Cytoplasmic inheritance analysis of citrus hybrid populations

Citrus is one of the most essential fruit crops worldwide, and it is generally considered that its cytoplasmic information is inherited from the maternal parent. Recent research has indicated that not all cytoplasmic genomes of citrus hybrids are derived from their female parent. However, the cytoplasmic inheritance pattern in citrus hybridization remains largely unexplored. In this study, we characterized the organelle genome diversity, nuclear-cytoplasmic evolutionary divergence and atypical genetic events in organelle genomes during hybridization in citrus by analyzing the phylogenetic relationship of organelle genomes in a natural citrus population. An F1 population was created from the cross with “CR038” (Citrus reticulata) as the maternal parent and “Pt005” (C. trifoliata) as the paternal parent. The complete organellar genomes (mitochondria and chloroplasts) of the parents were assembled using HiFi reads, and the draft organellar genomes of the offspring were also assembled using resequencing data. According to the analysis and identification results on phylogenetic relationship, comparative genome and recombination events, the cytoplasmic inheritance pattern of citrus could be classified into three types: maternal inheritance, biparental inheritance, and pseudo-paternal inheritance. This study is the first to reveal the cytoplasmic inheritance pattern in citrus based on the whole genome sequence data, which provides a novel insight into the genetic breeding in citrus.