Because cropping systems can greatly affect the establishment and spread of alien species populations, the design of cropping systems to control invasive weeds is an important approach for invasive species management in agro-ecosystems to avoid excessive increases in other control measures such as herbicides. The annual weed Phalaris minor Retz. (P. minor) is one of the most troublesome invasive weed species of winter crops in Yunnan Province, China, but the development of cropping systems for ecological control of this weed have received limited research attention. Here, we studied seed dormancy, germination characteristics and reproductive responses of P. minor to various cropping systems to show how cropping systems could be better designed to control P. minor in China. Our research showed that cropping systems significantly affected seed dormancy in submerged paddy fields. Phalaris minor seed remained dormant and the germination rates (less than 10%) were significantly lower (p < 0.05) than in maize fields and dry, bare soil conditions. Wheat, faba bean and rapeseed crops had no significant influence (p < 0.05) on the seed germination rate of P. minor, but increasing soil depth significantly decreased (p < 0.05) the germination rate and germination index of this weed. Total biomass, spike biomass, spike number and seed number of P. minor were significantly reduced (p < 0.05) with increasing proportions of the three crops (wheat, faba bean and rapeseed), with rapeseed having the strongest inhibition effects among the three crops. The reproductive allocation and reproductive investment of P. minor were also significantly reduced (p < 0.05) in mixed culture with wheat and rapeseed. With increasing proportions of wheat or rapeseed, the specific leaf area of P. minor significantly increased (p < 0.05), but the reverse was true for leaf area and specific leaf weight. Moreover, the net photosynthetic rate, stomatal conductance and transpiration rate for P. minor also decreased significantly (p < 0.05) when grown with wheat or rapeseed. These results suggest that optimal cropping systems design could involve planting rapeseed in conjunction with deep plowing and planting rice (continuous submergence underwater) in summer. Such a system could reduce the field populations and seed bank of P. minor, thus providing a sustainable and environmentally friendly means of suppressing P. minor.

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is among the oldest known bacterial diseases found for rice in Asia. It is the most serious bacterial disease in many rice growing regions of the world. A total of 47 resistance (R) genes (Xa1 to Xa47) have been identified. Nonetheless, these R genes could possibly be defeated to lose their qualitative nature and express intermediate phenotypes. The identification of sources of novel genetic loci regulating host plant resistance is crucial to develop an efficient control strategy. Wild ancestors of cultivated rice are a natural genetic resource contain a large number of excellent genes. Medicinal wild rice (Oryza officinalis) belongs to the CC genome and is a well-known wild rice in south China. In this study, O. officinalis was crossed with cultivated rice HY-8 and their hybrids were screened for BB resistance genes deployed through natural selection in wild rice germplasm. The molecular markers linked to R genes for BB were used to screen the genomic regions in wild parents and their recombinants. The gene coding and promoter regions of major R genes were inconsistently found in O. officinalis and its progenies. Oryza officinalis showed resistance to all thirty inoculated Xoo strains with non-availability of various known R genes. The results indicated the presence of novel genomic regions for BB resistance in O. officinalis. The present study not only provides a reference to investigate medicinal rice for R gene(s) identification against BB but also identified it as a new breeding material for BB resistance.

Using crops to control invasive weeds is an important approach for the long-term management of invasive species in agroecosystems. Nitrogen application can improve the yield and quality of crops, but may shift interactions of invasive weeds and crops, potentially affecting grass control ability. To explore the yield of a crop and its control efficacy of invasive weed under different nitrogen conditions, we studied the competitive effects of the high-value crop rapeseed (Brassica napus L.) on growth and photosynthetic characteristics of invasive species littleseed canarygrass in the field experiments. The results showed that the rapeseed yield and its control efficacy on littleseed canarygrass were significantly affected (p < 0.05) under different N regimes, and the control efficacy of littleseed canarygrass by rapeseed increased first and then decreased with the increase of basal nitrogen rates, while increasing topdressing N rates increased control efficacy of littleseed canarygrass by rapeseed. In fact, yield and weed control efficacy of rapeseed was most ideal when both basal and topdressing N was 90 kg·ha⁻¹. We also found that N significantly impacted the competitive ability of rapeseed toward littleseed canarygrass, and rapeseed had the highest competitive ability when both basal and topdressing N was 90 kg·ha⁻¹. With the increase of basal nitrogen rates, competitive balance index (CB) of rapeseed increased initially but decreased beyond an optimal level. CB continually increased with increasing topdressing N rates. Our research also showed level and period of N application had a significant effect (p < 0.01) on the photosynthetic rate (Pn) and chlorophyll content (Chl) of both rapeseed and littleseed canarygrass. Under the same N application regime, the Pn and Chl of littleseed canarygrass were higher than that of rapeseed in December, while the Pn and Chl of rapeseed was higher than that of littleseed canarygrass in February. Our study indicated that photosynthetic characteristics of rapeseed and littleseed canarygrass in different growth stages differ in their sensitivity to N regimes, creating a dynamic competitive relationship. Together, our results demonstrated that optimal application of fertilizer N could help rapeseed produce higher yields and greater weed control efficacy, suggesting that future modeling or experimental studies on utilizing crops to control invasive weeds should carefully consider both timing and placement of N.

