone-induced spawning of Channa bleheri have been effectively utilized in aquaculture and conservation with effective monitoring of genetic diversity and breeding performance to avoid inbreeding and healthy stocks (Nayak, 2020; Su et al., 2022). Such technology and systems are important for successful pedigree management and sustainable breeding of Channa in the long term.

3 Technical Systems and Progress in Artificial Breeding of Channa

3.1 Application and limitations of traditional selection methods

Traditional selection methods in Channa breeding, such as the application of natural spawning and selection for evident traits, are to be blamed for seed production and broodstock improvement. These activities are inexpensive and easy to carry out but with low genetic improvement, environmental susceptibility, as well as challenges in maintaining genetic diversity. Continued dependence on nature breeding for seed stock constrains Channa aquaculture scalability and reliability to require more emphasis on artificial seed production and better selection processes in a bid to respond to industry demands and deliver quality consistency (Debbarma et al., 2022).

3.2 Advances in hybrid breeding, sex control breeding, and polyploidy breeding

Some of the recent developments in breeding Channa are the application of artificial gynogenesis with successful induction of northern snakeheads as all-female populations with improved growth and commercial quality. It not only overcame the issue of deterioration of germplasm but also allowed introduction of favorable genetic material. Breeding protocols through hormone induction have also been improved for repeated spawnings within a year and improved fecundity rates. These hybridization, sex determination, and breeding cycle manipulations advances have augmented the genetic weaponry of Channa enhancement and render the enhanced strains accessible to aquaculture (Rath et al., 2023; Tang et al., 2024).

3.3 Exploration of disease-resistant breeding technologies

While direct genetic selection for Channa disease resistance is as yet incomplete, improvements in larval rearing, broodstock management, and artificial feeding schedules have made stocks healthier and more robust. Improvements in weaning regimes and environmental manipulations reduce stress and mortality, indirectly enhancing disease resistance. Coupling of these management practices with imminent genomic tools can provide for targeted development of disease-resistant strains of Channa (Debbarma et al., 2022).

3.4 Examples of Selected Superior Strains and Their Industrial Applications

Breeding schemes have evolved improved varieties of Channa using classical as well as new breeding methods. Northern snakehead gynogenetic strains show improved growth and commercial characteristics, and hormone-induced breeding schemes have allowed bulk production of Channa striata and Channa bleheri to meet food and aquaria needs. Such developments have increased the degree of reliance for seed supply, encouraged Channa culture, and aided in the conservation of threatened species by easing pressure on the wild population (Rath et al., 2023; Tang et al., 2024).

4 Progress in Genomic Studies of Channa

4.1 Construction and annotation of reference genomes in Channa

Outstanding success has also been achieved in the construction of high-quality reference Channa species genomes. An Illumina-assembled Northern snakehead (Channa argus) draft genome was constructed, yielding a 615.3 Mb genome with 19 877 predicted protein-coding genes, a valuable resource for functional and comparative study (Yi et al., 2017). There has been a recent chromosome-scale assembly of the albino strain of C. argus was acquired by PacBio and Hi-C technologies, offering a 644.1 Mb genome and 24 high-contiguity chromosomes to support genetic, evolutionary, and conservation research (Zhou et al., 2022). For Channa asiatica, 23-chromosome and 722 Mb high-quality assembly was constructed through Illumina, PacBio, and Hi-C sequencing integration, and 23 949 protein-coding genes were annotated with over 96% functionally characterized (Liu et al., 2024). These materials are a good base on which schemes for Channa genetic research and breeding can be developed.

4.2 Development of transcriptome, resequencing, and SNP resources

Transcriptome analysis was also coupled with genome sequencing to study functional genomics in Channa. Transcriptome analysis in C. asiatica indicated the induction of oxidative stress pathway under hypoxia, importance in mechanism studies of hypoxia tolerance (Liu et al., 2024). In C. argus, transcriptome sequencing with genome-wide association analysis (GWAS) identified sex-determining positions and candidate genes to facilitate the development of sex-specific markers for aquaculture breeding (Ou et al., 2024). In Channa maculata, a 50 K SNP array has facilitated the identification of nearly 46 000 good-quality SNPs, allowing population structure analysis, heritability estimation, and use of genomic selection models for growth traits (Cui et al., 2024). Such transcriptomic and SNP resource breakthroughs are fueling Channa's selective breeding and trait improvement.

