Conjoint Genome–Transcriptome Analysis to Identify the Conserved <i>ABCC3</i> Gene Involved in Glyphosate Resistance in <i>Lolium</i> spp.

Weeds in the <i>Lolium</i> genus, notably, <i>Lolium rigidum</i> and <i>Lolium multiflorum</i>, significantly threaten global crop yields and food production due to evolved glyphosate resistance from heavy reliance on this herbicide. However, the molecular basis for non-target site resistance (NTSR) remains unclear. Comprehensive genomic and transcriptomic analyses were performed on glyphosate-resistant and -susceptible biotypes of <i>L. rigidum</i> and <i>L. multiflorum</i> to identify key genes and regulatory networks linked to this resistance. Several key gene families were associated with herbicide detoxification: ABC transporters (ABCs), cytochrome P450s (CYP450s), aldo-keto reductases (AKRs), and glutathione <i>S</i>-transferases (GSTs). Notably, <i>ABCC3</i> emerged as a potential conserved NTSR gene in <i>Lolium</i> spp. Transgenic rice overexpressing <i>LrABCC3</i> exhibited enhanced glyphosate resistance, while candidate transcription factors potentially regulating <i>ABCC3</i> were identified, with LrB3 being validated to activate its promoter. This study identified <i>ABCC3</i> as the first conserved NTSR gene linked to glyphosate resistance in <i>Lolium</i> weeds.