Population genetic analysis of pyrethroid resistant grain aphid (Sitobion avenae) using high resolution microsatellite markers



Pyrethroid spray failures were first noted in cereal crops in June 2011 for some populations of the grain aphid (S. avenae). Samples of grain aphids were analysed for evidence of resistance and were shown to have a gene mutation that is associated with reduced sensitivity to pyrethroids (knockdown resistance, kdr). This was confirmed with bioassays showing a Resistance Factor of ~40. Additional testing of suction traps and field specimens found the resistance mechanism was reasonably widespread in the English grain aphid population.

Testing English grain aphid samples for the kdr mutation was funded by HGCA in 2012 and in 2013 the work was expanded to include samples from Scottish suction traps. The 2013 work was co-funded by AHDB Potatoes, as research on virus vectors of potyviruses, such as PVY, had shown that grain aphids are a more efficient vector of the viruses than previously thought. (See Project R428).

Molecular assays were also developed to determine the population structure of grain aphids. In the UK, grain aphids can develop sexually as well as asexually. This is distinct from the well understood insecticide-resistant aphid, the peach–potato aphid, Myzus persicae, which is thought to exist as a series of distinct asexual clones. It is possible that pyrethroid resistant grain aphids consist of one or a few clones however, it is also possible that the resistance gene has spread into grain aphids with many different genetic backgrounds. A better understanding of the situation will help interpret the spread of pyrethroid resistance in UK grain aphid populations.

Testing of samples of grain aphids from English and Scottish suction traps continued during summer 2014 with AHDB Potatoes funding. 


James Hutton Institute (JHI), Rothamsted Research (RRes)


Results 2013

In 2013, the frequency of the kdr mutation in grain aphid samples from the English suction traps was similar to that recorded in 2012. The frequency of the mutation varied between English sites in 2013 from 0% (at Starcross) to a maximum of just over 50% (at Kirton). Kirton consistently showed the highest frequency of the kdr mutation which may reflect a higher pyrethroid selection pressure in that area.

The frequency of the mutation in Scottish grain aphid samples was overall lower than in the English population and was  8% and 27% in the Edinburgh and Dundee traps, respectively, in 2013.

A subset of the grain aphid samples tested for the presence of the kdr mutation was also tested to understand their genetic make-up. If a genotype appears more than once during the analysis, this is considered as evidence of a clone (resulting from asexual reproduction). If a particular genotype appears to be unique then this suggests that the individual aphid has arisen from sexual reproduction.

In 2013, all of the grain aphids shown to have the kdr mutation (and therefore reduced sensitivity to pyrethroids) belong to a single clone (referred to as SA3). In addition to this clone, there were also at least seven other clones detected. These are all sensitive to pyrethroids (ie do not possess the kdr mutation). There were also many individual grain aphids that were a unique genotype.

England and Scotland differed in the proportion of the population that is clonal. In the areas of England sampled ~75% of the population was from one clone or another, whereas in Scotland, only ~10% was derived from a clone.

Results 2014

The SA3 clone was the dominant grain aphid genotype in 2014 in both England and Scotland. Two aphids from English suction traps that do not belong to the SA3 clone were also identified as having the kdr mutation. As in 2013, all the grain aphids that tested positive for the kdr mutation were heterozygotes (kdr-SR).

In Scotland, the genotypic diversity of the grain aphid population has decreased compared to 2013. In 2014, ~75% of the population was derived from a clone (compared to ~10% in 2013). The current belief is that genotypic diversity in S. avenae increases moving north where the conditions favour the sexual cycle and more individuals are derived from sexual reproduction. However, the results from 2014 suggest that selection pressure imposed by pyrethroid-based insecticide usage maybe altering the genotypic composition of the northern UK grain aphid populations.

Results 2015

A total of 1,003 individual grain aphids were tested for the kdr mutation in 2015. Overall frequencies in the English trap samples were similar to those reported in 2013 and 2014. In Scotland, kdr frequencies were similar to those found in 2014 with Dundee having the highest frequency (45%). All of the aphids that tested positive for the kdr mutation, both from England and Scotland, were heterozygotes (SR). As in previous years, no kdr homozygotes (RR) were identified in any of the samples.

A subset of samples (150 from England and 125 from Scotland) were successfully tested for their genetic variability by microsatellite analysis. As in 2013 and 2014, there was considerable genetic variation within these samples with a total of 102 different genotypes being detected. Clone SA3 was once again the dominant type occurring in 64 of the English aphids tested and 42 of the Scottish aphids. Unlike the study in 2014, there were no individuals identified with the kdr mutation that did not belong to the SA3 genotype.

In 2015, analysis of historical grain aphid DNA (collected in England in 1997 and 1998) did not identify the resistant SA3 clone, suggesting that it was not present (or present at a very low frequency) in the UK at that time. Several genotypes were identified that are still represented in current populations. Interestingly three very common clones found in 1997 and 1998 (A, C and E) are no longer found. The reasons for their demise are not known but the finding indicates that successful clones of the grain aphid, like successful clones of UK peach potato aphid (M. persicae), are subject to clonal turnover processes.

Project code:
01 July 2013 - 31 December 2015


R480 Final Report of 2014 season R480 Final Report_2015 season R480 Grain Aphid 2013

About this project

Aims and Objectives

Aim: To determine the genetic variation in relation to the insecticide resistance properties of S. avenae (grain aphid) in samples collected in the UK.

a) To establish the frequency and distribution of pyrethroid resistant grain aphid in the UK in 2013, 2014 and 2015.
b) To generate microsatellite profiles from DNA extracted from individual grain aphids known to carry pyrethroid resistance conferred by kdr and compare these to the remaining population.
c) To establish if the resistance has been acquired by one or a small number of successful lineages (clones) that have undergone clonal expansion and whether this has occurred in local clones
d) To establish if the kdr mutation has been inherited and spread by sexual reproduction into numerous lineages.