Abstract
To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two Zea mays L. lines traditionally bred in Poland. To overcome the complexity of the maize genome, two sequencing technologies were employed: Illumina and Single Molecule Real-Time (SMRT) PacBio. Eleven thousand structural variants, 4 million SNPs and approximately 800 thousand indels differentiating the two genomes were identified. Detailed analyses allowed to identify 20 variations within the EPSPS gene, but all of them were predicted to have moderate or unknown effects on gene expression. Other genes of the shikimate pathway encoding bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase and chorismate synthase were altered by variants predicted to have a high impact on gene expression. Additionally, high-impact variants located within the genes involved in the active transport of glyphosate through the cell membrane encoding phosphate transporters as well as multidrug and toxic compound extrusion have been identified.
Highlights
Maize (Zea mays L.) originates from Mexico and has adapted to a climate with high temperatures and high light intensity during the day and moderate temperatures at night [1]
In the face of increasing demands imposed by the impact of climate change and by a growing world population such improvement becomes necessity nowadays
The presented results from the sequencing of two maize inbred lines give us insight into the molecular pathways that may be potentially involved in the glyphosate tolerance trait
Summary
Maize (Zea mays L.) originates from Mexico and has adapted to a climate with high temperatures and high light intensity during the day and moderate temperatures at night [1]. Because of its high productivity, importance for food and feed production, and numerous industrial applications, maize has become one of the most important crop species worldwide; it is grown over a wide range of latitudes [2,3]. As a thermophilic plant, when grown in nonoptimal conditions, maize encounters environmental stresses and it is crucial to minimize the competition for water, light, and minerals [4] that occurs between maize seedlings and weeds growing in the field. The easiest way to eradicate weeds is the application of herbicides. One of the most popular and widely used (in the cultivation of maize and crops in general) herbicides of high economic value and effectiveness against a wide range of weeds is the nonselective foliar-applied Roundup® [5,6]. Glyphosate, the active ingredient in Roundup® , has its primary effect via the inhibition of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19) [7], an enzyme involved in one of the reactions in the shikimate pathway, Plants 2020, 9, 523; doi:10.3390/plants9040523 www.mdpi.com/journal/plants
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