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RNA ‐Seq transcriptome analysis to identify genes involved in metabolism‐based diclofop resistance in Lolium rigidum
Author(s) -
Gaines Todd A.,
Lorentz Lothar,
Figge Andrea,
Herrmann Johannes,
Maiwald Frank,
Ott MarkChristoph,
Han Heping,
Busi Roberto,
Yu Qin,
Powles Stephen B.,
Beffa Roland
Publication year - 2014
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.12514
Subject(s) - lolium rigidum , biology , transcriptome , genetics , contig , population , rna seq , gene , candidate gene , computational biology , gene expression , genome , herbicide resistance , demography , sociology
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 c DNA 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 F 2 population, including three CytP450, one nitronate monooxygenase ( NMO ), three GST , and one GT . Principal component analysis using these nine contigs differentiated F 2 ‐R from F 2 ‐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.