Identification of bZIP transcription factors and their responses to brown spot in pear

Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A₃ (GA₃). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in ‘Huangguan’ pear.

Keywords:
Pear; bZIP gene family; brown spot; hormone; expression profile

Authorship

Li Liu

Anhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China.Anhui Agricultural UniversityP.R. ChinaHefei, Anhui, P.R. ChinaAnhui Agricultural University, School of Horticulture, Hefei, Anhui, P.R. China.

Yuxin Zhang

Qi Wang

Xingyu Tao

Jing Fang

Wenjuan Zheng

Liwu Zhu

Bing Jia

Wei Heng

Shaowen Li

Anhui Agriculture University, School of Information and Computer Science, Hefei, Anhui, P. R. China.Anhui Agriculture UniversityP. R. ChinaHefei, Anhui, P. R. ChinaAnhui Agriculture University, School of Information and Computer Science, Hefei, Anhui, P. R. China.

http://orcid.org/0000-0002-2923-501X

Send correspondence to
Shaowen Li. Anhui Agriculture University, School of Information and Computer Science, West Changjiang Road No.130, Hefei, Anhui, China. E-mail: 553758852@qq.com.

Associate Editor:

Rogerio Margis

Conflict of Interest

The authors declare they have no conflict of interests.

Author Contributions

LL, WQ and JB conceived and designed the experiments; HW, ZYX and FJ collected fruits and prepared for RNA; ZYX and ZWJ performed RT-qPCR. TXY contributed to bioinformatic analysis; LL contributed to the writing of the manuscript and data analysis; LSW and ZLW revised the manuscript. All authors read and approved the final manuscript.

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Figures

Figures (4)

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Figure 1 -
Phylogenetic analysis of bZIPs from pear and Arabidopsis thaliana. The tree was constructed with IQ-TREE v.1.6 software. The bZIP TFs clustered into 13 distinct clades, marked by curves of different colors.

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Figure 2 -
Phylogenetic relationships, motif compositions and gene structures of PbbZIPs. (A) The phylogenetic tree was produced by MEGA using the neighbor-joining method with 1,000 bootstrap replicates. (B) A schematic representing the conserved motifs of the PbbZIPs identified by MEME. Each motif is indicated by a colored box numbered at the bottom. (C) Exon number distribution of the PbbZIP family TFs in white pear.

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Figure 3 -
The chromosomal locations of 77 PbbZIPs. The genes were mapped to the pear chromosomes by TBtools. The chromosomes of pear are shown arranged in a circle. The outer circle represents the chromosome. Heatmaps, scatterplots and histograms were used to record the gene density of each chromosome segment. The length of each chromosome segment was set at 500,000 bp.

Thumbnail

Figure 4 -
Phenotypic characteristics of BS, expression profiles of PbbZIP genes and a coexpression network and heatmap for PbbZIPs with GA signaling genes in pear. (A) Phenotypes of normal ‘Huangguan’ pear (CK), ‘Huangguan’ pear with BS disease and ‘Huangguan’ pear treated with GA₃. (B) The expression patterns of PbbZIP genes in ‘Huangguan’ pear. (C) Interaction network analysis of PbbZIPs with GA signaling genes in pear was performed using the STRING database. (D) Heatmap of GA signaling genes expressed in ‘Huangguan’ and ‘Huangguan’ with BS based on the fold change (log2) in FPKM values. The color scale at the top represents log2-FPKM values. (E) Relative expression profiles of PbbZIP genes in the exocarp of ‘Huangguan’ pear. Error bars represent the SE of three biological replicates. Lowercase letters indicate significant differences between treatments at the P < 0.05 level. CK: normal ‘Huangguan’ pear; BS: ‘Huangguan’ pear with BS; GA₃: ‘Huangguan’ pear treated with GA₃.

Figure 1 - Phylogenetic analysis of bZIPs from pear and Arabidopsis thaliana. The tree was constructed with IQ-TREE v.1.6 software. The bZIP TFs clustered into 13 distinct clades, marked by curves of different colors.

Figure 2 - Phylogenetic relationships, motif compositions and gene structures of PbbZIPs. (A) The phylogenetic tree was produced by MEGA using the neighbor-joining method with 1,000 bootstrap replicates. (B) A schematic representing the conserved motifs of the PbbZIPs identified by MEME. Each motif is indicated by a colored box numbered at the bottom. (C) Exon number distribution of the PbbZIP family TFs in white pear.

Figure 3 - The chromosomal locations of 77 PbbZIPs. The genes were mapped to the pear chromosomes by TBtools. The chromosomes of pear are shown arranged in a circle. The outer circle represents the chromosome. Heatmaps, scatterplots and histograms were used to record the gene density of each chromosome segment. The length of each chromosome segment was set at 500,000 bp.

Figure 4 - Phenotypic characteristics of BS, expression profiles of PbbZIP genes and a coexpression network and heatmap for PbbZIPs with GA signaling genes in pear. (A) Phenotypes of normal ‘Huangguan’ pear (CK), ‘Huangguan’ pear with BS disease and ‘Huangguan’ pear treated with GA₃. (B) The expression patterns of PbbZIP genes in ‘Huangguan’ pear. (C) Interaction network analysis of PbbZIPs with GA signaling genes in pear was performed using the STRING database. (D) Heatmap of GA signaling genes expressed in ‘Huangguan’ and ‘Huangguan’ with BS based on the fold change (log2) in FPKM values. The color scale at the top represents log2-FPKM values. (E) Relative expression profiles of PbbZIP genes in the exocarp of ‘Huangguan’ pear. Error bars represent the SE of three biological replicates. Lowercase letters indicate significant differences between treatments at the P < 0.05 level. CK: normal ‘Huangguan’ pear; BS: ‘Huangguan’ pear with BS; GA₃: ‘Huangguan’ pear treated with GA₃.

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Identification of bZIP transcription factors and their responses to brown spot in pear

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[1] Send correspondence to
Shaowen Li. Anhui Agriculture University, School of Information and Computer Science, West Changjiang Road No.130, Hefei, Anhui, China. E-mail: 553758852@qq.com.