A Two-in-One Strategy: Target and Nontarget Site Mechanisms Both Play Important Role in IMI-Resistant Weedy Rice.

The introduction of Clearfield technology allows the use of imidazolinone (IMI) herbicides to control weedy rice. Imidazolinone herbicides stop the acetolactate synthase (ALS) enzyme from synthesizing branched-chain amino acids, resulting in the death of the plant. Since the launch of Clearfield technology in Malaysia in 2010, many farmers have replaced traditional cultivars with Clearfield (CL) rice lines (MR220-CL1 and MR220-CL2). This technology was initially effective; however, in recent years, local farmers have reported the reduced efficacy of IMI herbicides in controlling the spread of weedy rice. Under IMI herbicide treatment, in previous weedy rice studies, the target-site resistance (TSR) mechanism of the ALS gene has been suggested as a key factor conferring herbicide resistance. In our study, a combination of ALS gene sequencing, enzyme colorimetric assay, and a genome-wide association study (GWAS) highlighted that a non-target-site resistance (NTSR) can be an alternative molecular mechanism in IMI-resistant weedy rice. This is supported by a series of evidence, including a weak correlation between single nucleotide polymorphisms (SNPs) within the ALS exonic region and ALS enzyme activity. Our findings suggest that the adaptability of weedy rice in Clearfield rice fields can be more complicated than previously found in other rice strains.

Impact of volunteer rice infestation on yield and grain quality of rice.

BACKGROUND: Volunteer rice (Oryza sativa L.) grains may differ in physicochemical traits from cultivated rice, which may reduce the quality of harvested rice grain. To evaluate the effect of volunteer rice on cultivated rice, fields were surveyed in Arkansas in 2012. RESULTS: Cropping history that included hybrid cultivars in the previous two years (2010 and 2011) had higher volunteer rice infestation (20%) compared with fields planted previously with inbred rice (5.5%). The total grain yield of rice was reduced by 0.4% for every 1% increase in volunteer rice density. The grain quality did not change in fields planted with the same cultivar for three years. Volunteer rice density of at least 7.6% negatively impacted the head rice and when infestation reached 17.7%, it also reduced the rice grain yield. The protein and amylose contents of rice were not affected until volunteer rice infestation exceeded 30%. CONCLUSION: Crop rotation systems that include hybrid rice are expected to have higher volunteer rice infestation than systems without hybrid rice. It is predicted that, at 8% infestation, volunteer rice will start to impact head rice yield and will reduce total yield at 18% infestation. It could alter the chemical quality of rice grain at >30% infestation. © 2016 Society of Chemical Industry.

One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L. )

Background Weedy rice (Oryza sativa L.) is a noxious form of cultivated rice (O. sativa L.) associated with intensive rice production and dry seeding. A cost-efficient strategy to control this weed is the Clearfield rice production system, which combines imidazolinone herbicides with mutant imidazolinone-resistant rice varieties. However, imidazolinone resistance mutations can be introgressed in weedy rice populations by natural outcrossing, reducing the life span of the Clearfield technology. Timely and accurate detection of imidazolinone resistance mutations in weedy rice may contribute to avoiding the multiplication and dispersion of resistant weeds and to protect the Clearfield system. Thus, highly sensitive and specific methods with high throughput and low cost are needed. KBioscience's Allele Specific PCR (KASP) is a codominant, competitive allele-specific PCR-based genotyping method. KASP enables both alleles to be detected in a single reaction in a closed-tube format. The aim of this work is to assess the suitability and validity of the KASP method for detection in weedy rice of the three imidazolinone resistance mutations reported to date in rice. Results Validation was carried out by determining the analytical performance of the new method and comparing it with conventional allele-specific PCR, when genotyping sets of cultivated and weedy rice samples. The conventional technique had a specificity of 0.97 and a sensibility of 0.95, whereas for the KASP method, both parameters were 1.00. Conclusions The new method has equal accuracy while being more informative and saving time and resources compared with conventional methods, which make it suitable for monitoring imidazolinone-resistant weedy rice in Clearfield rice fields.

Spread of herbicide-resistant weedy rice (red rice, Oryza sativa L.) after 5 years of Clearfield rice cultivation in Italy.

The weedy relative of cultivated rice, red rice, can invade and severely infest rice fields, as reported by rice farmers throughout the world. Because of its close genetic relationship to commercial rice, red rice has proven difficult to control. Clearfield (Cl) varieties, which are resistant to the inhibiting herbicides in the chemical group AHAS (acetohydroxyacid synthase), provide a highly efficient opportunity to control red rice infestations. In order to reduce the risk of herbicide resistance spreading from cultivated rice to red rice, stewardship guidelines are regularly released. In Italy, the cultivation of Cl cultivars started in 2006. In 2010, surveillance of the possible escape of herbicide resistance was carried out; 168 red rice plants were sampled in 16 fields from six locations containing Cl and traditional cultivars. A first subsample of 119 plants was analysed after herbicide treatment and the resistance was found in 62 plants. Of these 119 plants, 78 plants were randomly selected and analysed at the level of the AHAS gene to search for the Cl mutation determining the resistant genotype: the Cl mutation was present in all the resistant plants. Nuclear and chloroplast microsatellite markers revealed a high correlation between genetic similarity and herbicide resistance. The results clearly show that Cl herbicide-resistant red rice plants are present in the field, having genetic relationships with the Cl variety. Finding plants homozygous for the mutation suggests that the crossing event occurred relatively recently and that these plants are in the F2 or later generations. These observations raise the possibility that Cl red rice is already within the cultivated rice seed supply.