Key Genomic Differences of Citrus reticulata ‘Bendizao’ and Its Seedling Mutation Cultivar by Whole-Genome Resequencing

To investigate the genetic variation underlying the phenotypic differences between Citrus reticulata ‘Bendizao’ and its seedling mutation cultivar Citrus reticulata ‘Dongjiang Bendizao’, we performed whole-genome resequencing of both cultivars using high-throughput sequencing technology, achieving sequencing depths of 22× and 36×, respectively. Compared to the reference genome, we identified 4,150,080 and 4,081,142 single nucleotide polymorphism (SNP) loci in ‘Bendizao’ and ‘Dongjiang Bendizao’, of which only 5.41% and 5.52% were located in exonic regions. Exonic SNPs with nonsynonymous mutations or termination alteration effects yielded 3088 candidate genes. In addition, 664,149 and 627,686 insertions/deletions (InDel) loci were detected in the two cultivars, with only 1.50% and 1.57% in exonic regions, leading to the identification of 1065 genes based on differential exonic InDel loci. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the genetic variations were predominantly enriched in pathways such as RNA polymerase, phenylpropanoid biosynthesis, and plant–pathogen interaction. qRT-PCR validation of the five selected differentially expressed genes confirmed that three of them were significantly upregulated in ‘Dongjiang Bendizao’ compared with ‘Bendizao’, with fold changes ranging from approximately 4 to 13. Future functional validation of key candidates, including members of the TPS21, E2.1.1.104, RPS2, and CNGC genes, will help elucidate their regulatory networks and facilitate stress-tolerance breeding. Collectively, this study provides insights into the genomic variation between the two cultivars and establishes a theoretical foundation for cultivar identification and genetic improvement of local citrus germplasm.