Research status and prospect of genome breeding in China’s important cultured freshwater fish

A wide variety of aquatic types such as fish, shrimp, shellfish and algae have significantly enriched the structure of aquaculture in China, thereby supporting the diversified demands of the people for high-quality and nutritionally rich aquatic products. Fish constitute the cornerstone of China's aquaculture industry, and the production of the 25 major freshwater cultured fish species listed in the China Fisheries Statistical Yearbook accounted for nearly half of the total aquaculture output in 2024, making an irreplaceable and outstanding contribution to ensure a stable supply of high-quality protein for the nation. It also plays a vital role in regulating human dietary structure and fulfilling nutritional needs, whose industrial scale has already holden a leading position globally. In China, freshwater cultured fish are broadly categorized into two groups: commodity species and specialty species. Among these, commodity species account for the majority of total production. But specialty species are valued in the market for their exceptional tenderness and superior flavor profile. The rapid advancement of genome sequencing methods and the increasingly perfect application of genomic breeding technologies have strongly propelled the creation of new germplasm and the cultivation of new strains in major cultured freshwater fish, which solidifies the foundational role of freshwater aquaculture in ensuring the sustained supply of aquatic products in China, establishing a cutting-edge pathway to elevate the "gastronomic satisfaction" of the Chinese people. This article comprehensively reviews the current status of genomic resource exploration and utilization for major cultured freshwater fish, introduces fundamental biological information including the genome size, number of protein coding genes and genomic structural characteristics for 21 key freshwater cultured fish species. Targeting five high-profile economic traits, namely intermuscular bone-free, rapid growth, single sex, body color improvement, and disease resistance, the article summarizes the target genes and operational methodologies for genome editing using CRISPR-Cas9 technology across different major cultured freshwater fish species as well as reviews breakthrough research progress in creating new germplasm with superior economic traits. Focusing on the current application of genomic selection breeding technology in cultivating new strains in major cultured freshwater fish, this article retrospect its main effects and genetic gains through 4 fish species breeding course, in which, typical case contains genetic improvement of growth and disease resistance traits in common carp, disease resistance trait in rainbow trout, growth trait in Nile tilapia and channel catfish, respectively. From the perspective of further promoting genomic breeding research for major cultured freshwater fish, the paper proposes 5 key research direction in future, which including the development and application of genomic resources, the iteration and upgrading of genome editing technology, the innovation and optimization of genomic selection breeding technology, the testing and evaluation of comprehensive performance in new germplasm created via genome editing, and the building and popularizing of industrialization support system for genome breeding new strains. In summary, it is aimed to the information of this review could enhance the depth and breadth of genomic breeding research for China's major cultured freshwater fish, accelerate the breeding process and application effect of new varieties with superior economic traits, and contribute practical new technology and methodology to foster the high-quality development of the freshwater aquaculture industry in China.