Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq

Publication Overview
TitleRegulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
AuthorsPayá-Milans M, Nunez GH, Olmstead JW, Rinehart TA, Staton M
TypeJournal Article
Journal NameBMC genomics
Volume18
Issue1
Year2017
Page(s)580
CitationPayá-Milans M, Nunez GH, Olmstead JW, Rinehart TA, Staton M. Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq. BMC genomics. 2017 Aug 07; 18(1):580.

Abstract

BACKGROUND
Blueberries are one of the few horticultural crops adapted to grow in acidic soils. Neutral to basic soil pH is detrimental to all commonly cultivated blueberry species, including Vaccinium corymbosum (VC). In contrast, the wild species V. arboreum (VA) is able to tolerate a wider range of soil pH. To assess the molecular mechanisms involved in near neutral pH stress response, plants from pH-sensitive VC (tetraploid) and pH-tolerant VA (diploid) were grown at near neutral pH 6.5 and at the preferred pH of 4.5.

RESULTS
Transcriptome sequencing of root RNA was performed for 4 biological replications per species x pH level interaction, for a total of 16 samples. Reads were mapped to the reference genome from diploid V. corymbosum, transforming ~55% of the reads to gene counts. A quasi-likelihood F test identified differential expression due to pH stress in 337 and 4867 genes in VA and VC, respectively. Both species shared regulation of genes involved in nutrient homeostasis and cell wall metabolism. VA and VC exhibited differential regulation of signaling pathways related to abiotic/biotic stress, cellulose and lignin biosynthesis, and nutrient uptake.

CONCLUSIONS
The specific responses in VA likely facilitate tolerance to higher soil pH. In contrast, response in VC, despite affecting a greater number of genes, is not effective overcoming the stress induced by pH. Further inspection of those genes with differential expression that are specific in VA may provide insight on the mechanisms towards tolerance.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication Date2017 Aug 07
Journal AbbreviationBMC Genomics
DOI10.1186/s12864-017-3967-0
Elocation10.1186/s12864-017-3967-0
Journal CountryEngland
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
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PMID: PubMedPMID:28784085