TY - JOUR

T1 - Trait-directed de novo population transcriptome dissects genetic regulation of a balanced polymorphism in phosphorus nutrition/arsenate tolerance in a wild grass, Holcus lanatus

AU - Meharg, Caroline

AU - Khan, Bayezid

AU - Norton, Gareth

AU - Deacon, Claire

AU - Johnson, David

AU - Reinhardt, Richard

AU - Huettel, Bruno

AU - Meharg, Andrew A.

PY - 2014/1/31

Y1 - 2014/1/31

N2 - 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.

AB - 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.

KW - arsente

KW - Holcus lanatus

KW - phosphorus (P)

KW - tolerance

KW - transcriptome

U2 - 10.1111/nph.12491

DO - 10.1111/nph.12491

M3 - Journal article

VL - 201

SP - 144

EP - 154

JO - New Phytologist

JF - New Phytologist

SN - 0028-646X

IS - 1

ER -