De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like’ forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication.

Polypogon fugax is a common winter weed in China and other Asia countries. We have previously found a P. fugax biotype (R) resistant to acetyl co-enzyme A carboxylase (ACCase) herbicides also cannot be effectively controlled by some acetolactate synthase (ALS) herbicides. This study evaluated the level of resistance to four ALS herbicides (metsulfuron-methyl, chlorsulfuron, monosulfuron, pyribambenz isopropyl) in the R biotype and the associated resistance mechanism. The R biotype exhibited moderate level of resistance to metsulfuron-methyl (6.0-fold) compared with the sensitive biotype (S). Sequence analysis of ALS gene revealed that two ALS genes existed in P. fugax. However, no substitution associated with ALS resistance mechanism were found in ALS genes between the S and R biotypes. The activity of ALS enzyme isolated from the R biotype was inherently higher and less sensitive to metsulfuron-methyl than the S biotype. Glutathione S-transferases (GST) activity was also less sensitive to metsulfuron-methyl in the R than as the S biotypes. Malathion, a cytochrome P450 (CYP) monooxygenase inhibitor, had much greater synergistic effect with metsulfuron-methyl on the R than as the S plants, reducing the ED₅₀ value (herbicide dose to inhibit growth by 50%) of metsulfuron-methyl by 23- and 6-fold, respectively, suggesting that CYP mediated enhanced metabolism might contribute to the resistance to ALS herbicides. These results suggest that metsulfuron-methyl resistance in the R biotype was associated with the up-regulated ALS enzymatic activity and the GST and CYP-mediated enhanced herbicide metabolism.

Bipolaris eleusines was mixed with herbicides to improve the control of barnyardgrass (Echinochloa crus-galli), a noxious weed in rice fields. The compatibility of B. eleusines with herbicides was evaluated for toxic effects on spore germination and mycelium growth in vitro tests, and varied effects were observed with different chemical products. Briefly, 25 g/L penoxsulam OD plus 10% bensulfuron-methyl WP were much more compatible with B. eleusines, and there was no inhibition of spore germination but the promotion of mycelium growth of B. eleusines at all treatment rates. Under greenhouse conditions, the coefficient of the specificity of B. eleusines conidial agent was determined as 3.91, closer to the herbicidal control of 2.89, showing it is highly specific between rice and barnyardgrass. Field experiments in 2011 and 2012 showed that B. eleusines conidial agent displayed good activity on barnyardgrass, monochoria [Monochoria vaginalis (Burm.f.) Presl. Ex Kunth.], and small-flower umbrella sedge (Cyperus difformis L.) and had no negative impact on the rice plant. It also reduced the loss of rice yield when compared with the non-treated control and could make this pathogen a conidial agent for commercial bioherbicidal development in the future.

Echinochloa crus-galli (L.) P. Beauv (common name: barnyard grass) is a major weed in rice-growing areas and has evolved resistance to multiple herbicides. Florpyrauxifen-benzyl (trade name Rinskor) is a novel synthetic auxin herbicide that was approved in China in 2017 and is widely used in rice production to control resistant weeds, including barnyard grass. We identified a florpyrauxifen-benzyl-resistant E. crus-galli biotype with a resistance index (RI) of 11.89 using screen house herbicide experiments. To understand the phytotoxicity mechanisms of florpyrauxifen-benzyl, we used transcriptomics technologies to compare the gene expression profiles of florpyrauxifen-benzyl treatment on phytohormone transduction between florpyrauxifen-benzyl-resistant and -susceptible barnyard grasses (Echinochloa crus-galli (L.) P. Beauv). A total of 1810 DEGs were identified in the S comparison setting (FTS vs. UTS), and 915 DEGs were identified in the R comparison setting (FTR vs. UTR); 464 genes overlapped between the two comparison groups. Approximately sixty-nine hormone-related DEGs were detected after treatment with florpyrauxifen-benzyl in both R and S biotypes. At 24 h after florpyrauxifen-benzyl treatment, compared with the R biotype, the S biotype showed a stronger auxin response and higher expression of related genes involved in ethylene and abscisic acid biosynthesis and signal transduction. In addition, a brassinolide receptor gene was upregulated after florpyrauxifen-benzyl treatment and had higher expression in the S biotype than in the R biotype. This study is the first transcriptome analysis of the differential effects of florpyrauxifen-benzyl treatment between florpyrauxifen-benzyl-resistant and -susceptible E. crus-galli. It reflects the difference in phytohormone biosynthesis and signal transduction between R and S barnyard grasses in response to florpyrauxifen-benzyl treatment and will be helpful for understanding the phytotoxicity mechanisms of florpyrauxifen-benzyl.