Herbicide-resistant Weedy Rice Research Articles

Gene flow and spontaneous mutations are responsible for imidazolinone herbicide-resistant weedy rice (Oryza sativa L.)

For more than two decades, weedy rice (Oryza sativa L.) has been controlled in rice fields by using imidazolinone (IMI) herbicide-resistant rice technology (Clearfield®). Outcrossing in weedy rice populations and spontaneous mutations are potential problems with herbicide-resistant crop management technologies, such as the IMI-resistant rice. The aim of this study was to characterize the mechanism of IMI herbicide resistance in weedy rice through dose-response bioassay study and evaluating amino acid substitutions in acetolactate synthase (ALS) protein. A total of 118 suspected IMI-resistant weedy rice samples, which survived in the field after an IMI herbicide application, were collected at harvest time from Türkiye in 2020 and 2021. Single-dose imazamox application experiment revealed that 38 plants survived herbicide treatment. The imazamox resistance of the surviving plants was confirmed by dose-response experiment. ALS gene region underwent a sanger DNA partial sequencing. No substitution was found in 10 samples, however, amino acid substitutions were found in 26 samples with S563N, one sample with S653T, and one sample with E630D. The S653N point is the same substitution point that serves as the origin of resistance for the Clearfield® rice varieties that are commonly cultivated in the region. It has been hypothesized that the gene flow from IMI-resistant rice may be the cause of resistance in the IMI resistant weedy rice samples with S653N. The other substitution, S653T, were considered spontaneous mutation to IMI resistance. Interestingly, the S653T mutation was detected for the first time in weedy rice. The mechanism of resistance of 10 resistant weedy rice was not confirmed in this study, however, it may be a non-target resistance or another mutation point in target site, but evidently, they did not acquire resistance by gene flow from IMI-resistant rice. It has been concluded that the effectiveness of IMI-resistant rice technology in controlling weedy rice has drastically decreased due to possible gene flow, spontaneous mutation and non-target resistance. In addition to cultural controls like clean seed, clean machinery and crop rotation, other herbicide-tolerant rice systems such as Provisia® and Roxy-RPS® rice are needed to create a diverse weedy rice management ensemble available for rice production and move towards sustainable rice farming.

Presence of the HPPD Inhibitor Sensitive 1 Gene and ALSS653N Mutation in Weedy Oryza sativa Sensitive to Benzobicyclon.

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha−1, SC formulation) at 30 days after treatment (DAT). Thirty-four percent of plants were homozygous for the HIS1 allele and 98% of these plants exhibited field tolerance. However, the his1 genotype did not always correlate with field data. Only 52% of his1 plants were considered sensitive, indicating that the single nucleotide polymorphisms (SNPs) chosen in the KASP assay are not a reliable tool in predicting his1 homozygous plants. In an additional experiment, 86% of the 344 plants with at least one copy of the ALSS653N trait harbored a HIS1 allele, suggesting fields infested with IMI herbicide-resistant weedy rice are unlikely to be controlled with benzobicyclon.

Cross-Resistance to Imazapic and Imazapyr in a Weedy Rice (Oryza sativa) Biotype Found in Malaysia

ABSTRACT: The Clearfield® rice production system is an effective management tool for weedy rice and other weeds in the direct-seeded rice culture. However, if farmers cultivating the Clearfield® rice disregard stewardship recommendations, the industry could face a problem of herbicide-resistant weedy rice which would occur through the selection of outcrosses. This study aimed to confirm imidazolinone-resistant weedy rice in Malaysia. The resistant weedy rice (R-WR) was found to be 67 fold more resistant to OnDuty® (premix of imazapic and imazapyr) than the susceptible weedy rice (S-WR) based on the GR50 values (rate that causes 50% inhibition of shoot growth). The Clearfield® rice cultivar was 32-fold more tolerant to OnDuty® than the S-WR. Furthermore, the R-WR was 54 and 89 fold more resistant to imazapic and imazapyr applied separately than the S-WR, respectively. The Clearfield® rice was 140- and 40-fold more tolerant to imazapic and imazapyr, respectively than the S-WR. The R-WR biotype was susceptible to non-selective herbicides glyphosate and glufosinate, as well as the selective graminicide quizalofop. Oxadiazon controlled the R-WR biotype, but pretilachlor was ineffective. The present study documented the first case of weedy rice that was cross-resistant to imazapic and imazapyr in Malaysian Clearfield® rice field.

Feral rice from introgression of weedy rice genes into transgenic herbicide-resistant hybrid-rice progeny

Pollen-mediated transgenic flow of herbicide resistance occurs bidirectionally between transgenic cultivated rice and weedy rice. The potential risk of weedy traits introgressing into hybrid rice has been underestimated and is poorly understood. In this study, two glufosinate-resistant transgenic rice varieties, hybrid rice (F1), and their succeeding generations (F2-F4) were planted for 3 years in field plots free of weedy rice adjacent to experimental weedy-rice fields. Weedy-rice-like (feral) plants that were both glufosinate-resistant and had red-pericarp seed were initially found only among the F3 generations of the two glufosinate-resistant transgenic hybrid cultivars. The composite fitness (an index based on eight productivity and weediness traits) of the feral progeny was significantly higher than that of the glufosinate-resistant transgenic hybrid (the original female parent of the feral progeny) under monoculture common garden conditions. The hybrid rice progeny segregated into individuals of variable height and extended flowering. The hybrid rice F2 generations had higher outcrossing rates by pollen reception (0.96-1.65%) than their progenitors (0.07-0.98%). The results show that herbicide-resistant weedy rice can rapidly arise by pollen-mediated gene flow from weedy to transgenic hybrid rice, and their segregating pollen-receptive progeny pose a greater agro-ecological risk than transgenic varieties. The safety assessment and management regulations for transgenic hybrid rice should take into account the risk of bidirectional gene flow.

