Mitochondria and plastid response to genome duplication in diversified strategies to reconcile nucleo-cytoplasmic interaction in autotetraploid rice.

Whole-genome duplication is an important evolutionary mechanism in plants. Although numerous studies have morphologically characterized the polyploid plants, such as increased grain yield and enhanced resistance to pests and diseases, few studies are involved in the response of mitochondria and chloroplasts to the nuclear genome shock to reconcile the nucleo-cytoplasmic interactions in tetraploid rice. In this study, we employed the diploid rice cultivars Huang-Jin-Ke (HJK) and 032 and the artificially synthesized autotetraploid rice lines HJK-4n and 032-4n with normal fertility, to investigate their response of mitochondria and chloroplast genomes to the duplication of nuclear genome. Results revealed that, compared with diploid rice, autotetraploid rice exhibited extensive mitochondrial genome rearrangement and recombination, which led to significantly high expression of mitochondrial genes, and activity of mitochondrial respiratory chain complexes. Meanwhile, autotetraploid rice possessed a greater number of chloroplasts than diploid rice, leading to a significant increase in photosynthetic efficiency and biomass. Correspondingly, the nuclear genes associated with mitochondrial genome rearrangement and plastid duplication exhibited markedly elevated expression and high levels of H3K4me3 and H3K9me2 enrichment. This discovery reveals that the plastid and mitochondria reconcile the nucleo-cytoplasmic interaction in different ways in autotetraploid rice.