Dataset Information

Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance.

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.

SUBMITTER: Mahmoud M

PROVIDER: S-EPMC7238182 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance.

Mahmoud Medhat M Gracz-Bernaciak Joanna J Żywicki Marek M Karłowski Wojciech W Twardowski Tomasz T Tyczewska Agata A

Plants (Basel, Switzerland) 20200418 4

To study genetic variations between genomes of plants that are naturally tolerant and sensitive to glyphosate, we used two <i>Zea mays</i> 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 ...[more]

PMID: 32325671

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Project description:Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance.

Dataset Information

Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance.

Publications

Identification of Structural Variants in Two Novel Genomes of Maize Inbred Lines Possibly Related to Glyphosate Tolerance.

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