Molecular characterization of herbicide resistance in Palmer amaranth (Amaranthus palmeri S.Wats) populations in South Africa

Abstract

Weeds such as Palmer amaranth (Amaranthus palmeri S.Wats.) have over the years become problematic in the agricultural industry due to the proclivity to easily develop resistance to multiple herbicides. Reports of herbicide resistant Palmer amaranth invading most parts of North America and some parts of South America, Europe, Asia, and Africa are becoming more frequent. In 2018, A population of Palmer amaranth was found in a cotton field in the Northern Cape province of South Africa. A second population was also reported in 2019 in a field in the KwaZulu Natal Province of South Africa. Using molecular techniques, we set out to confirm the identity of the populations by sequencing the Internal transcribed spacer (ITS) region and to characterize the target site resistance mechanisms conferring resistance to Acetolactate (ALS), 5-enol pyruvylshikimate-3-phosphate synthase (EPSPS) and protoporphyrinogen oxidase (PPO) inhibitors. Preliminary genetic diversity studies were also carried out using microsatellite markers. Single nucleotide polymorphisms (SNP’s) were able to differentiate Palmer amaranth from smooth pigweed and Amaranthus standleyanus accessions. Resistance to ALS inhibitors was due to the amino acid change S653N in 9/29 accessions from the NC population and the presence of both the W574L (1/7) and S653N (7/7) amino acid changes in the KZN population. The two populations also differed in the EPSPS inhibitor resistance profiles as the NC population had the EPSPS gene duplication and the KZN population however had the rare amino acid change P106S but no gene duplication. Moreover, smooth pigweed accessions from the KZN population had the triple amino acid change TIPS-IVS. No target site resistance was observed in the PPO gene in both populations. Immediate genetic diversity was revealed by the microsatellite markers. Findings of this study confirmed the introduction of two different herbicide resistant Palmer amaranth populations in South Africa based on their resistance profiles. This study therefore serves as reference for the South African Herbicide Resistance Initiative when devising management strategies for the introduced population of Palmer amaranth.