Key Genomic Regions of Rice Cultivar GuiHeFeng and Its Derivatives Revealed by Genome-Wide Analysis

Rice is a widely cultivated staple crop that serves as the primary source of carbohydrates for more than half of the global population. Elite parents with superior agronomic traits play a crucial role in rice breeding systems. In this study, we performed whole-genome resequencing of the rice cultivar GuiHeFeng and its nine derivative lines, identifying a total of 6,633,507 high-quality single-nucleotide polymorphisms (SNPs). The percentage of GuiHeFeng traceable blocks (GTBs) in the 9 derivatives ranged from 48.94% to 63.2%. Based on SNP analysis, we found 1310 key GuiHeFeng traceable blocks, which were derived from GuiHeFeng and present in all 9 derivatives. Moreover, 375 selective sweeps (SSWs) were identified, of which 20 were also located within the kGTBs. These 20 SSWs were regarded as key genomic regions for rice breeding. After the association test, 20 alleles including 17 genes were identified on the kGTBs, and 38 significant genes were found within the key genomic regions. A total of 295 SNPs related to agronomic traits were detected by GWAS analysis. This research identifies genomic segments and agronomically important genes/QTLs that will serve as essential targets for genomic selection in rice breeding.