Genome-wide genetic variation and comparative transcriptome analyses of citrus mutant Jedae-unshiu and wild-type Citrus unshiu

‘Miyagawa-wase’ mandarin ( Citrus. unshiu Marc. cv. Miyagawa-wase) is one of the most widely cultivated citrus varieties in Korea. Previously, we used γ-irradiation to develop new citrus varieties by mutation breeding, a useful tool for increasing genetic diversity in a short time. One of the new citrus varieties we generated, Jedae-unshiu , produces uniquely shaped fruit with vertical troughs on the flavedo. Although comparative analyses of genome-wide variation and transcriptomics have been reported for seedless or color-change citrus variants, little is known regarding genetic variants linked to morphological variation in citrus fruits. In this study, genome-wide single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variants were identified in Jedae-unshiu by whole-genome re-sequencing and subjected to functional annotation by gene ontology (GO) analysis. The results show that InDel-containing genes are more highly represented in the GO database than SNP-containing genes. In addition, we compared Jedae-unshiu and wild-type control transcriptomes to identify candidate genetic determinants of the unique fruit phenotype of Jedae-unshiu . A total of 641 unique, differentially expressed genes (DEGs) were identified in Jedae-unshiu relative to wild-type control, including 388 up-regulated and 253 down-regulated genes. The DEGs were mapped to GO terms and subjected to Kyoto Encyclopedia of Genes and Genomes pathway analysis to identify DEGs involved in cellular processes potentially linked to the unique phenotype of Jedae-unshiu fruit. The expression of 10 DEGs (5 up- and 5 down-regulated) was quantified by reverse transcriptase-polymerase chain reaction (RT-PCR). Our findings provide insight into putative genetic determinants of fruit morphology in citrus.