Trait directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass Holcus lanatus

Caroline Meharg*, Bayezid Khan, Gareth Norton, Claire Deacon, David Johnson, Richard Reinhardt, Bruno Huettel, Andrew A. Meharg

*Corresponding author for this work

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3 Citations (Scopus)
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Abstract

The aim of this study was to characterize the transcriptome of a balanced polymorphism, under the regulation of a single gene, for phosphate fertilizer responsiveness/arsenate toler- ance in wild grass Holcus lanatus genotypes screened from the same habitat.

De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide poly- morphism (SNP) calling were conducted on RNA extracted from H.lanatus. Roche 454 sequencing data were assembled into c. 22 000 isotigs, and paired-end Illumina reads for phosphorus-starved (P) and phosphorus-treated (P+) genovars of tolerant (T) and nontoler- ant (N) phenotypes were mapped to this reference transcriptome.

Heatmaps of the gene expression data showed strong clustering of each P+/P treated genovar, as well as clustering by N/T phenotype. Statistical analysis identified 87 isotigs to be significantly differentially expressed between N and T phenotypes and 258 between P+ and P treated plants. SNPs and transcript expression that systematically differed between N and T phenotypes had regulatory function, namely proteases, kinases and ribonuclear RNA- binding protein and transposable elements.

A single gene for arsenate tolerance led to distinct phenotype transcriptomes and SNP pro- files, with large differences in upstream post-translational and post-transcriptional regulatory genes rather than in genes directly involved in P nutrition transport and metabolism per se.
Original languageEnglish
Pages (from-to)144-154
Number of pages11
JournalNew Phytologist
Volume201
Issue number1
Early online date18 Sep 2013
DOIs
Publication statusPublished - Jan 2014

Keywords

  • arsente
  • Holcus lanatus
  • phosphorus (P)
  • tolerance
  • transcriptome
  • RNA EDITING SITES
  • ARSENATE TOLERANCE
  • TRANSPOSABLE ELEMENTS
  • PHOSPHATE DEFICIENCY
  • SEQUENCE ALIGNMENT
  • YORKSHIRE FOG
  • IANATUS L
  • PLANTS
  • GENOME
  • IDENTIFICATION

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