Transcriptomics analysis of the flowering regulatory genes involved in the herbicide resistance of Asia minor bluegrass (Polypogon fugax)

Comprehensive insights into herbicide resistance mechanisms in weeds: a synergistic integration of transcriptomic and metabolomic analyses

Omics techniques, including genomics, transcriptomics, proteomics, and metabolomics have smoothed the researcher's ability to generate hypotheses and discover various agronomically relevant functions and mechanisms, as well as their implications and associations. With a significant increase in the number of cases with resistance to multiple herbicide modes of action, studies on herbicide resistance are currently one of the predominant areas of research within the field of weed science. High-throughput technologies have already started revolutionizing the current molecular weed biology studies. The evolution of herbicide resistance in weeds (particularly via non-target site resistance mechanism) is a perfect example of a complex, multi-pathway integration-induced response. To date, functional genomics, including transcriptomic and metabolomic studies have been used separately in herbicide resistance research, however there is a substantial lack of integrated approach. Hence, despite the ability of omics technologies to provide significant insights into the molecular functioning of weeds, using a single omics can sometimes be misleading. This mini-review will aim to discuss the current progress of transcriptome-based and metabolome-based approaches in herbicide resistance research, along with their systematic integration.

Overexpression of AGAMOUS-like gene PfAG5 promotes early flowering in Polypogon fugax

Herbicides are the major tool for controlling large populations of yield depleting weeds. However, over-reliance on herbicides has resulted in weed adaptation and herbicide resistance. In recent years, early flowering weed species related to herbicide resistance is emerging, which may cause seed loss before crop harvest, creating a new problem for non-chemical weed management. In this study, a homologue gene of AGAMOUS sub-family (referred to as PfAG5) of the MADS-box family was cloned from plants of an early flowering Polypogon fugax Nees ex Steud. population resistant to the ACCase inhibitor herbicide (clodinafop-propargyl). The PfAG5 gene was functionally characterised in Arabidopsis thaliana L. Overexpression of the PfAG5 gene in Arabidopsis resulted in early flowering, abnormal flowers (e.g. small petals), short plants and reduced seed set, compared with the wild type. The expression of the PfAG5 gene was high in leaves and flowers, but low in pods in transgenic Arabidopsis. The PfAG5 gene was expressed earlier and higher in the resistant (R) than the susceptible (S) P. fugax plants. Furthermore, one protein (FRIGIDA-like) with relevance to flowering time regulation and interacts with PfAG5 in resistant (R) P. fugax was identified by the yeast two-hybrid and pull-down assays. These results suggest that the PfAG5 gene is involved in modulating early flowering in P. fugax.

Comparative Transcriptome Analysis Revealing the Different Germination Process in Aryloxyphenoxypropionate-Resistant and APP-Susceptible Asia Minor Bluegrass (Polypogon fugax)

Herbicide-resistant mutations are predicted to exhibit fitness cost under herbicide-free conditions. Asia minor bluegrass (Polypogon fugax) is a common weed species in the winter crops. Our previous study established a P. fugax accession (LR) resistant to aryloxyphenoxypropionate (APP) herbicides, which also exhibited germination delay relative to the susceptible accession (LS). A comparative transcriptome was conducted to analyze the gene expression profile of LS and LR at two germination time points. A total of 11,856 and 23,123 differentially expressed genes (DEGs) were respectively identified in LS and LR. Most DEGs were involved in lipid metabolism, carbohydrate metabolism, amino acid metabolism, and secondary metabolites biosynthesis. Twenty-four genes involved in carbohydrate and fatty acid metabolism had higher relative expression levels in LS than LR during germination. Nine genes involved in gibberellin (GA) and abscisic acid (ABA) signal transduction showed different expression patterns in LS and LR, consistent with their different sensitivity to exogenous hormones treatments. This study first provided insight into transcriptional changes and interaction in the seed germination process of P. fugax. It compared the differential expression profile between APP herbicides resistance and susceptible accessions during germination, which contributed to understanding the association between herbicide resistance and fitness cost.

StMADS11 Subfamily Gene PfMADS16 From Polypogon fugax Regulates Early Flowering and Seed Development

The evolution of herbicide resistance in weedy plants leads to various adaptation traits including flowering time and seed germination. In our previous studies, we found an association of the early flowering phenotype with the ACCase inhibitor herbicide resistance genotype in a population of Polypogon fugax. MADS-box transcription factors are known to play pivotal roles in regulating plant flowering time. In this study, a SHORT VEGETATIVE PHASE (SVP)-like gene, belonging to the StMADS11 subfamily in the MADS-box family, was cloned from the early flowering P. fugax population (referred to as PfMADS16) and resistant to the herbicide clodinafop- propargyl. Overexpression of the SVP-like gene PfMADS16 in Arabidopsis thaliana resulted in early flowering and seed abortion. This is consistent with the phenotypic characters of resistant P. fugax plants, but contrary to the conventional role of SVP-like genes that usually suppress flowering. In addition, down regulation of the seed formation gene AtKTN1 in flowers of PfMADS16 transgenic Arabidopsis plants indicates that PfMADS16 may be indirectly associated with seed viability. Furthermore, one protein (PfMADS2) from the APETALA1 (AP1) subfamily interacting with PfMADS16 in P. fugax was identified with relevance to flowering time regulation. These results suggest that the PfMADS16 gene is an early flowering regulation gene associated with seed formation and viability in resistant P. fugax population. Our study provides potential application of PfMADS16 for integrated weed management (such as genetic-based weed control strategies) aiming to reduce the soil weed seedbank.