Research Article: Mutations in the plastidic ACCase gene endowing resistance to ACCase-inhibiting herbicide in Phalaris minor populations from India

Date Published: January 5, 2016

Publisher: Springer Berlin Heidelberg

Author(s): Nishu Raghav, Rajender Singh, Rajender Singh Chhokar, Davinder Sharma, Raman Kumar.


Littleseed canarygrass (Phalaris minor Retz.) is one of the most common and troublesome weeds infesting wheat crop in India. Repeated use during the last two decades of the ACCase-inhibiting herbicide (clodinafop) to control this weed has resulted in the occurrence of resistance. Fifty-three P. minor populations were collected from wheat fields in Haryana and Punjab states of India. The dose–response assays indicated that 29 populations were resistant, 23 populations were susceptible and one population was moderately resistant to clodinafop. Sequence analysis of the CT domain of ACCase gene among resistant and susceptible populations revealed two non-synonymous mutations, Trp2027 to Cys and Ile2041 to Asn in the resistant populations. Allele-specific PCR markers were developed to differentiate between wild-type and resistant codons at positions 2027 and 2041 of ACCase in P. minor which enables molecular assays for rapid detection and resistance diagnosis for efficient weed management in wheat. This is the first report from India of a target site mutation corresponding to resistance to clodinafop in P. minor.

Partial Text

Littleseed canarygrass (Phalaris minor Retz.) is the most dominant winter season weed in wheat and widely distributed in wheat growing regions of the world. This weed has been reported from Macronesia to Mediterranean, Irano-Turanic and Saharo-Sindic regions, eastern and South Africa, North and South America, Australia and the Far East (Singh et al. 1999). In India, it is the major weed of the north-western and eastern Indo-Gangetic Plains (Chhokar and Sharma 2008). Up until the early 1990s, P. minor was effectively controlled by isoproturon, a substituted urea herbicide, but after long period of continuous and heavy spraying along with poor application rates, spray techniques and timing led to the evolution of isoproturon resistance in P. minor (Malik and Singh 1995; Chhokar and Malik 2002). In 1997–1978, four alternative herbicides (sulfosulfuron, clodinafop, fenoxaprop and tralkoxydim) were recommended for its control and the majority of farmers accepted clodinafop due to excellent crop safety and efficacy against this weed. The excessive dependence on clodinafop resulted in evolution of weed resistance against this herbicide. At present, this weed has evolved multiple herbicide resistance across three modes of actions: photosynthesis at the photosystem II site A, acetyl CoA carboxylase and acetolactate synthase inhibition (Chhokar and Sharma 2008). Herbicide resistance in weeds is an evolutionary process and its dynamics and impact are dependent on several factors such as genetics and biology of weeds along with herbicidal, operational and other biological components (Powels and Yu 2010). There are currently 418 unique cases (species x site of action) of herbicide-resistant weeds globally, with 224 species (129 dicots and 95 monocots). Weeds have evolved resistance to 21 of the 25 known herbicide sites of action and to 149 different herbicides. Herbicide-resistant weeds have been reported in 73 crops in 61 countries (Heap 2014).

The variable crop phytotoxicity to clodinafop treatments were observed in the weed populations. The resistant populations were not affected by recommended dose (X dose) of clodinafop (60 g/ha), whereas susceptible populations were effectively controlled by ½ X dose (30 g/ha) of clodinafop (Table 2). The dose–response assays indicated that 29 populations were resistant, 23 populations were susceptible and one population was moderately resistant to clodinafop.Table 2Response of various populations of P. minor to clodinafopVisual phytotoxicity (%)Clodinafop (30 g/ha)Clodinafop (60 g/ha)0–25–H-14, H-15, H-16, H-17, H-19, H-20, H-21, H-22, H-26, H-28, H-31, H-34, H-40, P-5, P-12, P-17, P-38, P-49, P-54, P-75, P-76, G-8, G-21, G-29, G-34, G-43, N-5, N-8, N-926–50–H-1351–75––76–100H-8, H-23, H-27, H-68, P-8, P13, P-14, P-26, P-30, P-35, P-43, P-60, P-63, P-69, G-2, G-6, G-18, G-39, G-40, G-42, G-46, G-47, N-4–

The continuous adoption of rice–wheat cropping system in wheat growing regions has led to the problem of Phalaris minor as a troublesome weed of wheat causing yield reductions. Reliable, fast, simple detection of herbicide resistance is necessary for farmers to adopt timely alternative herbicide application strategies to prevent further spread of herbicide-resistant weeds. DNA-based diagnostic markers have the advantage of quickly detecting resistant plants compared with conducting pot assays, which are time and space consuming, and labor intensive. The primary aim of the study was to find the mutations in CT domain of plastidic ACCase gene conferring herbicide resistance in P. minor. The allele-specific PCR marker developed based on SNP will help in identification clodinafop-resistant and susceptible populations.




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