A 2.9 Mb Chromosomal Segment Deletion Is Responsible for Early Ripening and Deep Red Fruit in Citrus sinensis

Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The present study identified a novel navel orange accession, designated as Ganhong, with early ripening and deep red fruit traits. DNA sequence analysis showed a 2.9 Mb deletion in one copy of chromosome 7 in Ganhong navel orange. Flesh samples from Ganhong and its parental variety, Newhall navel orange, were sampled for RNA sequence analysis 200 days after flowering; 958 differentially expressed genes (DEGs) were identified between the two varieties. Functional enrichment analysis indicated that these DEGs were mainly enriched in phytohormones, particularly abscisic acid (ABA), related to fruit ripening. The deletion interval has 343 annotated genes, among which 4 genes (Cs_ont_7g018990, Cs_ont_7g019400, Cs_ont_7g019650, and Cs_ont_7g019820) were inferred to be candidate causal genes for early ripening and deep red fruit traits based on gene functionality and gene expression analysis. The present study laid a foundation for further elucidation of the mechanisms underlying the early ripening and deep red fruit trait in Ganhong navel orange.