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

Research output: Contribution to journalArticle

2 Citations (Scopus)

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 tolerance in wild grass Holcus lanatus genotypes screened from the same habitat. De novo transcriptome sequencing, RNAseq (RNA sequencing) and single nucleotide polymorphism (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 nontolerant (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 profiles, 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

Fingerprint

Holcus
Holcus lanatus
arsenates
Poaceae
Transcriptome
transcriptome
Phosphorus
genetic polymorphism
nutrition
grasses
Phenotype
phenotype
phosphorus
Single Nucleotide Polymorphism
Population
single nucleotide polymorphism
Cluster Analysis
Genes
RNA Sequence Analysis
RNA-binding proteins

Keywords

  • arsenate
  • Holcus lanatus
  • phosphorus (P)
  • tolerance
  • transcriptome

Cite this

Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus. / Meharg, Caroline; Khan, Bayezid; Norton, Gareth; Deacon, Claire; Johnson, David; Reinhardt, Richard; Huettel, Bruno; Meharg, Andrew A.

In: New Phytologist, Vol. 201, No. 1, 01.2014, p. 144-154.

Research output: Contribution to journalArticle

Meharg, Caroline ; Khan, Bayezid ; Norton, Gareth ; Deacon, Claire ; Johnson, David ; Reinhardt, Richard ; Huettel, Bruno ; Meharg, Andrew A. / Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus. In: New Phytologist. 2014 ; Vol. 201, No. 1. pp. 144-154.
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