On the morning of September 8, The Paper learned from the Center for Excellence in Molecular Plant Science of the Chinese Academy of Sciences that on the 7th, the team of academician Han Bin of the center published an online report entitled "The structure and function of rice hybrid genomes reveal genetic" in the international academic journal Nature Genetics basis and optimal performance of heterosis).
Based on the excellent materials of hybrid breeding, this study extracts and summarizes the theoretical basis, and then uses the theory to feed back the practice, which provides theoretical guidance and valuable resources for promoting the innovation of hybrid rice breeding technology.
This study evaluates the achievements of hybrid breeding in the past half century from the time dimension, identifies the molecular imprint of improved breeding, quantifies the dominant degree and phenotypic contribution rate of key sites of improved breeding, summarizes the genetic law of breeding, deeply analyzes the genetic basis of heterogeneity between subspecies, and constructs a genome selection model to quickly screen excellent hybrid combinations and shorten the hybrid breeding cycle.
The division of three breeding stages and the phenotypic trend analysis of materials at different breeding stages.
Looking back at half a century of hybrid rice breeding achievements
In the early 70s of last century, Mr. Yuan Longping and his assistants discovered a natural sterile individual in the wild rice population, which promoted the commercialization of hybrid rice breeding. Hybrid rice breeding has greatly increased the yield of rice, achieving a second jump in yield after semi-dwarf stalk breeding, which is known as the "second green revolution".
In the past half century, a large number of hybrid rice varieties have been bred, if the genome and phenotypic information of a large number of excellent hybrid rice varieties can be analyzed, it can help to analyze the genetic basis of the formation of hybrid rice varieties, analyze the changes in the genome structure of hybrid rice varieties from the time dimension, and help explore the law of hybrid advantage in improved breeding.
The team of Han Bin, researcher of the Center for Excellence in Molecular Plant Science of the Chinese Academy of Sciences and academician of the Chinese Academy of Sciences, together with Yang Shihua, researcher of the China Rice Research Institute, and Gong Junyi, associate researcher, collected 2839 hybrid rice germplasm resources. These resources cover the entire history of hybrid rice breeding in China, and are also the largest hybrid rice germplasm resource set reported so far. Eighteen representative hybrid rice materials were selected to construct an F2 population containing 10,000 individuals.
Based on the genotype and phenotypic data of the above more than 10,000 materials, the study constructed a genomic selection model. The model can predict the field performance of materials based on the genomic genetic variation information of the hybrid combination, and carry out multi-trait selection in combination with the prediction results of seven important agronomic traits, so as to realize the efficient screening of individuals with breeding potential, help breeders formulate hybridization plans, shorten the breeding cycle, and save labor and time costs.
In addition, since the training set contains a large number of F2 individuals derived from interspecific hybrid rice, the model can effectively process the genotype data of interspecific hybrid rice, so as to be suitable for interspecific hybrid combination selection, which is expected to promote the development of interspecific hybrid rice breeding.
By analyzing the phenotypic change trend of 2839 hybrid rice varieties, this study reviewed the achievements of improved breeding: 1. The bank organ was significantly enlarged, including the number of grains per panicle and the number of effective panicles. The enlargement of the bank organ has built a high-yield shelf for the material, laying the foundation for the yield increase. 2. In order to match the enlarged library organ, the source organ is significantly enlarged, including the leaf length and leaf width of the main photosynthetic organ sword leaf, to improve the filling capacity of the source organ; 3. The ear pumping period is slightly shortened. The climatic conditions in the late growth period (filling stage) of rice are changeable, and extreme weather may affect the yield of rice, or even lead to no harvest of grains. The slightly shortened ear pumping period can reduce the risk of extreme weather in the late growth period, thereby improving the stable yield performance of the material; 4. The cooking quality and appearance quality of the grain have been significantly improved. The quality of rice in early hybrid rice was poor, but through the unremitting improvement of breeders, the quality of rice was significantly improved.
The shortening of the ear pumping period and the improvement of rice quality pose great challenges to increasing or maintaining existing production levels. The study found that hybrid rice breeding was improved synergistically through the source bank, and the yield per plant not only did not decrease, but achieved a slight increase.
How to avoid "dragging behind" genotypes: genome inflection, or synergistic modification of both parents
The study found that the gradual increase in genomic genetic diversity of hybrid rice population in the process of improved breeding of hybrid rice is related to the gradual increase in the number of TJ (Twoline-Jap) type hybrid rice. According to previous reports by Han Bin's team, this type of hybrid rice belongs to the two-line hybrid seed system, mostly indica-indica hybrid rice type, but contains japonica-type organelles, and lineage tracking shows that the ancestral material of this type of hybrid rice is japonica rice type (Nongken 58S) (Gu et al., 2021).
The newly published study found that TJ hybrid rice has a higher nuclear genome than WA (wild abortion type, three-line hybrid breeding) hybrid rice, and the excellent allele variation of japonica rice source is used more frequently.
Therefore, the researchers believe that the development of novel germplasm resources and seed preparation systems will help introduce and widely use excellent allele variants through genome introgression.
In addition, genome-wide association analysis was used to locate the main potential sites regulating the yield and quality of hybrid rice. The study pointed out that breeding uses genetic effects at sites to select appropriate genotypes for trait improvement. Taking rice quality as an example, most of the main potential sites exhibit negative dominant effects, which is consistent with the inherent impression that quality is difficult to show heterogeneous advantages, and also means that heterozygous genotypes will "drag their feet". Therefore, improved breeding enables F1 (offspring) to acquire a dominant homozygous genotype by synergistic modification of both parents, equipping both parents with dominant alleles at the target locus. This also provides some enlightenment for hybrid rice breeding: for dominant (partially dominant) effect sites, only one parent can be modified, the superdominant site needs to make the parents have different genotypes, and the additive effect or negative dominant effect site must achieve synergistic improvement of both parents to maximize the heterogeneous advantageous effect.
Most of the rice-related main genes showed negative dominant effects and the dominant allele frequencies of the four main loci increased synergistically in both parents.
Bin Han and Shihua Yang are co-corresponding authors of the paper. Gu Zhoulin, postdoctoral fellow of the Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Gong Junyi, associate researcher of China Rice Research Institute, and Zhou Zhu and Zhen Li, doctoral students of the Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, are co-first authors of the paper. Professor Huang Xuehui of Shanghai Normal University, Professor Yang Jian of Westlake University and Professor Dale Sanders of the John Innes Centre provided constructive suggestions and important guidance for the study. The research was supported by the National Natural Science Foundation of China, the Pilot Special Project of the Chinese Academy of Sciences (Category B), the Shanghai Municipal Science and Technology Commission, and the China Postdoctoral Science Foundation.
Link to the paper: https://www.nature.com/articles/s41588-023-01495-8