RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum

Todd Gaines; L. Lorentz; A. Figge; J. Herrmann; F. Maiwald; M.C. Ott; Heping Han; Roberto Busi; Qin Yu; Stephen B. Powles; R.S. Beffa

doi:10.1111/tpj.12514

RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum

Todd Gaines, L. Lorentz, A. Figge, J. Herrmann, F. Maiwald, M.C. Ott, Heping Han, Roberto Busi, Qin Yu, Stephen B. Powles, R.S. Beffa

UWA School of Agriculture and Environment

Research output: Contribution to journal › Article

115 Citations (Scopus)

Abstract

Summary Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism-based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA-Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop-resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant-only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up-regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2-R from F2-S individuals. In a physiological validation experiment in which 2,4-D pre-treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field-evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Original language	English
Pages (from-to)	865-876
Journal	The Plant Journal
Volume	78
Issue number	5
DOIs	https://doi.org/10.1111/tpj.12514
Publication status	Published - Jun 2014

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@article{49131f12da9f418880495db5e7c839d7,

title = "RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum",

abstract = "Summary Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism-based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA-Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop-resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant-only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up-regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2-R from F2-S individuals. In a physiological validation experiment in which 2,4-D pre-treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field-evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance. {\textcopyright} 2014 The Authors The Plant Journal {\textcopyright} 2014 John Wiley & Sons Ltd.",

author = "Todd Gaines and L. Lorentz and A. Figge and J. Herrmann and F. Maiwald and M.C. Ott and Heping Han and Roberto Busi and Qin Yu and Powles, {Stephen B.} and R.S. Beffa",

year = "2014",

month = jun,

doi = "10.1111/tpj.12514",

language = "English",

volume = "78",

pages = "865--876",

journal = "The Plant Journal",

issn = "0960-7412",

publisher = "John Wiley & Sons",

number = "5",

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RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum. / Gaines, Todd; Lorentz, L.; Figge, A.; Herrmann, J.; Maiwald, F.; Ott, M.C.; Han, Heping ; Busi, Roberto ; Yu, Qin ; Powles, Stephen B.; Beffa, R.S.

In: The Plant Journal, Vol. 78, No. 5, 06.2014, p. 865-876.

Research output: Contribution to journal › Article

TY - JOUR

T1 - RNA-Seq transcriptome analysis to identify genes involved in metabolism-based diclofop resistance in Lolium rigidum

AU - Gaines, Todd

AU - Lorentz, L.

AU - Figge, A.

AU - Herrmann, J.

AU - Maiwald, F.

AU - Ott, M.C.

AU - Han, Heping

AU - Busi, Roberto

AU - Yu, Qin

AU - Powles, Stephen B.

AU - Beffa, R.S.

PY - 2014/6

Y1 - 2014/6

N2 - Summary Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism-based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA-Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop-resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant-only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up-regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2-R from F2-S individuals. In a physiological validation experiment in which 2,4-D pre-treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field-evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

AB - Summary Weed control failures due to herbicide resistance are an increasing and worldwide problem that significantly affect crop yields. Metabolism-based herbicide resistance (referred to as metabolic resistance) in weeds is not well characterized at the genetic level. An RNA-Seq transcriptome analysis was used to find candidate genes that conferred metabolic resistance to the herbicide diclofop in a diclofop-resistant population (R) of the major global weed Lolium rigidum. A reference cDNA transcriptome (19 623 contigs) was assembled and assigned putative annotations. Global gene expression was measured using Illumina reads from untreated control, adjuvant-only control, and diclofop treatment of R and susceptible (S). Contigs that showed constitutive expression differences between untreated R and untreated S were selected for further validation analysis, including 11 contigs putatively annotated as cytochrome P450 (CytP450), glutathione transferase (GST), or glucosyltransferase (GT), and 17 additional contigs with annotations related to metabolism or signal transduction. In a forward genetics validation experiment, nine contigs had constitutive up-regulation in R individuals from a segregating F2 population, including three CytP450, one nitronate monooxygenase (NMO), three GST, and one GT. Principal component analysis using these nine contigs differentiated F2-R from F2-S individuals. In a physiological validation experiment in which 2,4-D pre-treatment induced diclofop protection in S individuals due to increased metabolism, seven of the nine genetically validated contigs were induced significantly. Four contigs (two CytP450, NMO, and GT) were consistently highly expressed in nine field-evolved metabolic resistant L. rigidum populations. These four contigs were strongly associated with the resistance phenotype and are major candidates for contributing to metabolic diclofop resistance. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

U2 - 10.1111/tpj.12514

DO - 10.1111/tpj.12514

M3 - Article

C2 - 24654891

VL - 78

SP - 865

EP - 876

JO - The Plant Journal

JF - The Plant Journal

SN - 0960-7412

IS - 5

ER -