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Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis

Overview of attention for article published in BMC Plant Biology, January 2015
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Title
Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis
Published in
BMC Plant Biology, January 2015
DOI 10.1186/s12870-014-0356-6
Pubmed ID
Authors

Romina Petersen, Haris Djozgic, Benjamin Rieger, Steffen Rapp, Erwin Schmidt

Abstract

BackgroundPrimary roots (radicles) represent the first visible developmental stages of the plant and are crucial for nutrient supply and the integration of environmental signals. Few studies have analyzed primary roots at a molecular level, and were mostly limited to Arabidopsis. Here we study the primary root transcriptomes of standard type, heterozygous columnar and homozygous columnar apple (Malus x domestica) by RNA-Seq and quantitative real-time PCR. The columnar growth habit is characterized by a stunted main axis and the development of short fruit spurs instead of long lateral branches. This compact growth possesses economic potential because it allows high density planting and mechanical harvesting of the trees. Its molecular basis has been identified as a nested Gypsy-44 retrotransposon insertion; however the link between the insertion and the phenotype as well as the timing of the phenotype emergence are as yet unclear. We extend the transcriptomic studies of columnar tissues to the radicles, which are the earliest developmental stage and investigate whether homozygous columnar seedlings are viable.ResultsRadicles mainly express genes associated with primary metabolism, growth and development. About 200 genes show differential regulation in a comparison of heterozygous columnar radicles with non-columnar radicles, whereas the comparison of homozygous columnar radicles with non-columnar radicles yields about 300 differentially regulated genes. Genes involved in cellulose and phenylpropanoid biosynthesis, cell wall modification, transcription and translation, ethylene and jasmonate biosynthesis are upregulated in columnar radicles. Genes in the vicinity of the columnar-specific Gypsy-44 insertion experience an especially strong differential regulation: the direct downstream neighbor, dmr6-like, is downregulated in heterozygous columnar radicles, but strongly upregulated in columnar shoot apical meristems.ConclusionsThe transcriptomic profile of primary roots reflects their pivotal role in growth and development. Homozygous columnar embryos are viable and form normal radicles under natural conditions, and selection towards heterozygous plants most likely occurs due to breeders¿ preferences. Cell wall and phytohormone biosynthesis and metabolism experience differential regulation in columnar radicles. Presumably the first step of the differential regulation most likely happens within the region of the retrotransposon insertion and its tissue-specificity suggests involvement of one (or several) tissue-specific regulator(s).

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Mendeley readers

The data shown below were compiled from readership statistics for 31 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Chile 1 3%
Sri Lanka 1 3%
Unknown 29 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 9 29%
Student > Ph. D. Student 8 26%
Student > Master 6 19%
Professor 3 10%
Lecturer > Senior Lecturer 1 3%
Other 4 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 23 74%
Biochemistry, Genetics and Molecular Biology 3 10%
Environmental Science 1 3%
Computer Science 1 3%
Chemistry 1 3%
Other 0 0%
Unknown 2 6%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 February 2015.
All research outputs
#14,675,892
of 16,638,522 outputs
Outputs from BMC Plant Biology
#1,841
of 2,429 outputs
Outputs of similar age
#239,013
of 292,607 outputs
Outputs of similar age from BMC Plant Biology
#54
of 64 outputs
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