Table 2.
The candidate gene list for involvement in glyphosate-resistance mechanisms in Lolium multiflorum obtained from differential expression analysis from RNA-seq in glyphosate-resistant (GR) and glyphosate-sensitive (GS) biotypes in response to glyphosate treatment. The fold-change ratio represents the ratio of the gene expression between GR/GS biotypes in response to glyphosate treatment ((GRt1/GRt0)/(GSt1/GSt0)).
| Contig ID | Uniprot ID | Functional Annotation—Gene | Putative Localization | 1 Log2 FC GR t1/t0 | 1 Log2 FC GS t1/t0 | Fold-Change GR/GS * |
|---|---|---|---|---|---|---|
| Upregulated Genes | ||||||
| DN140736_c3_g2 | Q9STT5 | ABC transporter A family member 7-ABCA7 | Multi-pass membrane protein | 4.8 | 1.9 | 2.5 |
| DN134601_c1_g3 | P53832 | Cell wall integrity and stress response-WSC2 | Plasma membrane | 6.6 | 4.5 | 1.4 |
| DN140896_c3_g3 | Q8GZ17 | COBRA-like protein 7-COBL7 | Cell membrane | 4.6 | 2.8 | 1.7 |
| DN138383_c1_g1 | A0A3B6IQ15 | Fe2OG dioxygenase domain-containing protein | Unknown | 4.0 | 2.4 | 1.7 |
| DN112601_c0_g2 | Q39111 | Gibberellin 20 oxidase 2-GA20OX2 | Unknown | 4.9 | 0.6 | 8.7 |
| DN137545_c0_g2 | P52409 | Glucan endo-1,3-beta-glucosidase-GLC1 | Component of plasma membrane | 3.7 | 2.3 | 1.6 |
| DN130084_c1_g4 | M0Y4P1 | Glycosyltransferase UDP UGT13248 | Intracellular-membrane-bound | 3.5 | 2.7 | 1.3 |
| DN125138_c7_g3 | Q7XT97 | Glycosyltransferase UDP 79 UGT79 | Intracellular-membrane-bound | 3.8 | 2.9 | 1.3 |
| DN123097_c0_g1 | A0A3B6PNF9 | Glycosyltransferase | Unknown | 4.8 | 2.7 | 1.8 |
| DN111587_c0_g1 | P82977 | Subtilisin-chymotrypsin inhibitor-WSCI | Extracellular region or secreted | 5.9 | 3.7 | 1.6 |
| DN135754_c1_g1 | Q9MAX3 | Sulfate transporter 1.2 | Multi-pass membrane protein | 3.6 | 2.1 | 1.7 |
| DN120520_c4_g4 | P69326 | Ubiquitin | Nucleus and cytoplasm | 6.3 | 3.4 | 1.8 |
| DN123915_c1_g2 | P0CH35 | Ubiquitin-60S ribosomal protein L40-2 Ub-CEP52-2 | Nucleus and cytoplasm | 6.4 | N/A | 6.4 |
| DN141149_c4_g5 | A0A3B6THG7 | Uncharacterized protein | Integral component of membrane | 4.9 | 0.5 | 9.9 |
| Downregulated Genes | ||||||
| DN134059_c0_g2 | A0A3B6MSN4 | DAO domain-containing protein | Unknown | −3.1 | −1.2 | 2.5 |
| DN119890_c0_g2 | P17816 | Glycine-rich cell wall structural protein-GRP | Cell wall | −4.5 | −2.0 | 2.2 |
| DN137034_c0_g1 | A0A3B5Y7P6 | RNA polymerase sigma factor | Chloroplast | −2.9 | −1.3 | 2.2 |
| DN136212_c1_g1 | P27626 | Senescence-associated protein-DIN1 | Unknown | −5.2 | N/A | 5.2 |
| DN134440_c0_g3 | Q41558 | Transcription factor-HBP-1b(c1) | Nucleus | −3.5 | −1.5 | 2.4 |
| DN124989_c0_g4 | W5D4P6 | Uncharacterized protein-TRAES_3BF019300240CFD_c1 | Unknown | −5.4 | N/A | 5.4 |
| DN127114_c0_g3 | Q9LPN5 | Vacuolar protein sorting-associated-VPS60-1 | Endosome | −4.1 | −2.1 | 2.0 |
1 Positive numbers indicate upregulated genes, whereas negative numbers indicate downregulated genes in response to glyphosate treatment using the log2 FC criteria (numbers <1 and >0 will be negative). * The fold-change results were significant by the F test (p ≤ 0.05). The results of differential expression were filtered using the thresholds of false discovery rate (FDR) and p-value set at ≤0.05, as well as log2 FC of ≥2 for upregulated and ≤−2 for downregulated genes. N/A indicates gene expression not detected. t0 = without glyphosate treatment; t1 = with glyphosate treatment at 24 h after treatment. Two biotypes originating from the same geographical region (São Valentin, RS, Brazil) were used, one GR and the other GS.