Gene flow from single and stacked herbicide-resistant rice (Oryza sativa): modeling occurrence of multiple herbicide-resistant weedy rice.

Provisia™ rice (PV), a non-genetically engineered (GE) quizalofop-resistant rice, will provide growers with an additional option for weed management to use in conjunction with Clearfield® rice (CL) production. Modeling compared the impact of stacking resistance traits versus single traits in rice on introgression of the resistance trait to weedy rice (also called red rice). Common weed management practices were applied to 2-, 3- and 4-year crop rotations, and resistant and multiple-resistant weedy rice seeds, seedlings and mature plants were tracked for 15 years. Two-year crop rotations resulted in resistant weedy rice after 2 years with abundant populations (exceeding 0.4 weedy rice plants m-2 ) occurring after 7 years. When stacked trait rice was rotated with soybeans in a 3-year rotation and with soybeans and CL in a 4-year rotation, multiple-resistance occurred after 2-5 years with abundant populations present in 4-9 years. When CL rice, PV rice, and soybeans were used in 3- and 4-year rotations, the median time of first appearance of multiple-resistance was 7-11 years and reached abundant levels in 10-15 years. Maintaining separate CL and PV rice systems, in rotation with other crops and herbicides, minimized the evolution of multiple herbicide-resistant weedy rice through gene flow compared to stacking herbicide resistance traits. © 2017 Society of Chemical Industry.

Introgression of Clearfield™ rice crop traits into weedy red rice outcrosses

Studies were conducted to determine the impact of introgression of crop alleles into weedy rice populations. Seeds of 89 weedy rice accessions collected from Arkansas fields in 11 counties, with a history of Clearfield™ rice production, were planted in 2011 and sprayed twice with imazethapyr (0.071kg ai ha−1). Survivors were genotyped using an allele-specific PCR assay to detect the presence of resistance-endowing als mutations, S653N and G654E, in herbicide-resistant (HR) weedy rice that could have originated from Clearfield™ cultivars planted in the state. Hybridization between Clearfield™ rice and weedy rice was verified using four DNA markers RM 215, RM 220, and RM 234 microsatellites, and the and RID12 indel. Two to five HR plants, representing different plant types per accession per replication (698 plants total) were characterized for 16 morphological and biological traits. Seventy-nine percent of accessions were resistant to imazethapyr. The HR weedy rice plants carried the S653N mutation and were confirmed as outcrosses with Clearfield™ rice using DNA markers. Ten weedy rice accessions (nearly 25% of confirmed outcrosses) harbored multiple alleles from rice cultivars, indicating previous hybridization events with multiple cultivars or outcrossing with weedy rice. The majority of HR weedy rice accessions were similar to cultivated rice in height, culm angle, flag leaf length and width, days to flower, seed shattering and dormancy. Kernels of 20% of the parent weedy rice accessions were segregating for white and red bran color. Two of the parent weedy rice accessions with gold hull were homozygous for white bran and produced progenies with 100% white-bran kernels; thus, weedy rice was no longer exclusively red. Therefore, HR weedy rice outcrosses generally had acquired crop-like traits, which make it easier to deplete from the soil seedbank, but also difficult to scout.

Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil.

Several studies have expressed concerns about the effects of gene flow from transgenic herbicide‐resistant crops to their wild relatives, but no major problems have been observed. This review describes a case study in which what has been feared in transgenics regarding gene flow has actually changed biodiversity and people's lives. Nontransgenic imidazolinone‐resistant rice (IMI‐rice) cultivars increased the rice grain yield by 50% in southern Brazil. This increase was beneficial for life quality of the farmers and also improved the regional economy. However, weedy rice resistant to imidazolinone herbicides started to evolve three years after the first use of IMI‐rice cultivars. Population genetic studies indicate that the herbicide‐resistant weedy rice was mainly originated from gene flow from resistant cultivars and distributed by seed migration. The problems related with herbicide‐resistant weedy rice increased the production costs of rice that forced farmers to sell or rent their land. Gene flow from cultivated rice to weedy rice has proven to be a large agricultural, economic, and social constraint in the use of herbicide‐resistant technologies in rice. This problem must be taken into account for the development of new transgenic or nontransgenic rice technologies.

The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice.

The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.

Risk Assessment of Herbicide-Resistant Crops: A Latin American Perspective Using Rice (Oryza sativa) as a Model1

Herbicide-resistant crops (HRCs), particularly glyphosate-resistant soybean, are increasingly important in Latin America. Prior to commercial release of these crops, their short- and long-term risks should be thoroughly assessed. A risk assessment should include the identification and characterization of potential hazards and an estimation of the likelihood of these hazards occurring. For HRCs the agro-ecological hazards are mostly related to the occurrence of herbicide-resistant (HR) weeds and crop volunteers and the adverse effects from the use of pesticides within the agricultural area. Herbicide-resistant rice is used as a case study to visualize the key components of such a risk assessment. For this purpose, a model that simulates a typical rain-fed rice production system in Central America was developed. The model was used to investigate the selection of HR weedy rice populations under various scenarios. Scenarios included contrasting weed management practices, hybridization levels between the comme...