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SUMMARY The repeated evolution of high seed shattering during multiple independent de‐domestications of cultivated Asian rice (Oryza sativa) into weedy rice (Oryzaspp.) is a prime example of convergent evolution. Weedy rice populations converge in histological features of the abscission zone (AZ), a crucial structure for seed abscission, while ancestral cultivated rice populations exhibit varied AZ morphology and levels of shattering. However, the genetic bases of these phenotypic patterns remain unclear. We examined the expression profiles of the AZ region and its surrounding tissues at three developmental stages in two low‐shattering cultivars ofausandtemperate japonicadomesticated groups and in two genotypes of their derived high‐shattering weed groups, Blackhull Awned (BHA) and Spanish Weedy Rice (SWR), respectively. Consistent with the greater alteration of AZ morphology during the de‐domestication of SWR than BHA, fewer genes exhibited a comparable AZ‐region exclusive expression pattern between weed and crop in thetemperate japonicalineage than in theauslineage. Transcription factors related to the repression of lignin and secondary cell wall deposition, such as,OsWRKY102andOsXND‐1‐like, along with certain known shattering genes involved in AZ formation, likely played a role in maintaining AZ region identity in both lineages. Meanwhile, most genes exhibiting AZ‐region exclusive expression patterns do not overlap between the two lineages and the genes exhibiting differential expression in the AZ region between weed and crop across the two lineages are enriched for different gene ontology terms. Our findings suggest genetic flexibility in shaping AZ morphology, while genetic constraints on AZ identity determination in these two lineages. 

ABSTRACT Weedy rice is a close relative of cultivated rice (Oryza sativa) that infests rice fields worldwide and drastically reduces yields. To combat this agricultural pest, rice farmers in the southern US began to grow herbicide‐resistant (HR) rice cultivars in the early 2000s, which permitted the application of herbicides that selectively targeted weedy rice without harming the crop. The widespread adoption of HR rice coincided with increased reliance on hybrid rice cultivars in place of traditional inbred varieties. Although both cultivated and weedy rice are predominantly self‐fertilising, the combined introductions of HR and hybrid rice dramatically altered the opportunities and selective pressure for crop‐weed hybridization and adaptive introgression. In this study, we generated genotyping‐by‐sequencing data for 178 weedy rice samples collected from across the rice growing region of the southern US; these were analysed together with previously published rice and weedy rice genome sequences to determine the recent genomic and population genetic consequences of adaptive introgression and selection for herbicide resistance in US weedy rice populations. We find a reshaped geographical structure of southern US weedy rice as well as purging of crop‐derived alleles in some weed strains of crop‐weed hybrid origin. Furthermore, we uncover evidence that related weedy rice strains have made use of different genetic mechanisms to respond to selection. Lastly, we identify widespread presence of HR alleles in both hybrid‐derived and nonadmixed samples, which further supports an overall picture of weedy rice evolution and adaptation through diverse genetic mechanisms. 

Abstract The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages. 

Abstract One of the common mechanisms to trigger plant innate immunity is recognition of pathogen avirulence gene products directly by products of major resistance (R) genes in a gene for gene manner. In the USA, theRgenes,Pik-s, PiKh/m, andPi-ta, Pi-39(t), andPtrgenes have been effectively deployed to prevent the infections ofM. oryzaeraces, IB49, and IC17 for some time.Pi-9is only recently being deployed to provide overlapped and complimentary resistance toMagnaporthe oryzaeraces IB49, IC17 and IE1k in the USA. Pi-ta, Pi-39(t), Pi9 are major nuclear binding site-leucine rich (NLR) proteins, and Ptr is an atypical R protein with 4 armadillo repeats. AlphaFold is an artificial intelligence system that predicts a protein 3D structure from its amino acid sequence. Here we report genome sequence analyses of the effectors and avirulence (AVR) genes,AVR-PitaandAVR-Pik, andAVR-Pi9, in 3 differentialM. oryzaeraces. Using AlphaFold 2 and 3 we find strong evidence of direct interactions of products of resistance genesPi-taandPikwithM. oryzaeavirulence (AVR) genes,AVR-PitaandAVR-Pikrespectively. We also found that AVR-Pita interacts with Pi-39(t) and Ptr, and Pi9 interacts with both AVR-Pi9 and AVR-Pik. Validation of direct interactions of two pairs of R and AVR proteins supported a direct interaction mechanism of plant innate immunity. Detecting interaction of both Ptr and Pi39(t) with AVR-Pita, and Pi-9 with both AVR-Pi9 and AVR-Pik, revealed a new insight into recognition of pathogen signaling molecules by these host R genes in triggering plant innate immunity. 

