Organelle genomes of progeny of Tripidium arundinaceum × Saccharum spontaneum and sugarcane cultivar revealed their inheritance and characterization after hybridization

Sugarcane (Saccharum spp.) breeding often involves hybridization with distantly related wild species (such as Tripidium arundinaceum) to improve stress resistance, but mitochondrial and chloroplast inheritance across multiple backcross generations remains poorly understood. In this study, we employed PacBio and Illumina sequencing to assemble and compare the mitochondrial genomes (mitogenomes) and chloroplast genome of four genotypes: an distant hybrid F₁ GXAS 07–6-1 (Tripidium arundinaceum × Saccharum spontaneum), a subsequent hybrid F₁ GXASF₁ 08–2-28, a first-generation backcross GXASBC₁ 12-A6–3, and a second-generation backcross GXASBC₂ 15–114. Maternal inheritance preserves key co-linear gene clusters, whereas MTPT content varies, indicating post-hybridization structural adjustments. Our study confirms strict maternal inheritance of mitochondrial and chloroplast genomes across hybrid and backcross generations and validates mitochondrial transmission using organelle-specific markers, providing insights into organellar inheritance and references for sugarcane breeding.