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

瑞士黑麦草 生物 转录组 遗传学 康蒂格 人口 RNA序列 基因 候选基因 计算生物学 基因表达 基因组 抗除草剂 社会学 人口学
作者
Todd A. Gaines,Lothar Lorentz,Andrea Figge,Johannes Herrmann,Frank Maiwald,Mark‐Christoph Ott,Heping Han,Roberto Busi,Qin Yu,Stephen B. Powles,Roland Beffa
出处
期刊:Plant Journal [Wiley]
卷期号:78 (5): 865-876 被引量:196
标识
DOI:10.1111/tpj.12514
摘要

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.
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