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Genome-wide identification and expression analysis of the bZIP gene family in apple (Malus domestica)

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Abstract

The basic leucine zipper (bZIP) family is one of the largest transcription factor (TF) families in plants, which play crucial roles in plant growth and development. bZIP proteins are involved in multiple biological processes, as well as responses to various biotic/abiotic stresses. Although genome-wide analysis of the bZIP gene family has been conducted in several plant species, only few comprehensive characterization of this gene family has been reported in apple (Malus domestica), an important tree fruit in the Rosaceae family. In this study, we identified 114 bZIP genes from the apple genome, which were divided into 10 subgroups based on their sequences. We further characterized these MdbZIP genes in terms of gene structure, protein model, and chromosomal distribution. Genome-wide expression profile of MdbZIP genes indicated that 14 MdbZIPs were highly expressed during apple fruit development, and 17 MdbZIPs showed differential expression in leaves and mature apple fruit. Analysis of the expression of 16 MdbZIPs under drought and salt stresses in apple leaves and roots using quantitative real-time PCR (qRT-PCR) indicated that they all exhibited differential transcript levels in both treatments, suggesting that MdbZIP genes are involved in abiotic stress responses. The genome-wide identification, characterization, and expression analysis of apple bZIP genes provide new insights into the roles of the bZIP TF family and lay a solid foundation for future cloning and functional analysis of this gene family, which may be used to manipulate apple growth and development and improve its stress tolerance.

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Authors and Affiliations

  1. Department of Horticulture, Cornell University, 134A Plant Science, Ithaca, NY, 14853, USA

    Yuan-Yuan Li, Dong Meng, Mingjun Li & Lailiang Cheng

  2. College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, 271018, China

    Yuan-Yuan Li

  3. College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China

    Mingjun Li

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  1. Yuan-Yuan Li
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  2. Dong Meng
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Correspondence to Lailiang Cheng.

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Data archiving statement

The apple bZIP gene family sequences have been submitted to GDR (Genome Database for Rosaceae), and the accession number been shown in the Table 1.

Additional information

Communicated by V. Decroocq

Yuan-Yuan Li and Dong Meng contributed equally to this work.

Electronic supplementary material

Fig. S1

Phylogenetic tree that added four reference’s bZIP apple genes (JPEG 153 kb)

High-resolution image (TIFF 1551 kb)

Fig. S2

Phylogenetic tree made by full length of bZIP proteins (JPEG 147 kb)

High-resolution image (TIFF 1461 kb)

Table S1

Quantitative real-time PCR primers for expression analysis of MdbZIP genes (DOCX 14 kb)

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Li, YY., Meng, D., Li, M. et al. Genome-wide identification and expression analysis of the bZIP gene family in apple (Malus domestica). Tree Genetics & Genomes 12, 82 (2016). https://doi.org/10.1007/s11295-016-1043-6

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  • DOI: https://doi.org/10.1007/s11295-016-1043-6

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