4.3 Analysis of population genetic structure and genome-wide diversity

Population genetic analysis with genome-wide SNPs and mitochondrial DNA markers has also shed more light on the genetic structure and diversity of Channa species. SNP-based analysis in C. maculata illustrated population structure and relatedness and illustrated that SNP panels selected by GWAS have the potential to greatly improve genomic selection accuracy for growth (Cui et al., 2024). Mitochondrial genome sequencing and phylogenetic reconstruction of Channa species revealed evolutionary associations, species limits, and genetic differentiation, and guided conservation and aquaculture management (Figure 2) (Zhou et al., 2019; Liu et al., 2023; Fatima et al., 2024; Purohit et al., 2024). The research concludes the importance of integrative genomic and molecular data to account for population diversity and breeding program planning in Channa.

5 Prospects of Genomic Selection in Channa Breeding

5.1 Principles and workflow of genomic selection (GS)

Genomic selection (GS) uses genome-wide genetic markers such as SNPs to predict breeding values of individuals for quantitative traits. The typical protocol is to genotype a reference population, fit marker effects with statistical models, and derive the genetic merit of selection candidates from their marker profiles. The process enables more accurate and quicker selection compared to traditional methods, especially for traits with moderate heritability (Hu et al., 2018; Cui et al., 2024).

5.2 Identification of quantitative trait loci (QTL) and genome-wide association studies (GWAS) for target traits

Genome-wide association studies (GWAS) are required to map quantitative trait loci (QTL) of economically important traits by genome scanning for marker-trait associations. GWAS have been applied in growth traits in Channa maculata and identified SNPs highly associated with weight and total length. These SNPs selected by GWAS also enhance the accuracy of GS models by selecting those with the best predictive power towards target traits (Fernández-González et al., 2024).

5.3 Case studies on the application of gs in growth, disease resistance, and sex control

One such recent investigation of the blotched snakehead (Channa maculata) for GS growth potential had earlier reported GS potential. Using a 50K SNP array, researchers were able to detect around 46 000 good-quality SNPs and reported that GS models, particularly when augmented with GWAS-selected SNPs, considerably improved predictions for weight and total length. The research found that even low-density panels of SNPs are of high predictive accuracy and therefore can be an effective tool for selective breeding in Channa. While growth was an issue of concern, the approach and outcome provide a foundation for the application of GS for other characteristics such as disease resistance and sex control in subsequent research (Zhang et al., 2017).

5.4 Integration potential of GS with MAS and conventional breeding strategies

The integration of GS with MAS and conventional breeding is employed to enhance the genetic improvement. The GWAS-selected SNPs can be integrated into traditional markers in MAS, and GS can offer multi-trait selection in parallel with hastening the cycle of breeding (Wang and Chen, 2024). Together, the approaches can enhance Channa breeding programme productivity and efficiency to enable development of high-quality strains for aquaculture (Fernández-González et al., 2024).

6 Current Challenges and Technical Bottlenecks

6.1 Precision and standardization issues in phenotypic data collection

Reliable and uniform collection of phenotypic data is an ongoing problem in Channa breeding. Difference in measurement procedures, environmental conditions, and qualitative assessment techniques can lead to variable results, reducing the validity of the trait assessment and hindering the effectiveness of genomic selection and association studies. Lack of standard phenotyping among different research groups as well as breeding programs also complicates integration and data comparison, with ultimate effects on the accuracy of selection decisions (Nord and Li, 2018; Pollio et al., 2019).

6.2 Limitations in the quality and representativeness of reference genomes

Although highly quality reference genomes have been constructed for several Channa species, there is still room for improvement in completeness, accuracy of the annotation, and coverage of the genetic diversity. Some assemblies may be lacking repetitive or difficult-to-assemble genomic components, and reference genomes consist of one individual or population, and these may not represent the entire scope of genetic variability of the species. These limitations can decrease the detection of useful functional genes and decrease the efficiency of subsequent activities such as GWAS and marker development (Juels et al., 2016; Zhou, 2024).

