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Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera

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Abstract

In plants, the transcription factor families have been implicated in many important biological processes. These processes include morphogenesis, signal transduction and environmental stress responses. Proteins containing the lateral organ boundaries domain (LBD), which encodes a zinc finger-like domain are only found in plants. This finding indicates that this unique gene family regulates only plant-specific biological processes. LBD genes play crucial roles in the growth and development of plants such as Arabidopsis, Oryza sativa, Zea mays, poplar, apple and tomato. However, relatively little is known about the LBD genes in grape (Vitis vinifera). In this study, we identified 40 LBD genes in the grape genome. A complete overview of the chromosomal locations, phylogenetic relationships, structures and expression profiles of this gene family during development in grape is presented here. Phylogenetic analysis showed that the LBD genes could be divided into classes I and II, together with LBDs from Arabidopsis. We mapped the 40 LBD genes on the grape chromosomes (chr1–chr19) and found that 37 of the predicted grape LBD genes were distributed in different densities across 12 chromosomes. Grape LBDs were found to share a similar intron/exon structure and gene length within the same class. The expression profiles of grape LBD genes at different developmental stages were analysed using microarray data. Results showed that 21 grape LBD genes may be involved in grape developmental processes, including preveraison, veraison and ripening. Finally, we analysed the expression patterns of six LBD genes through quantitative real-time polymerase chain reation analysis. The six LBD genes showed differential expression patterns among the three representative grape tissues, and five of these genes were found to be involved in responses to mannitol, sodium chloride, heat stress and low temperature treatments. To our knowledge, this is the first study to analyse the LBD gene family in grape and provides valuable information for classification and functional investigation of this gene family.

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Acknowledgements

This work was supported by the National Natural Science Foundation (grant no. 31400225), Shandong Province Natural Science Foundation (grant no. ZR2011CM032), and the Shandong Province Young and Middle-aged Scientists Research Awards Fund (grant no. BS2014SW014) in China.

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  1. Key Laboratory of Biology and Molecular Biology in University of Shandong, Weifang University, Weifang, Shandong, 261061, China

    HUI CAO, CAI-YUN LIU, CHUN-XIANG LIU, YUE-LING ZHAO & RUI-RUI XU

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  1. HUI CAO
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Correspondence to YUE-LING ZHAO or RUI-RUI XU.

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[Cao H., Liu C.-Y., Liu C.-X., Zhao Y.-L. and Xu R.-R. 2016 Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera. J. Genet. 95, xx–xx]

RX led and coordinated the project and carried out the bioinformatics analyses, CL conducted the RNA extraction and qRT-PCR experiments, RX and YZ wrote the manuscript, HC revised the manuscript. All authors read and agreed with the final manuscript.

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CAO, H., LIU, CY., LIU, CX. et al. Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera . J Genet 95, 515–526 (2016). https://doi.org/10.1007/s12041-016-0660-z

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