Italian ryegrass (Lolium multiflorum; LOLMU) is one of the most troublesome weeds in temperate regions in the world. This weed species interfere with wheat, corn, rye, and oat, causing significant crop yield losses. This species has evolved glyphosate resistance, making it difficult to control. The mechanisms of glyphosate resistance are still unknown, and an understanding thereof will favor the development of new strategies of management. The present study is the first transcriptome study in LOLMU using glyphosate-resistant and -sensitive biotypes, aiming to identify and to provide a list of the candidate target genes related to glyphosate resistance mechanism. The transcriptome was assembled de novo, producing 87,433 contigs with an N50 of 740 bp and an average length of 575 bp. There were 92 and 54 up- and down-regulated genes, respectively, in the resistant biotype, while a total of 1683 were differentially expressed in the sensitive biotype in response to glyphosate treatment. We selected 14 highly induced genes and seven with repressed expression in the resistant biotype in response to glyphosate. Of these genes, a significant proportion were related to the plasma membrane, indicating that there is a barrier making it difficult for glyphosate to enter the cell.

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

Background: Rice, one of the main foods in Brazil and the world, is sensitive to chilling (0–15 °C), especially in the germination and reproductive stages. Chilling causes delayed germination and affects coleoptile elongation at the S3 stage (needlepoint), causing poor plant establishment, stunted growth, and non-vigorous plants, also impacting weed management. Elucidating the mechanisms responsible for resilience under cold conditions helps the development of tolerant cultivars. Transcription factors (TFs) act in stress response signaling, making them indispensable in the tolerance mechanism. Objective: Thus, this study aimed to identify and characterize the expression profile of transcription factors in the response to chilling stress in rice at the germination stage. Methods: To determine the transcriptional profile of 2408 genes belonging to 56 TF families, RNAseq was performed on the shoot tissue of seedlings of Oro (chilling-tolerant) and Tio Taka (chilling-sensitive) genotypes grown under control conditions (25 °C) and chilling stress (13 °C) until the S3 stage. Results: Of the total genes analyzed, 22% showed significant differential expression in the analyzed cultivars. There were 117 genes that showed significant differential expression in the tolerant cultivar, 60 of which were downregulated and 57 upregulated. In the sensitive cultivar, 248 genes had a significant differential expression, of which 98 genes were downregulated and 150 genes were upregulated. A total of 170 genes encoding TFs were commonly and significantly differentially expressed in the tolerant and sensitive genotypes. Conclusions: Here, we revealed potential new targets involved in the regulation of chilling stress in rice at the S3 stage.