Transcriptome profiling reveals auxin suppressed anthocyanin biosynthesis in red-fleshed apple callus (Malus sieversii f. niedzwetzkyana)

Abstract

Anthocyanin biosynthesis in callus culture in vitro is strongly influenced by exogenous auxin concentrations. However, the mechanisms by which auxin regulates anthocyanin biosynthesis are largely unknown. To understand the molecular basis of this phenomenon, global gene expression was analyzed in red-fleshed apple calli treated with 1-naphthaleneacetic acid (NAA; 0.3 and 10 mg/L) and 2,4-dichlorophenoxyacetic acid (2,4-D; 0.03 and 0.6 mg/L) using RNA-seq. A total of 3070 and 2533 genes were differently expressed (log2 ratio ≥ 2 at P < 0.0001) in the 2,4-D and NAA treatments, respectively. Thereof, 937 genes were up-regulated and 902 genes were both down-regulated. Genes involved in anthocyanin and flavonoid synthesis and transport into the vacuole were generally down-regulated. Higher concentrations of 2,4-D and NAA facilitated the transport of auxin and induced the expressions of genes involved in the homeostatic feedback regulatory loop. In the auxin signaling pathway, nine Aux/IAA family genes and seven ARF family genes were up-regulated. Moreover, 298 transcription factors were differentially expressed in the NAA and 2,4-D treatments. Among them, some members of MYB, bHLH, and WD40 families that directly regulate anthocyanin and flavonoid synthesis, such as MYB75 (MdMYB10), MYB12, MYB111, MYB113, TT2, and TT8 (MdbHLH3), were down-regulated by NAA and 2,4-D. Auxin also affected gene expression in other plant hormone signaling pathways, such as the cytokinin, ethylene, and gibberellic acid pathways, which also influenced anthocyanin biosynthesis. This study provides a valuable overview of transcriptome changes and gives insight into the molecular mechanism by which auxin inhibits anthocyanin biosynthesis in red-fleshed apple calli.