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes’ expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.

Endophytic bacteria play crucial roles in plant pathogen protection and growth. Oryza eichingeri is a unique wild rice species rich with genetic resources. Studies have explored beneficial endophytic bacteria and investigated the synergistic interaction between microbes and wild rice. However, the endophytic bacterial community of Oryza eichingeri and their plant growth-promoting (PGP) abilities characteristics remain largely unknown. Here, endophytic bacteria in the root, stem, and leaf tissues of Oryza eichingeri were characterized using metagenomic Illumina 16S rRNA gene sequencing. Additionally, culturable endophytic bacteria were isolated. The metagenomic analysis showed that, compared to those in other tissue compartments, the endophytic bacterial community in the roots had a more complex structure and enhanced functions, and each compartment had its own specific endophytic bacterial biomarkers. A total of 94 endophytic bacteria were isolated from Oryza eichingeri, among which 80 strains possessed PGP traits including increasing phosphate solubilization, siderophore production, IAA production, and nitrogen fixation. These strains displayed good PGP effects on cultivated rice seedlings, promoting the formation of strong root systems, stimulating biomass accumulation, and increasing root length and plant height. These findings provide insights into the composition of the bacterial endosphere of Oryza eichingeri and potential applications of the dominant PGP bacteria in rice cultivation.

Background/Objectives: Bacterial blight (BB) represents one of the most devastating diseases threatening global rice production. Exploring and characterizing disease resistance (R) genes provides an effective strategy for controlling BB and enhancing rice resilience. Common wild rice (Oryza rufipogon) serves as a valuable reservoir of genetic diversity and disease resistance resources. In this study, we identified and functionally characterized a novel NLR gene, YPR1, from common wild rice (Oryza rufipogon), which exhibited significant spatial, temporal, and tissue-specific expression patterns. Methods: Using a combination of conventional PCR, RT-PCR, bioinformatics, transgenic analysis, and CRISPR/Cas9 gene-editing approaches, the full-length YPR1 sequence was successfully cloned. Results: The gene spans 4689 bp with a coding sequence (CDS) of 2979 bp, encoding a 992-amino acid protein. Protein domain prediction revealed that YPR1 is a typical CNL-type NLR protein, comprising RX-CC_like, NB-ARC, and LRR domains. The predicted molecular weight of the protein is 112.43 kDa, and the theoretical isoelectric point (pI) is 8.36. The absence of both signal peptide and transmembrane domains suggests that YPR1 functions intracellularly. Furthermore, the presence of multiple phosphorylation sites across diverse residues implies a potential role for post-translational regulation in its signal transduction function. Sequence alignment showed that YPR1 shared 94.02% similarity with Os09g34160 and up to 96.47% identity with its closest homolog in the NCBI database, confirming that YPR1 is a previously unreported gene. To verify its role in disease resistance, an overexpression vector (Ubi–YPR1) was constructed and introduced into the BB-susceptible rice cultivar JG30 via Agrobacterium tumefaciens-mediated transformation. T₁ transgenic lines were subsequently inoculated with 15 highly virulent Xanthomonas oryzae pv. oryzae (Xoo) strains. The transgenic plants exhibited strong resistance to eight strains (YM1, YM187, C1, C5, C6, T7147, PB, and HZhj19), demonstrating a broad-spectrum resistance pattern. Conversely, CRISPR/Cas9-mediated knockout of YPR1 in common wild rice resulted in increased susceptibility to most Xoo strains. Although the resistance of knockout lines to strains C7 and YM187 was comparable to that of the wild type (YP^WT), the majority of knockout plants exhibited more severe symptoms and significantly lower YPR1 expression levels compared with YP^WT. Conclusions: Collectively, these findings demonstrate that YPR1 plays a crucial role in bacterial blight resistance in common wild rice. As a novel CNL-type NLR gene conferring specific resistance to multiple Xoo strains, YPR1 provides a promising genetic resource for the molecular breeding of BB-resistant rice varieties.