RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide.
RNA-Seq transcriptome analysis of Amaranthus palmeri with differential tolerance to glufosinate herbicide.
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DOI：
10.1371/journal.pone.0195488
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发表时间：
2018
期刊：
影响因子：
3.7
通讯作者：
Roma-Burgos N
中科院分区：
文献类型：
--
作者：
Salas-Perez RA;Saski CA;Noorai RE;Srivastava SK;Lawton-Rauh AL;Nichols RL;Roma-Burgos N
长穗苋是一种危害严重的杂草，在某些情况下严重威胁着北美农业生产的可持续性。抗草甘膦的苋属物种分布广泛，促使使用草甘膦的替代品，如草铵膦，与抗草铵膦作物品种结合，以帮助控制抗草甘膦杂草。本实验对A. palmeri植物暴露于0.55 kg ha-1草铵膦后存活。由于在采集地点没有使用草铵膦的记录，种群中植物的存活可能是由于选择之前的遗传表达;在杂草科学的正式说法中，这被描述为自然耐受性。在处理后24小时（HAT）收获来自草铵膦处理的和未处理的幼苗的叶组织用于RNA-Seq分析。使用Illumina DNA序列读数测量来自未处理和处理的存活（推测耐受，T）和易感（S）植物的全局基因表达。使用相同的植物来确定赋予对草铵膦的差异耐受性的机制。S植物积累的氨是T植物的两倍，24 HAT。草铵膦靶基因GS 2的相对拷贝数在T和S植物之间没有差异，在两种生物型中均具有1至3个GS 2拷贝。组装了由72，780个重叠群组成的参考cDNA转录组，其中65，282个序列进行了注释。来自转录组组装的GS 2序列不具有耐受植物所特有的多态性。567个基因在处理的T和S植物之间差异表达。在经处理的T植物中的上调基因中，210个比经处理的S植物中的上调基因被更高度地诱导。草铵膦耐受植物对ABC转运蛋白、谷胱甘肽S-转移酶（GST）、NAC转录因子、硝酸单加氧酶（NMO）、几丁质激发子受体激酶（CERK 1）、热休克蛋白83、乙烯转录因子、热应激转录因子、NADH-泛醌氧化还原酶、阿坝8 '-羟化酶和细胞色素P450基因（CYP 72 A、CYP 94 A1）的诱导作用更强。选择7个候选基因进行定量真实的时间PCR验证。虽然GST在至少一个群体中的处理的耐受植物中上调，但CYP 72 A219在所有处理的耐受生物型中一致高度表达。这些基因是对草铵膦产生耐受性的候选基因。总之，这些结果表明，在人口中的压力保护基因的差异诱导，可以使一些人生存除草剂的应用。解毒相关基因的高表达可以在具有持续选择压力的群体中得到固定，从而导致抗性的进化。或者，持续的选择压力可以选择具有相同结果的GS 2基因中的突变。
Amaranthus palmeri (Amaranthaceae) is a noxious weed in several agroecosystems and in some cases seriously threatens the sustainability of crop production in North America. Glyphosate-resistant Amaranthus species are widespread, prompting the use of alternatives to glyphosate such as glufosinate, in conjunction with glufosinate-resistant crop cultivars, to help control glyphosate-resistant weeds. An experiment was conducted to analyze the transcriptome of A. palmeri plants that survived exposure to 0.55 kg ha-1 glufosinate. Since there was no record of glufosinate use at the collection site, survival of plants within the population are likely due to genetic expression that pre-dates selection; in the formal parlance of weed science this is described as natural tolerance. Leaf tissues from glufosinate-treated and non-treated seedlings were harvested 24 h after treatment (HAT) for RNA-Seq analysis. Global gene expression was measured using Illumina DNA sequence reads from non-treated and treated surviving (presumably tolerant, T) and susceptible (S) plants. The same plants were used to determine the mechanisms conferring differential tolerance to glufosinate. The S plants accumulated twice as much ammonia as did the T plants, 24 HAT. The relative copy number of the glufosinate target gene GS2 did not differ between T and S plants, with 1 to 3 GS2 copies in both biotypes. A reference cDNA transcriptome consisting of 72,780 contigs was assembled, with 65,282 sequences putatively annotated. Sequences of GS2 from the transcriptome assembly did not have polymorphisms unique to the tolerant plants. Five hundred sixty-seven genes were differentially expressed between treated T and S plants. Of the upregulated genes in treated T plants, 210 were more highly induced than were the upregulated genes in the treated S plants. Glufosinate-tolerant plants had greater induction of ABC transporter, glutathione S-transferase (GST), NAC transcription factor, nitronate monooxygenase (NMO), chitin elicitor receptor kinase (CERK1), heat shock protein 83, ethylene transcription factor, heat stress transcription factor, NADH-ubiquinone oxidoreductase, ABA 8’-hydroxylase, and cytochrome P450 genes (CYP72A, CYP94A1). Seven candidate genes were selected for validation using quantitative real time-PCR. While GST was upregulated in treated tolerant plants in at least one population, CYP72A219 was consistently highly expressed in all treated tolerant biotypes. These genes are candidates for contributing tolerance to glufosinate. Taken together, these results show that differential induction of stress-protection genes in a population can enable some individuals to survive herbicide application. Elevated expression of detoxification-related genes can get fixed in a population with sustained selection pressure, leading to evolution of resistance. Alternatively, sustained selection pressure could select for mutation(s) in the GS2 gene with the same consequence.
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