Crop production faces major challenges, including climate change, biodiversity loss, and global food insecurity, with the need to produce more food under increasingly difficult climatic conditions without negatively impacting ecosystems. Weeds are plants that have adapted to cropping systems despite intensive management efforts over centuries. We propose that weeds possess novel and useful sources of genetic variation that can be used to improve crops for abiotic and biotic stress tolerance. We discuss the potential advantages and disadvantages associated with this approach and outline the interdisciplinary research that will be necessary to successfully identify and utilize this genetic diversity to improve crops. Although the concept of utilizing weedy traits in crops has been put forward previously, recent advances in weed genomics resources, bioinformatics tools to identify the genetic basis of adaptive traits, and genome editing methods now combine to make this approach more feasible.

Bacterial blight (BB), caused by Xanthomonas oryzae pathovar oryzae (Xoo), is a major rice disease in Asia and Africa. Xoo possesses virulence factors for pathogenicity and race differentiation that complicate resistance breeding of rice. The availability of 48 BB resistance (R) genes (Xa/xa) portends the selection of R genes for broad and durable resistance. To establish durable resistance, understanding the pathogen virulence spectrum and host resistance mechanisms is required. This review examines the global distribution and diversity of Xoo populations, highlights the different resistance mechanisms of 15 Xa/xa genes, and identifies the three effective resistance genes for 24 countries. The review proposes strategies for durable, broad-spectrum resistance to BB.

Rhizoctonia solani is a necrotrophic fungus that causes sheath blight (ShB) in rice, resulting in substantial yield losses. A major challenge in managing this disease is the lack of fully resistant rice varieties. While some germplasms show partial resistance, the underlying mechanisms remain poorly understood. In this study, we used quantitative proteomics to investigate host-pathogen interactions and identify differentially abundant proteins (DAPs) in response to R. solani infection. Label-free quantitative proteomics (LC-MS/MS) was employed to compare the proteomes of the moderately resistant variety CR 1014 and the susceptible variety Swarna-Sub1, revealing 753, 681, 680, and 992 differentially abundant proteins (DAPs) at 12, 24, 48, and 72 h post-infection, respectively. Our results indicate that CR 1014 exhibits enhanced redox homeostasis, with a significant upregulation of reactive oxygen species (ROS)-scavenging proteins, such as peroxidases and glutathione S-transferases, compared to Swarna-Sub1. CR 1014 also demonstrated robust activation of carbohydrate metabolism, the phenylpropanoid pathway, and the quinate pathway-key processes involved in lignification and the synthesis of defense-related compounds. Additionally, pathogenesis-related proteins, such as chitinases and PR10 family members, were strongly induced in CR 1014, reinforcing its heightened defense response. In contrast, Swarna-Sub1 showed an insufficient induction of key defense enzymes like phenylalanine ammonia-lyase and chorismate mutase. Furthermore, its susceptibility was reflected in impaired photosynthesis and fatty acid metabolism. These findings provide valuable insights into the proteomic landscape of rice during R. solani infection and highlight potential targets for improving ShB resistance. This study establishes a framework for understanding the molecular mechanisms underlying resistance and susceptibility to this destructive pathogen.

