Genome-Wide Profiling of the Genes Related to Leaf Discoloration in Zelkova schneideriana

Zelkova schneideriana is a landscaping flowering and deciduous plant whose leaf color changes in the fall season. In the discoloration period, the anthocyanin content in the red lines of Z. schneideriana is 3.52 times greater than that in the green lines, whereas the chlorophyll content in the red lines is 20.10 times lower. To understand the molecular mechanism of the leaf discoloration, transcriptome sequencing was performed. A total of 3965 differentially expressed genes (DEGs) were identified between the red and green lines in the discoloration period. These DEGs were mainly involved in plant–pathogen interactions, the MAPK signaling pathway, plant hormone signal transduction, flavonoid biosynthesis, and anthocyanin biosynthesis. Among them, three downregulated genes were involved in chlorophyll synthesis; these genes exhibited a maximum decrease in the red lines that was 11.13 times greater than their expression in the green lines. In contrast, 33 upregulated genes were involved in anthocyanin biosynthesis; they exhibited a maximum increase in the red lines 4645.33 times greater than their expression in the green lines. The results of an association analysis revealed that four transcription factors, including ZeBHLH42, ZeMYB123, ZeMYB113, and ZeWRKY44, positively regulated the anthocyanin synthesis genes. These results explained the mechanism underlying the discoloration of Zelkova leaves and provided a basis for molecular breeding programs of colorful plants.