Comparative transcriptome analysis reveals candidate genes for leaf color formation in a thermo-sensitive leaf-color mutant generated by carbon-ion beam in green wandering Jew (Tradescantia fluminensis)

Abstract

• Altered levels of chlorophyll and anthocyanin contents, and abnormal ultrastructural features of chloroplasts were detected in the thermo-sensitive leaf-color mutant of green wandering Jew. • RNA-Seq analysis identified 42 candidate genes involved in photosynthesis, 14 candidate genes for chlorophyll biosynthesis, and 13 candidate genes for flavonoid and anthocyanin biosynthetic pathways. • Chlorophyll fluorescence signals, and HPLC confirmed the gene expression levels obtained by RNA-Seq. Leaf color is considered a valuable trait when breeding ornamental plants. In this study, a novel thermo-sensitive leaf-color mutant ( mt ) of green wandering Jew was obtained through carbon-ion beam irradiation. Young leaves of the mt plant exhibited pink coloration under low temperature ( mt _7 ℃) and green coloration under normal temperature ( mt _25 ℃). However, young leaves of the wild type (WT) remained green under low and normal temperatures. Here, we compared the mt and WT in terms of their anatomical, physiological, transcriptomic, and metabolomic characteristics at 7 ℃ and 25 ℃. Histological analyses showed that the upper epidermis and palisade parenchyma of mt were fewer and smaller. Chloroplasts of mt _25 ℃ were abnormally inflated, and leucoplasts were present instead of chloroplasts in mt _7 ℃ leaves. Physiological experiments also showed that mt _7 ℃ had lower chlorophyll and carotenoid contents, and higher anthocyanin contents; however, the chlorophyll content in mt _25 ℃ leaves were higher than that in the WT. Transcriptome profiling revealed that 99 differentially expressed genes (DEGs) and 1597 transcription factors (TFs) are involved in photosynthesis, chlorophyll biosynthesis, and flavonoid and anthocyanin biosyntheses. This study identified 8 candidate genes associated with the PS Ⅱ reaction center, 13 genes related to PS Ⅰ, 15 genes for LHC, 4 genes for PET/Cyt b6/f, and 2 genes for ATP synthase; these genes were differentially expressed at 7 ℃. DEGs related to photosynthesis and chlorophyll biosynthesis were down-regulated in the pink leaves of mt _7 ℃, whereas DEGs involved in flavonoid and anthocyanin biosyntheses were up-regulated in mt _7 ℃ and mt _25 ℃ leaves. Differential expression levels were further confirmed by qRT-PCR, Chlorophyll fluorescence signals, and previous HPLC results the. The anthocyanin content of mt _7 ℃ was 20-fold higher than that of the other pigments resulting in pink coloration at low temperature. This study provides a systematic evaluation of thermo-sensitive color variation in the mt . Based on these results, we identified key pathways related to thermo-sensitive leaf-color change in green wandering Jew.