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Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies

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Abstract

The columnar phenotype of apple trees (Malus x domestica) is characterized by a compact growth habit with fruit spurs instead of lateral branches. These properties provide significant economic advantages by enabling high density plantings. The columnar growth results from the presence of a dominant allele of the gene Columnar (Co) located on chromosome 10 which can appear in a heterozygous (Co/co) or homozygous (Co/Co) state. Although two deep sequencing approaches could shed some light on the transcriptome of columnar shoot apical meristems (SAMs), the molecular mechanisms of columnar growth are not yet elaborated. Since the influence of phytohormones is believed to have a pivotal role in the establishment of the phenotype, we performed RNA-Seq experiments to study genes associated with hormone homeostasis and clearly affected by the presence of Co. Our results provide a molecular explanation for earlier findings on the hormonal state of columnar apple trees. Additionally, they allow hypotheses on how the columnar phenotype might develop. Furthermore, we show a statistically approved enrichment of differentially regulated genes on chromosome 10 in the course of validating RNA-Seq results using additional gene expression studies.

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Abbreviations

Co:

Columnar

NGS:

Next generation sequencing

SAM:

Shoot apical meristem

IAA:

Indole-3-acetic acid

CK:

Cytokinin

ABA:

Abscisic acid

GA:

Gibberellic acid

JA:

Jasmonic acid

A14:

A14-190-93 (non-columnar type apple)

P28:

Procats 28 (columnar type apple)

BR:

Brassinosteroid

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Acknowledgments

We thank Benjamin Rieger and Dr. Steffen Rapp for their work in the development of Perl scripts and their bioinformatics support. We are grateful to Dr. Walker Jackson for his many helpful comments on the manuscript. The work was supported by grants of the Federal Ministry of Agriculture and Nutrition (Nr. 511-06.01-28-1-43.042-07 and Nr. 313-06.01-28-1-43.042-07).

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Molecular Genetics, University of Mainz, 55128, Mainz, Germany

    Clemens Krost, Romina Petersen, Stefanie Lokan & Erwin R. Schmidt

  2. Geisenheim Research Center, Von-Lade-Straße 1, 65366, Geisenheim, Germany

    Bastienne Brauksiepe & Peter Braun

  3. Institut für Molekulargenetik, Johannes Gutenberg-Universität, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany

    Erwin R. Schmidt

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  1. Clemens Krost
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  2. Romina Petersen
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  6. Erwin R. Schmidt
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Correspondence to Erwin R. Schmidt.

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11103_2012_9992_MOESM1_ESM.xlsx

Results from DESeq analysis The table contains 1173 differentially regulated genes with p < 0.005 and fold change > 3.0 obtained from DESeq analysis. For every gene, Malus x domestica UniGene database ID, Malus x domestica genome project ID and Populus trichocarpa genome project ID (used for MAPMAN visualization) is provided. Log2 fold change values are highlighted in green and red representing up or down regulation, respectively. All entries are sorted by base mean values (XLSX 174 kb)

11103_2012_9992_MOESM2_ESM.tif

MAPMAN analysis of differentially regulated genes The figure visualizes all genes found to be differentially expressed by DESeq for metabolic processes (A) and various functional categories (B). Overrepresented categories that confirm earlier findings (Krost et al. 2012) are framed in red. Red and green boxes represent repressed and induced genes, respectively. Values in the key imply log2 of normalized Illumina read counts(TIFF 1665 kb)

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Krost, C., Petersen, R., Lokan, S. et al. Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies. Plant Mol Biol 81, 211–220 (2013). https://doi.org/10.1007/s11103-012-9992-0

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