Researcher Li Zhong from the Yangtze River Fisheries Research Institute of the Chinese Academy of Fishery Sciences conducted a study on the chromosome map of the rice field eel genome and obtained the first high-quality genome reference map.”G3:Genes/Genomes/Genetics” was published online. This is another important achievement made by the team on the basis of the first complete artificial large-scale breeding of rice field eel in China, and laid an important foundation for the accelerated breeding of new rice field eel varieties.
The research used Illumina second-generation sequencing, PacBio SeqII third-generation sequencing and Hi-C technology, combined with advanced assembly strategies to obtain a complete and continuous high-quality rice field eel genome. The genome size is 799 Mb (Contig N50=2.4 Mb, Scaffold N50=67.24 Mb), 12 chromosomal sequences were assembled, covering 99.26%of the predicted genome size; 36,802 microsatellite (SSR) sites were identified 287,189 candidate SSR markers were obtained, and a high-density physical map was constructed using the identified SSR markers, and some molecular markers were verified. The development and utilization of molecular markers will greatly accelerate the process of assisted breeding. Through the analysis of the genome, it was found that the rice field eel and the giant spur loach differentiated between 4.99 million years ago, and then 769 gene families of the rice field eel were amplified. The functional annotations showed that they focused on the immune system-related pathways, sensory systems such as olfactory conduction, signal transmission, etc. system. These findings provide important data for research on the evolution of rice field eel karyotype, epidermal respiration and its unique reversal characteristics.
Monopterus albus is an important freshwater breeding species. In 2019, the national output was 319,000 tons and the basic output value exceeded 20 billion yuan. It is an important starting point for comprehensively promoting the rural revitalization strategy. At the same time, the rice field eel is a unique hermaphrodite and first maturing female sex-reversing fish, which has extremely high value for sex research. Like the eel industry, the rice field eel industry has been re-cultivating by catching wild seed, and the industry has always been stuck in the amount of resources that cannot be expanded; the bottleneck of artificial propagation has also restricted the advancement of basic scientific research. In recent years, Researcher Li Zhong has carried out research on fully artificial large-scale breeding. In 2019, it passed the on-site acceptance by the expert team of 11 teaching/scientific research units organized by the Yangtze River Research Institute and the People’s Government of Xiantao City. Relevant research results have carried out industrial demonstrations in Xiantao, Hubei and Yibin, Sichuan, and achieved excellent demonstration effects and industrial influence, opening the way for scientific research and industrial upgrading.
At present, the germplasm resources of rice field eel are mixed, including black spot eel, yellow spot eel, gray eel, etc. The large yellow spot eel has three stripes on the back, golden abdomen, and bright body color. It has obvious advantages in growth and disease resistance, and is deeply loved by farmers and consumers. According to the needs of farmers and consumers, the team of researcher Li Zhong used family selection and breeding methods to carry out the selection and breeding of new varieties of eel. The third generation has been selected and the consistency rate of body color has reached more than 80%. The breakthrough in the complete artificial breeding technology of rice field eel and the analysis and utilization of high-quality genome will greatly promote the progress of variety selection, and the new variety of the large yellow spot is expected to pass the national examination and approval in recent years.
The first author of this paper is Dr. Haifeng Tian, and the corresponding author is Researcher Li Zhong. The research was funded by the basic scientific research business expenses of the Chinese Academy of Fishery Sciences. The specific link of the paper is https://doi.org/10.1093/g3journal/jkaa032.