Research on the Creation of Genomically Reconstructed, Highly Resistant and High-Yielding New Polyploids

Sexual reproduction is the primary mode of reproduction in eukaryotes. During sexual reproduction, homologous recombination in meiosis and the fusion of male and female gametes generate genetic diversity in offspring. This diversity forms the basis of agricultural selective breeding. However, the desirable traits obtained through sexual reproduction, especially heterosis, tend to segregate in subsequent generations. Therefore, fixing advantageous genotypes rapidly through asexual clonal reproduction to prevent trait segregation and permanently maintain heterosis is considered the "Holy Grail" of agricultural breeding. More importantly, the combination of asexual reproduction and polyploid breeding technologies has shown potential in crop breeding. However, the application of this strategy in animals still faces challenges.

On July 11, the team of Academician Gui Jianfang from the Institute of Hydrobiology, Chinese Academy of Sciences, utilized asexual-sexual reproduction conversion in animal breeding to construct genomically reconstructed polyploids with desirable traits, providing technical support for the breeding of the heterozygous gibel carp "Zhongke No. 6".

In previous work, the team used the heterozygous gibel carp "Zhongke No. 3" as a base variety and leveraged the reproductive potential of gynogenetic gibel carp to integrate the paternal genome to form higher ploidy polyploids. They introduced a set of paternal double-diploid red crucian carp genomes into double-triploid gibel carp, creating a few double-tetraploid males with restored sexual reproduction ability, revealing the genetic mechanism of ploidy variation driving reproductive mode conversion and clonal diversity formation in crucian carp. Based on this, the team used naturally herpesvirus-resistant double-diploid white crucian carp as the maternal line and crossed them with double-tetraploid males to create a new polyploid population. Whole haplotype genome assembly and analysis showed that the new polyploid inherited a complete chromosome set from the maternal white crucian carp and two chromosome sets from the paternal double-tetraploid. Among the paternal-derived chromosomes, some homologous chromosomes between gibel carp and red crucian carp underwent one or two recombination events, indicating that the new polyploid is a genomically reconstructed double-triploid.

From the double-triploid population, the researchers selected three large-sized, phenotypically superior females as maternal lines. Using the females' restored gynogenetic ability and Xingguo red carp as the paternal line, they created three gynogenetic clonal lines, named Clonal Line-1, Clonal Line-2, and Clonal Line-3. Artificial herpesvirus infection experiments showed varying antiviral capacities among the clonal lines. All individuals in Clonal Line-1 survived, approximately 38.9% of Clonal Line-2 survived, while all individuals in Clonal Line-3 and "Zhongke No. 3" died within 12 days post-infection; about 58.0% of individuals in the white crucian carp population survived. Moreover, transcriptome and physiological-biochemical analyses revealed a positive correlation between hemoglobin synthesis, blood oxygen homeostasis, and herpesvirus resistance in the clonal lines. Further genetic analysis of extreme resistant and susceptible individuals in the double-triploid population linked herpesvirus resistance to a ~11.0 Mb genomic hotspot on chromosome 12B of the white crucian carp, indicating that chromosome 12B contains a resistant haplotype and a susceptible haplotype. When the resistant haplotype from white crucian carp is transferred into the double-triploid females, it can be fixed through gynogenesis to form resistant clonal lines.

The study found that through ploidy changes and reproductive mode conversion driving multi-genomic reconstruction, both the natural gynogenetic ability of gibel carp and the herpesvirus resistance of white crucian carp can be introduced into genomically reconstructed double-triploids. The formation of gynogenetic ability is achieved through an "ameiotic pathway" during oogenesis, while antiviral capacity is highly associated with hemoglobin synthesis and oxygen homeostasis during infection. Differences in antiviral capacity among double-triploid individuals are due to two distinct white crucian haplotypes. Growth comparison experiments showed that Clonal Line-2 exhibited superior growth compared to the base variety "Zhongke No. 3", while Clonal Line-1 and Clonal Line-3 showed slower growth than "Zhongke No. 3". Therefore, Clonal Line-2, which combines antiviral resistance and growth advantages, has been selected as the candidate new variety "Zhongke No. 6".

This study demonstrates that asexual-sexual reproduction conversion can achieve precise genome design breeding in animal polyploids, laying a theoretical foundation for cultivating new gibel carp varieties with high resistance and high yield.

The related research results were published in Advanced Science. The work was supported by the National Key R&D Program, the National Natural Science Foundation of China, the Strategic Priority Research Program of the Chinese Academy of Sciences, and the Youth Talent Support Program of the China Association for Science and Technology.