Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice.

Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop-weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide-resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping-by-sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy-related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS-inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus-indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus-like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.

Insights into the genetic spatial structure of Nicaraguan weedy rice and control of its seed spread.

BACKGROUND: The genetic backgrounds and occurrence patterns of weedy rice (WR, Oryza sativa) are highly diverse, and so are the challenges facing its control among countries. WR control is difficult because it is similar to cultivated rice and manual removal is one of the few options for control. Understanding the ecology of WR will aid efforts to break its life cycle and establish long-term management strategies under both irrigated and rainfed systems. RESULTS: Nicaraguan WR (NWR) plants were genetically closer to the AUS and Indica pools in terms of to genetic distance. A map of admixture coefficients suggested a pattern of long-distance dispersal and spread of NWR across Nicaragua, which has likely been facilitated by commercial activities and sharing of harvesting equipment between border cities or important trading ports and inland regions. Moreover, the NWR plants from the soil seedbank in irrigated regions showed different habitats and lower grain number per panicle compared with plants spread by seed-mediated contamination. In addition, grain indexes showed that length-to-width ratio was a better indicator than awn length for distinguishing between NWR and Nicaraguan Indica cultivars. CONCLUSION: Analysis of the population structure and habitats of NWR revealed five clusters derived from seed-mediated contamination in rainfed upland regions, plants from the soil seedbank in irrigated double-cropping regions, and pollen-mediated contamination across both regions. Field weed management before harvesting and seed purification based on the length-to-width ratio can be conducted to improve the efficiency of long-term control of WR in Nicaragua. © 2022 Society of Chemical Industry.

Snorkeling Strategy: Tolerance to Flooding in Rice and Potential Application for Weed Management.

Flooding is an important strategy for weed control in paddy rice fields. However, terrestrial weeds had evolved mechanisms of tolerance to flooding, resulting in new 'snorkeling' ecotypes. The aim of this review is to discuss the mechanisms of flooding tolerance in cultivated and weedy rice at different plant stages and the putative utility of this trait for weed management. Knowledge about flooding tolerance is derived primarily from crop models, mainly rice. The rice model informs us about the possible flooding tolerance mechanisms in weedy rice, Echinochloa species, and other weeds. During germination, the gene related to carbohydrate mobilization and energy intake (RAmy3D), and genes involved in metabolism maintenance under anoxia (ADH, PDC, and OsB12D1) are the most important for flooding tolerance. Flooding tolerance during emergence involved responses promoted by ethylene and induction of RAmy3D, ADH, PDC, and OsB12D1. Plant species tolerant to complete submersion also employ escape strategies or the ability to become quiescent during the submergence period. In weedy rice, the expression of PDC1, SUS3, and SUB1 genes is not directly related to flooding tolerance, contrary to what was learned in cultivated rice. Mitigation of flooding tolerance in weeds could be achieved with biotechnological approaches and genetic manipulation of flood tolerance genes through RNAi and transposons, providing a potential new tool for weed management.

A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing.

PREMISE OF THE STUDY: We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. METHODS: A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. RESULTS: From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. DISCUSSION: We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought.