Multi-omics analysis of somatic mutants reveals TCP7 allelically regulates multiple carotenogenic genes in citrus.

Somatic mutations are widespread in all organisms and cause abundant phenotypic changes, constituting an important source of variation especially for clonally propagated plants. Somatic mutants can serve as a mutation-introducing method for exploring the regulatory mechanism of mutated trait formation in clonally propagated plants. Red-fleshed and orange-fleshed pomelo varieties derive from independent mutations of the wild-type white-fleshed Guanxi honey pomelo (Citrus grandis), offering an ideal system for dissecting core regulatory transcription factors behind the fruit color trait. Here, we performed a meta-analysis comprising genome, transcriptome, DNA methylome and chromatin accessibility assays of the two color mutants and their wild type, resulting in haplotype-scaled pan-genome. The chromatin openness analysis suggested that binding sites for TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors are significantly enriched in the differentially open regions, with different footprint patterns in the mutants and wild type. We identified CgTCP3, CgTCP7, and CgTCP20 as regulators of key carotenogenic genes including ZDS, BCH, and NCED2. Furthermore, CgTCP7 underwent positive selection in pomelo germplasm, with various alleles differentially affecting carotenogenic gene expression and modulating carotenoid accumulation. We therefore identified the core transcription factor genes responsible for color trait formation, providing resources for breeding varieties with diversified phenotypes.