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.

Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

“…Additionally, two out of seven genes in the shikimate pathway were differentially methylated as a result of the herbicide stress. Herein, we did not detect changes in the methylation pattern in genes encoding shikimate pathway enzymes; however, previous changes in the coding sequences of two shikimate pathways enzymes (bifunctional 3-dehydroquinate dehydratase/ shikimate dehydrogenase and chorismate synthase) in the two tested Z. mays lines (TL and SL) were detected (Mahmoud et al 2020).…”

“…Previously, it was shown that herbicidal stress influences miRNA expression (Żywicki et al 2015) and that some of the traits related to herbicide resistance may be encoded in the genome (Mahmoud et al 2020). Here, we focused our efforts on analyzing the influence of herbicidal stress on changes in DNA methylation in the same two Z. mays lines, which are differentially susceptible to the systemic herbicide Roundup®.…”

“…mays lines were chosen based on the results of field tests conducted to verify the response of 25 Z. mays inbred lines to Roundup® stress (K. Adamczewski, data not published). Based on these tests, we chose the S79757 line (sensitive to Roundup®, SL) as it showed the most prominent response to herbicide stress and the S245 line (tolerant to Roundup®, TL) as one of the most resistant (Supplementary Figure 1 in Mahmoud et al (2020)). When the highest concentration of herbicide (Roundup® 360 SL) was used (300 g, 1.0 l/ha), the level of injuries to the TL variety was 40%, while it reached 85% in the SL 3 weeks after the application of the herbicide (rating is done based on phenotypic analyses of leaf chlorosis and wilting, inhibition of plant growth) (K. Adamczewski, data not published).…”

“…Seeds from both lines were obtained from a local breeder (HR Smolice, Poland). The same two lines were used in the analyses described in Mahmoud et al (2020) and Żywicki et al (2015).…”

“…The seedlings were grown in a greenhouse in controlled temperature (22 o C), humidity, and light conditions (16 h/8 h-light/dark) (Mahmoud et al 2020;Żywicki et al 2015). Uniform seedlings from both lines were selected and divided into two groups: one was sprayed with the herbicide Roundup® (1.0 l/ha, 300 g glyphosate) with adjuvant AS 500 SL (4.0 l/ha) 2 weeks after plants' emergence (at the stage of 4-5 leaves), and the other (control) group was cultured without the herbicide treatment.…”