6.3 Influence of genetic background differences and genotype-by-environment interactions on selection efficiency

Genetic heterogeneity within populations and large genotype-by-environment (G×E) interactions will have profound impacts on selection efficiency of Channa breeding. Selection characters achieved in one population or under some conditions may be useless under other conditions, which will reduce genetic gain and make breeding results unpredictable. This calls for multi-environment and multi-population testing, as well as the creation of valid statistical models to estimate G×E effects in genomic selection (Xu et al., 2021; Zhuravkov et al., 2024).

6.4 Technical costs and constraints in commercial application

The high cost of large-scale genotyping, sequencing, and analysis remains a barrier to the general application of sophisticated genomic tools in commercial Channa breeding. In addition, the requirement for experts, expertise facilities, and bioinformatics laboratories can limit the utilization of these technologies, especially for small- and medium-scale farmers. These constraints hinder the conversion of research advances to real breeding advances and limit scalability of genomic selection schemes (Pollio et al., 2019; Mahmoodi et al., 2022).

7 Development Directions and Strategic Recommendations for Molecular Breeding in Channa

7.1 Promote multi-omics data integration to improve the resolution of complex trait analysis

Integration of multi-omics data including genomics, transcriptomics, and phenomics can give a much higher resolution of dissection of complex traits in Channa. Integration of such levels of information can enable scientists to improve detection of the genetic architecture of economically important traits, improve accuracy of breeding value, and detect major regulatory modules. This approach gives more precise selection and improves genetic progress in breeding schemes (Xu et al., 2017).

7.2 Develop high-throughput marker screening platforms and breeding databases for Channa

Creation of high-throughput SNP genotyping platforms such as 50 K SNP arrays facilitates massive and cost-effective Channa genetic marker screening. Coupled with precise breeding databases, they enable genotypic and phenotypic data management, perform population structure analysis, and enable convenient selection of outstanding breeding candidates. Such infrastructures are the pillars of Channa modernization and evidence-based decision-making (Cui et al., 2024).

7.3 Explore integrated breeding systems combining genomic selection, MAS, and phenotypic selection

Co-implementation of GS, MAS, and phenotypic selection can realize the highest genetic gain and breeding efficiency (Han, 2024). For example, integration of GWAS-selected SNPs with GS models has been found to significantly improve the precision of predictions of Channa maculata growth traits using low-density SNP panels. The integrated approach allows simultaneous selection of several characters and high-performance strains to be rapidly bred (Xu et al., 2017).

7.4 Facilitate the adoption of cost-effective genomic technologies in grassroots breeding units

For broader use, cheap genomic technologies and easy platforms have to be pushed from the farm gate. The application of low-density SNP panels, which are highly efficient in prediction, can maintain genotyping cost low and make advanced breeding tools accessible to small- and medium-scale farmers. Roll-out of technology has to be accompanied by training and capacity development to maximize its effect (Cui et al., 2024).

8 Concluding Remarks

Recent years have witnessed unprecedented technology development in Channa breeding, including success in the development of high-quality reference genomes for a number of species, development of high-density SNP arrays, and inclusion of transcriptomic and genomic resources. This has enabled the identification of significant genes and markers for economically important traits, improved the population genetic structure knowledge, and enabled the utilization of genomic tools in selective breeding programs.

Genomic selection (GS) has transformed Channa breeding by making it possible to accurately predict breeding values and bulk selection of numerous complex traits. The application of GWAS-selected SNPs and high-density genotyping arrays has greatly improved the speed and accuracy of growth, disease resistance, and sex control selection. GS models have also been highly accurate for prediction using low-density marker panels and thus are cost-efficient for research and commercial breeding.

To achieve the full potential of molecular breeding, integration of research advancements with industry needs should be augmented. It encompasses the development of user-friendly breeding databases, the development of cost-effective genotyping technologies, and institutional capacity-building in grassroot breeding stations. The joint efforts of industry stakeholders and researchers will facilitate quick takeoff of genomic tools, allow for the development of better Channa strains, and generate sustainable aquaculture growth.

Acknowledgments

The authors thank the animal research team for their support and help in data collection and analysis. The authors also thank the anonymous reviewers for their insightful and constructive comments on the manuscript.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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