Bn.YCO affects chloroplast development in Brassica napus L.

Mature chloroplasts, as the main sites of photosynthesis, are essential for seedling growth in higher plants. Loss of function of genes involved in chloroplast development changes plant phenotype. We obtained a YELLOW COTYLEDON (YCO) mutant in rapeseed (Brassica napus L.) using CRISPR-Cas9. Bn.YCO, a gene of unknown function, has two homologous copies (BnaA01.YCO and BnaC01.YCO) in B. napus. Homozygous mutation of these two homologs resulted in yellow cotyledons and chlorotic true leaves. Transmission electron microscopy revealed that the formation of thylakoid membranes was inhibited in yellow cotyledons. Sequence similarity search revealed that YCO was conserved in different species, and a subcellular location assay verified that Bn.YCO was located in the chloroplast. Bn.YCO was expressed in multiple tissues, most highly in cotyledons. Knockout of Bn.YCO blocked the transcription of plastid genes, especially those of photosystem genes transcribed by plastid-encoded polymerase. Transcriptome sequencing showed that the majority of genes involved in ribosome assembly and photosynthesis were down-regulated in Bn.yco mutants. These results suggested that loss of function of Bn.YCO affected plastid gene transcription, which influenced chloroplast biogenesis in rapeseed seedlings.