Abstract High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative. 

Abstract Weedy rice (Oryzaspp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved fromauscultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL‐seq approach that combines bulked segregant analysis and high‐throughput whole genome resequencing to map the three important weediness traits in an F₂population derived from a cross between BHA weedy rice with an ancestralauscultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop,indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor–descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa. 

Abstract Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21^stcentury introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance geneALS, but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States. 

Societal Impact StatementWeedy plants are a major constraint on agricultural productivity. Weedy rice is a weed that invades rice fields worldwide and is responsible for reductions in rice yields. Studies to date have detected multiple independent weedy rice origins in different parts of the world. We investigated the origin of weedy rice in Spain and Portugal and found that it has evolved from a cultivated rice variety group grown locally. Iberian weeds carry mutations that reverse domesticated pericarp color to its ancestral red color. Our results imply that management strategies are needed to prevent the evolution of troublesome weeds from cultivated ancestors. SummaryWeedy rice, a damaging conspecific weed of cultivated rice, has arisen multiple times independently around the world. Understanding all weedy rice origins is necessary to create more effective weed management strategies. The origins of weedy rice in Spain and Portugal, where there are no nativeOryzaspecies, are unknown. In this study, we try to identify the likely ancestors of Iberian weedy rice and the mechanisms involved in the evolution of two weedy traits, seed shattering, and red pericarps.We used genotyping by sequencing to understand the origin of Iberian weedy rice and its relationship to other weedy, wild, and cultivated rice groups worldwide. We also genotyped candidate genes for shattering and pericarp color.We find that weedy rice in the Iberian Peninsula has primarily evolved through de‐domestication oftemperate japonicacultivars, with minor origins from exotic weedy rice. Iberian weeds have evolved the capacity to shatter seeds via novel loci and have acquired red pericarps via compensatory mutations in theRcdomestication gene. Our results suggest the Iberian weeds have experienced selection at multiple locations in the genome to establish as weeds, likely targeting male fertility genes among other functions.Our characterization of Iberian weedy rice adds to the growing evidence that de‐domestication of cultivated rice varieties is the main source of weedy rice worldwide. Their evolutionary versatility explains why weedy rice continues to be one of the most problematic weeds of cultivated rice. 

Abstract Two mapping populations were developed from crosses of the Asianindicarice (Oryza sativaL.) cultivar ‘Dee Geo Woo Gen’ (DGWG; PI 699210 Parent, PI 699212 Parent) and two weedy rice ecotypes, an early‐flowering straw hull (SH) biotype AR‐2000‐1135‐01 (PI 699209 Parent) collected in Arkansas and a late‐flowering black hull (BHA) biotype MS‐1996‐9 (PI 699211 Parent) collected in Mississippi. The weed and crop‐based rice recombinant inbred line (RIL) mapping populations have been used to identify genomic regions associated with weedy traits as well as resistance to sheath blight and rice blast diseases. The mapping population consists of 185 (DGWG/SH; Reg. no. MP‐9, NSL 541035 MAP) and 234 (BHA/DGWG; Reg. no. MP‐10, NSL 541036 MAP) F₈RILs, of which 175 (DGWG/SH) and 224 (BHA/DGWG) were used to construct two linkage maps using single nucleotide polymorphic markers to identify weedy traits, sheath blight, and blast resistance loci. These mapping populations and related datasets represent a valuable resource for basic rice evolutionary genomic research and applied marker‐assisted breeding efforts in disease resistance. 

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have greatly advanced the genetic analysis of blast resistance. To date, approximately 122 blast-resistance genes have been identified, with 39 of these genes cloned and molecularly characterized. The application of these findings in marker-assisted selection (MAS) has significantly improved rice breeding, allowing for the efficient integration of multiple resistance genes into elite cultivars, enhancing both the durability and spectrum of resistance. Pangenomic studies, along with AI-driven tools like AlphaFold2, RoseTTAFold, and AlphaFold3, have further accelerated the identification and functional characterization of resistance genes, expediting the breeding process. Future rice blast disease management will depend on leveraging these advanced genomic and computational technologies. Emphasis should be placed on enhancing computational tools for the large-scale screening of resistance genes and utilizing gene editing technologies such as CRISPR-Cas9 for functional validation and targeted resistance enhancement and deployment. These approaches will be crucial for advancing rice blast resistance, ensuring food security, and promoting agricultural sustainability.