Multi-omic insights into genetic diversity and chilling-tolerant potential in the somatic hybrid Citrus aurantium + Citrus sinensis

Somatic hybridization has been used to overcome sexual incompatibility, enabling the integration of nuclear and cytoplasmic genomes from distantly related species and facilitating the development of diverse germplasm for crop improvement. In citrus, somatic hybrids have been characterized morphologically and cytologically, but the genetic basis of their expanded diversity remains unclear. Here, we performed an integrated analysis of a somatic hybrid (Ca + Cs) generated by protoplast fusion between Citrus aurantium (Ca) and Citrus sinensis (Cs), including morphological assessment, karyotyping, transcriptome, and DNA methylation profiling. The hybrid exhibited a vigorous root system, thicker stems and leaves, altered chromosome structure, and co-expression of parental 45S rDNA loci. Transcriptome profiling revealed subgenome-biased expression favoring the Cs-derived genome. DNA methylation profiling uncovered asymmetric epigenetic reprogramming, with hypomethylation of genes related to genomic stability in the Ca-derived genome and of genes involved in defense against genomic intrusion in the Cs-derived genome. Under chilling stress, the somatic hybrid displayed a more rapid transcriptional response than either parent. Together, these results suggest coordinated transcriptional and epigenetic remodeling in citrus somatic hybrids, providing insights into subgenomic interactions with implications for future evaluation of their potential in rootstock improvement.