Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress

Abstract

The bHLH (basic helix-loop-helix) transcription factor family is the second largest in plants. It occurs in all three eukaryotic kingdoms, and plays important roles in regulating growth and development. However, family members have not previously been studied in apple. Here, we identified 188 MdbHLH proteins in apple "Golden Delicious" (Malus × domestica Borkh.), which could be classified into 18 groups. We also investigated the gene structures and 12 conserved motifs in these MdbHLHs. Coupled with expression analysis and protein interaction network prediction, we identified several genes that might be responsible for abiotic stress responses. This study provides insight and rich resources for subsequent investigations of such proteins in apple.

Keywords: apple; bHLH transcription factor; drought and salt stress; expression analysis; genome-wide analysis; regulation networks.

Figure 1

Summary information for the 188 MdbHLH genes. (A) Locations of 188 MdbHLHs on 17 chromosomes. (B) Distribution of 188 MdbHLHs on chromosomes. (C) Functional annotation (Gene Ontology) of MdbHLH proteins. Segmented duplicate homologous blocks are indicated with gray shadow.

Figure 2

Phylogenetic analysis (original tree) and subgroup classifications of MdbHLH proteins.

Figure 3

Expression analysis of MdbHLH orthologs in Arabidopsis. Expression patterns of MdbHLH orthologs under drought (A,B) and salt (C,D) stress. Different colors indicate genes with expression patterns that are similar between tissue types (stars) or treatments (dots).

Figure 4

Protein interaction network for MdbHLHs based on MdbHLH orthologs in Arabidopsis. This network was predicted by online software STRING. Red lines indicate proteins that are predicted to interact with more than four other bHLH proteins. MdbHLH proteins are shown in brackets with Arabidopsis orthologs.

Figure 5

Relative expression analysis of select genes along the time series. Analysis (2^−ΔΔCT method) of 30 selected MdbHLHs expressed in response to induced drought (PEG6000; blue line) or salt stress (NaCl; red line).

Figure 6

Protein interaction networks prediction for crucial MdbHLH proteins. Protein interaction network predictions of MdbHLH24 (A), MdbHLH74 (B), and MdbHLH4 (C), based on MdbHLH orthologs in Arabidopsis. MdbHLH proteins are shown in brackets with Arabidopsis orthologs.