Annotation And Breeding Application Of Major Functional Genes Of Rice Principal Parents

With the rapid development of rice functional genomics,over 4,000 main-effect functional genes associated with agronomic traits have been cloned.Additionally,the largescale sequencing of rice germplasm populations has provided abundant information for the exploration and utilization of functional genes.Utilizing favorable allele genes from different rice varieties is an effective approach to breed high-quality rice varieties.The objective of this project is to functionally annotate the main-effect genes in the backbone parents of rice through gene functional loci,providing information and references for breeding work.The main results obtained from this work are as follows:(1)Initially,we collected and organized relevant information on 102 main-effect functional genes and 2,494 whole-genome sequencing data of rice through literature review and other means.We performed genotype identification and functional annotation of these genes using 202 functional loci,defining different allele genes as dominant genotypes,recessive genotypes,and neutral genotypes based on their phenotypic effects.We also collected a substantial number of published rice genome sequencing datasets for functional annotation,including 533 accessions of the core germplasm population,1,961 breeding parent populations,and 592 hybrid rice populations.(2)Structural analysis of the three populations revealed that hybrid rice exhibited the highest number of dominant genotypes,and genes related to reproductive stages and fertility were heterozygous at different periods.There were significant structural differences between indica and japonica rice,with clear geographic clustering in japonica rice,while no distinct differences were observed among different parent types in indica rice.Through linkage group analysis,we identified 45 different functional genes between the indica and japonica subgroups.We identified 71 functional genes under selection during the breeding process in indica rice and 54 functional genes in japonica rice,with the ancestral population of the breeding population being the 533 group.Based on the functional annotation results,we constructed a functional gene annotation map and identified three selection patterns of functional genes during breeding:A)simultaneous selection of dominant and recessive genotypes;B)selection of only dominant genotypes;C)selection of only recessive genotypes.These results indicate that many potential advantageous allele loci in the genome are yet to be explored.(3)We provided relevant strategies for future genomic breeding models and conducted practical validation.We utilized the aromatic rice variety and the sterile line Kongyu131 and Daohuaxiang as parents to construct F2 populations and recombinant inbred line populations,validating the annotation results of functional genes.Additionally,we successfully bred high-quality rice varieties with excellent appearance traits adapted to different ecological regions.This project collected and integrated information on main-effect genes related to rice agronomic traits,performed functional gene annotation on different populations,analyzed functional gene information in backbone parents,and proposed different gene locus improvement recommendations for indica and japonica rice subgroups.We also provided suggestions on establishing standardized and engineered genomic breeding processes,which were applied in breeding practice to cultivate high-quality rice varieties adapted to different ecological regions.