Recently, the rice molecular design technology and application innovation team of the Institute of Crop Science, Chinese Academy of Agricultural Sciences has constructed a genome-wide gene function haplotype (gcHap) data set, comprehensive Revealed the natural variation characteristics of Asian cultivated rice gene functional haplotypes, proposed the multi-origin (domesticated) hypothesis of Asian cultivated rice, and developed a software package-HAPS suitable for the whole genome association analysis and whole genome prediction of functional haplotype data. The related research results were published in”Molecular Plant” on February 10.
According to researcher Xu Jianlong, accelerating the breeding process, enhancing high yield potential and stability, and taking into account quality improvement are the current urgent needs of rice production. In order to accelerate the integration of rice functional genome research and rice molecular breeding, the team took the lead in completing the”3000 Rice Genome Project” in 2018, revealing the genomic diversity of rice core germplasm from three main aspects, one is more than 3,200 Ten thousand high-quality SNPs; the second is the existence-deletion mutations in more than 30,000 rice encoding genes; the third is more than 93,000 structural variations. However, as another important aspect of genetic diversity within rice species, the variation characteristics of functional haplotypes (functional alleles) of gene coding regions in rice germplasm resources are still unclear.
In this study, based on the annotation information of the Nipponbare reference genome, the researchers constructed a data based on 3010 non-synonymous SNP data of the coding regions of rice core germplasm genes. A genome-wide gene function haplotype data set consisting of 45,963 genes. It fully revealed the natural variation characteristics of the functional haplotypes of Asian cultivated rice genes, proposed the multi-origin (domesticated) hypothesis of Asian cultivated rice, and assessed the influence of modern breeding on the diversity of the genome-wide functional haplotypes. The ploidy was dug in depth. It is found that the genome-wide association analysis based on functional haplotype data has greater power than SNP data, and has higher predictive power on most traits, and has developed a genome-wide association analysis and genome-wide prediction suitable for functional haplotype data The software package”HAPS” of the company will provide great convenience for the basic research of rice genes and the discovery of favorable alleles for complex traits in the future, and will fully assist rice molecular design and breeding. At the same time, it also has reference significance for other crop population genomes, functional genomes and design breeding research.
The yield-related gene”favorable” gcHap was bred in Indica and Japonica Frequency in variety and its distribution in germplasm resources
The research was funded by the National Key Research and Development Program, the National Natural Science Foundation of China, and the Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences.