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Herbicide Resistance: Mechanisms, Inheritance, and Molecular Genetics

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Target-site Based Resistance

Target-site mutations have been identified in weeds resistant to herbicides that inhibit Photosystem II (PSII), microtubule assembly, and the enzymes, acetolactate synthase (ALS), acetyl-CoA carboxylase (ACCase) and 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. Most often there is a point mutation responsible for resistance. This is a change in one nuleotide in the DNA sequence of the gene that results in a single amino acid change in the protein target site. The shape of the site where the herbicide binds is changed so the herbicide can no longer bind. The plants with the mutation will not be affected by the herbicide. Although many weed species are resistant to the same herbicide, resistance may not be due to the same mutation.


Target Site Resistance Animation

Photosystem II Resistance

Triazine, phenylurea, and uracil herbicides inhibit photosynthesis by binding to the D1 protein and blocking transport of the electrons to the plastoquinone in Photosystem II. (For more detailed information on PSII herbicide mode of action Click Here)

Although all of these herbicides inhibit PSII, the binding sites for different families vary slightly so a single mutation will not provide resistance to PSII inhibitors. In resistant weeds, there is a mutation in the psbA gene that codes for the D1 protein. This mutation prevents the binding of the herbicides.

Photosystem II Resistance Animation

In most species, the resistance is due to a change in one amino acid of the D1 protein where glycine is substitued for serine at position 264. The mutation provides resistance to symmetrical triazine herbicides but not to other herbicides that inhibit PS II.

An isoleucine for Val219 substitution in Poa annua was responsible for resistance to the phenylurea, diuron, and to metribuzin (an asymmetrical triazine). In Portulaca oleacea a Ser264 to threonine substitution provided resistance to the phenylurea, linuron, and to the symmetrical triazine herbicide families.

Target-site based resistance to the PSII inhibitors is maternally inherited because the mutation is encoded by chloroplast DNA. Maternal inheritance decreases the movement of the resistance trait because it is not moved with pollen. The mutation reduces the efficiency of photosynthesis in resistant plants, which results in reduced fitness.

Microtubule Assembly Resistance

Dinitroanaline herbicides, such as prodiamide, oryzalin, and trifluralin, bind to tubulin and block the formation of microtubules, which are important in cell division. There are two types of tubulin, α and β. In dinitroanaline-resistant plants, there is a point mutation in the gene that encodes α-tubulin. The mutation either changes the target-site so the herbicides can no longer bind or it changes the interaction between the α- and β-tubulins, which affect microtubule formation. Dinitroanaline resistance has been reported to be controlled by a single, recessive nuclear gene. This is in contrast to most reports of herbicide resistance being controlled by a dominant or semi-dominant gene. Since the dinitroanaline resistance trait is recessive, it will take longer for it to build up in the population because only homozygous recessive plants will be resistant to the herbicide. In the following tables (Punnett Squares), the shaded cells are the plants that would survive herbicide treatment. If the gene is dominant then 3 of 4 plants would survive treatment, where as if the gene is recessive only 1/4 of the plants would survive.

Dominant Gene

  R r
r Rr rr


Recessive Gene
  R r
r Rr rr

ALS Resistance

The 5 different chemical families that inhibit ALS are the imidazolinones (IMI), pyrimidinylthiobenzoates (PTB), sulfonylaminocarbonyltriazolinones (SCT), sulfonylureas (SU), and triazolopyrimidines (TP). Most commercially available herbicides in these families belong to either the IMIs or the SUs. ALS is the first common enzyme in the biochemical pathway that produces the branched chain amino acids.

Multiple mutations are responsible for ALS resistance. For example, mutations in the gene that encodes ALS which result in any one of five different amino acids changes will result in resistance to the ALS inhibitors. The particular mutation determines to which ALS inhibitor family the weed will be resistant. For example, a change in Pro197 provides high resistance to the sulfonylurea herbicides but not to the imidazolinone herbicides. A substitution at Ala122 results in resistance to only the imidazolinone herbicides. A Trp591 mutation provides resistance to both classes of herbicides. It is possible to have more than one mutation in the ALS gene which provides a greater level of resistance to multiple ALS inhibitor families. The different resistance patterns for ALS inhibitors suggest that the binding sites for the different families of herbicides are not identical but rather they bind to different areas of the herbicide binding site. For more information on mutations responsible for ALS inhibitor resistance see Tranel, P.J., Wright, T.R, and Heap, I.M. ALS mutations from herbicide-resistant weeds. Available

Resistance to the ALS inhibitors has been reported to be controlled by a single, dominant or semi-dominant, nuclear encoded gene. The inheritance of the trait is not influenced by the particular mutation. Heterozygous (Rr) plants often are injured by the application of an ALS inhibitor but they do not die. Since the trait is nuclear-encoded, the resistance gene will move with pollen. Unlike Photosystem II resistance, plants resistant to the ALS inhibitors do not have reduced fitness. Therefore, the resistant populations build up quickly.

ACCase Resistance

There are two herbicide chemical families, aryloxyphenoxypropionates (AOPP) and cyclohexanediones (CHD), that bind to ACCase, an enzyme that is found in chloroplasts. ACCase catalyses the first committed step of fatty acid biosynthesis. The molecular mechanism of ACCase inhibition has not yet been determined. These herbicides kill monocot weeds but do not affect dicot weeds. The ACCase of dicots is not sensitive to inhibition from the herbicides.

The herbicides are in these two families are structurally different but may have overlapping binding sites since the binding of a herbicide from one class prevents binding of a herbicide from the other class. It is also possible that once a herbicide from one class binds, the structure of ACCase could be changed and the binding site for the other herbicide class would be modified so it could no longer bind. It has been difficult to predict cross-resistance patterns between the AOPP and CHD herbicides. A plant with resistance to either the AOPP or CHD herbicides may or may not be resistant to herbicides in the same family.

A point mutation has been identified in the ACCase-resistant grasses, Alopecurus myosuroides, Lolium rigidum, and Setaria viridis. In Setaria viridis, the substitution of leucine for isoleucine provided resistance to sethoxydim, a CHD. The substitution was in chloroplastic ACCase at position 1780.

Inheritance of the resistant trait is controlled by a single, semi-dominant gene. In most cases, effects of the resistance trait on fitness have not been evaluated.


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