In August 2021, bacterial leaf blight-like symptoms were observed on 14 out of 570 rice genotypes (Oryza sativa) in research field plots of global rice germplasm grown in Arkansas (eXtra Figure S1. A & B). The disease was characterized by spreading lesions on leaves, panicle sterility and reduced yield in highly susceptible, mature rice germplasm. No spread of disease to nearby plants was observed. Isolations were performed at Colorado State University, where soakates from symptomatic leaves were spread onto nutrient agar. After 72 h at 28°C, uniform, distinct, yellow-colored bacterial colonies were observed. To screen for the presence of common rice bacterial pathogens, PCR amplification directly from colonies or from DNA isolated from symptomatic field-collected leaves was performed. Primers specific for Xanthomonas oryzae pvs. oryzae and oryzicola (Lang et al., 2010), Burkholderia glumae (Echeverri-Rico et al., 2021), and Pseudomonas fuscovaginae (Ash et al., 2014) did not amplify indicating these organisms were not present. Sequencing of 16S rRNA gene (Weisburg et al., 1991) amplicons suggested the bacteria belonged to the genera Pantoea and Sphingomonas (NCBI accession no. OP683332 and OP683333, respectively). Amplicons resulting from primers specific to the gyrB gene region of P. ananatis (Kini et al., 2021) were sequenced and the fragment was compared to the P. ananatis PA13 reference genome using a BLAST analysis. One candidate (AR358) showed 100% identity with the P. ananatis gyrB region. Primers specific for Sphingomonas sp. (Bangratz et al., 2020) confirmed the second candidate (AR359) as a Sphingomonas sp. The identity of P. ananatis was confirmed by the Plant Pathogen Confirmatory Diagnostics Laboratory (Beltsville, MD, USA). To determine pathogenicity, leaves from 7-day-old seedlings of rice (Oryza sativa) cultivar Kitaake were scissor-clip inoculated (Kauffman et al., 1973) with four different treatments and compared to control leaves inoculated with sterile water. Treatments for the experiment consisted of bacterial suspensions (108 CFU/ml) of the two candidate organisms, P. ananatis (strain AR358) or Sphingomonas sp. (strain AR359), individually or in a 1:1 ratio of P. ananatis:Sphingomonas sp., or soakate from infected field tissue. Lesions similar to those observed in the field were only detected on leaves inoculated with P. ananatis or infected field tissue soakate at 7-days post-inoculation (eXtra Figure S1. C). Bacteria were recovered from the leaves of the artificially inoculated seedlings from three treatments (P. ananatis, P. ananatis:Sphingomonas sp. and soakate from the infected field tissue) and were determined to be P. ananatis based on colony morphology, amplification of 16s rRNA, and gyrB sequence data. Our results confirm the pathogenicity of P. ananatis to rice and fulfill Koch's postulates. P. ananatis was also recovered from several similarly diseased rice breeding lines at the University of Arkansas System Division of Agriculture Rice Research and Extension Center. We conclude that P. ananatis is the causal pathogen for leaf blight-like symptoms observed in the global rice cultivars grown in Arkansas. P. ananatis was previously reported as a pathogen on rice in several rice growing regions, including China (Yu et al., 2021), India (Reshma et al., 2022), and Africa (Kini et al., 2017), however, this is the first report of P. ananatis as a pathogen of rice in the United States.

Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host–pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science–policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems. In this Review, Singh et al. explore the impact of future climate scenarios on plant pathogen burden and biogeography, their interaction with the plant microbiome and the consequences on plant disease and productivity in different ecosystems. They propose different approaches to ensure long-term global food security.

AbstractIntroductionCitrus greening (aka Huanglongbing, HLB) caused primarily by the bacterial pathogenCandidatusLiberibacter asiaticus (CLas) has devastating effects on the global citrus industry. Agricultural management‐induced changes in microbial communities are hypothesised to contribute toward HLB resistance by reducing pathogen titre and increasing root and soil health. However, we have a limited understanding of the impacts of management practices on the soil microbiome, making the extent of HLB management uncertain.Material and MethodsHere we investigated the effect of agricultural management practices on reducingCLas titer via changes in rhizosphere‐associated bacterial communities. Rhizosphere and root samples were collected from two sites in Florida where different management practices (e.g., metalized reflective mulch ground covers, compost application and microbial inoculations) are currently being implemented to prevent HLB. Management‐induced changes in the rhizosphere bacterial community were assessed using amplicon sequencing. qPCR assays were used to quantify the titer of the pathogenCLas in roots. In addition, we measured soil properties and the activities of microbial enzymes involved in soil nutrient cycling.ResultsOur results indicated that certain management practices lead to shifts in the community structure of rhizosphere bacterial communities that negatively interact with the HLB pathogen. Management practices improved soil quality and reducedCLas titer. Additionally, we found that Actinobacteria were frequently enriched in the successful treatment sites, suggesting that Actinobacteria taxa could be indicators for HLB suppression properties in the soil.ConclusionOur results suggest that microbiome manipulation, either through changes in the management practices or microbial amendment, can increase the suppressive potential of soils, resulting in the reduction inCLas titer and potentially leading to HLB suppression in citrus groves.

Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for ...Read More

Biotic stresses, including diseases, severely affect rice production, compromising producers' ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.

Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the main concerns for rice production in the Americas since bacterial infection can interfere with the grain-filling process and under severe conditions can result in high sterility. B. glumae has been detected in several rice-growing areas of Colombia and other countries of Central and Andean regions in Latin America, although evidence of its involvement in decreasing yield under these conditions is lacking. Analysis of different parameters in trials established in three rice-growing areas showed that, despite BPB presence, severity did not explain the sterility observed in fields. PCR tests for B. glumae confirmed low infection in all sites and genotypes, only 21.4% of the analyzed samples were positive for B. glumae. Climate parameters showed that Montería and Saldaña registered maximum temperature above 34°C, minimum temperature above 23°C, and Relative Humidity above 80%, conditions that favor the invasion model described for this pathogen in Asia. Our study found that in Colombia, minimum temperature above 23°C during 10 days after flowering is the condition that correlates with disease incidence. Therefore, this correlation, and the fact that Montería and Saldaña had a higher level of infected samples according to PCR tests, high minimum temperature, but not maximum temperature, seems to be determinant for B. glumae colonization under studied field conditions. This knowledge is a solid base line to design strategies for disease control, and is also a key element for breeders to develop strategies aimed to decrease the effect of B. glumae and high night-temperature on rice yield under tropical conditions.

Harnessing plant-associated microbiomes offers an invaluable strategy to help agricultural production become more sustainable while also meeting growing demands for food, feed, and fiber. A plethora of interconnected interactions among the host, environment, and microbes, occurring both above- and below-ground, drive recognition, recruitment, and colonization of plant-associated microbes, resulting in activation of downstream host responses and functionality. Dissecting these complex interactions by integrating multi-omic approaches, high-throughput culturing, and computational and synthetic biology advances is providing deeper understanding of the structure and function of native microbial communities. Such insights are paving the way towards development of microbial products as well as microbiomes engineered with synthetic microbial communities capable of delivering agronomic solutions. While there is a growing market for microbial-based solutions to improve crop productivity, challenges with commercialization of these products remain. The continued translation of plant-associated microbiome knowledge into real-world scenarios will require concerted transdisciplinary research, cross-training of a next generation of scientists, and targeted educational efforts to prime growers and the general public for successful adoption of these innovative technologies.

Prime editing is an adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase fusion and a guide RNA amended with template and primer binding site sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of prime editing in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for prime editing in dicots as well as monocots, their validation in Nicotiana benthamiana , rice, and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.

Summary Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae ( Xoo ), on cultivated rice varieties. Fundamental to this pathogens’ virulence is transcription activator‐like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor‐effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo . To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi‐parent advanced generation inter‐cross (MAGIC) population. Of 18 QTL revealed by genome‐wide association studies and interval mapping analysis, six were specific to Tal7b (qBB‐ tal7b ). Overall, 150 predicted Tal7b gene targets overlapped with qBB‐ tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b‐specific QTL, qBB‐ tal7b ‐8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor‐effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.

To more sustainably mitigate the impact of crop diseases on plant health and productivity, there is a need for broader spectrum, long-lasting resistance traits. Defense response (DR) genes, located throughout the genome, participate in cellular and system-wide defense mechanisms to stave off infection by diverse pathogens. This multigenic resistance avoids rapid evolution of a pathogen to overcome host resistance. DR genes reside within resistance-associated quantitative trait loci (QTL), and alleles of DR genes in resistant varieties are more active during pathogen attack relative to susceptible haplotypes. Differential expression of DR genes results from polymorphisms in their regulatory regions, that includes cis-regulatory elements such as transcription factor binding sites as well as features that influence epigenetic structural changes to modulate chromatin accessibility during infection. Many of these elements are found in clusters, known as cis-regulatory modules (CRMs), which are distributed throughout the host genome. Regulatory regions involved in plant-pathogen interactions may also contain pathogen effector binding elements that regulate DR gene expression, and that, when mutated, result in a change in the plants' response. We posit that CRMs and the multiple regulatory elements that comprise them are potential targets for marker-assisted breeding for broad-spectrum, durable disease resistance.