Comparative transcriptome profiling of genes and pathways involved in leaf-patterning of Clivia miniata var. variegata

Clivia miniata var. variegata (Cmvv) typically possesses yellow- and green-striped leaves. The striped plant not only has a high ornamental value but also be suitable for photosynthesis and chloroplast development research. Our previous study had revealed that yellow stripes (YSs) of Cmvv leaves contain chlorophyll-less ineffective chloroplasts. However, mechanism of Cmvv variegation is yet to be investigated. In the study, transcriptomes of both the YSs and green stripes (GSs) from single Cmvv leaves were compared using high-throughput sequencing. A total of 688 differential expression genes (DEGs) were identified based on biological replications. The qRT-PCR results indicated that transcriptome profiles accurately reflected global transcriptome differences between YSs and GSs. Subcellular localization analysis suggested that 56 DEG proteins were targeted to chloroplasts, and might be involved in anterograde signaling and leaf patterning. Moreover, the DEGs were mostly enriched in photosynthesis and plant-pathogen interaction KEGG pathways. Meanwhile, there should be coordination interaction between the two pathways. Seven of the eight DEGs involved in photosynthesis KEGG pathway were chloroplast-encoded genes and distributed among different cistrons of chloroplast DNA (cpDNA) large single copy regions (LSC) which are more prone to mutation. It was proposed that the YSs were caused by mutation(s) in cpDNA LSC. Thus, when the primary zygote of Cmvv was chimeric in LSC, leaf might be yellow- and green-striped. The study would give new insights into plant variegation and offers candidate genes to guide future research attempting to breed variegated plants.