Skim sequencing of nuclear and organelar genomes in three maize cytolines

Crops are under constant pressure due to global warming. Nowadays' technologies offer a unique opportunity to probe how maize responds to this process from an omics perspective and speed up the breeding programs accordingly. Recently, an atlas of gene expression responses to heat stress in various tissues of maize was developed (He et al., 2019). Complementary to testing the response to heat stress of a single nucleus hosted in a single cytoplasm, here we use three maize cytolines (i.e., the same nucleus but different cytoplasms) (i) to probe how one nucleus performs in different cytoplasmic environments and (ii) to link different gene expression patterns to existing genetic variability in the organellar genomes. There is a consistent common response as differentially expressed genes (DEG) and enriched GO terms in all three cytolines, but the cytoplasm donor lines trigger the expression of new genes that are not DEG in the nucleus-donor line. Cytoline-specific DEG may be linked to the existing variability at the mitochondrial level. A SNP in the mitochondrial Atp4 gene seems to impact the proper functioning of its protein, explaining the tremendous difference in gene expression of one cytoline vs. the other two. By corroborating gene expression data with the existing polymorphisms at organellar genomes and measurements of photosynthesis rates in the three cytolines, our results offer a unique perspective on the existing interplay between one nucleus and three different cytoplasms. Our results contribute molecular data to the paradigm used to explain the impact of transferring elite nuclei into cytoplasms that confer heat resistance as an alternative to traditional breeding in the context of global warming.