Species identification, phylogenetic analysis and detection of herbicide-resistant biotypes of Amaranthus based on ALS and ITS

Han Xu,Shuifang Zhu,Cong Wang,Rieks D Van Klinken,Ke Chen,Yan Chen,Xubin Pan

doi:10.1038/s41598-020-68541-x

Abstract

The taxonomically challenging genus Amaranthus (Family Amaranthaceae) includes important agricultural weed species that are being spread globally as grain contaminants. We hypothesized that the ALS gene will help resolve these taxonomic challenges and identify potentially harmful resistant biotypes. We obtained 153 samples representing 26 species from three Amaranthus subgenera and included in that incorporated ITS, ALS (domains C, A and D) and ALS (domains B and E) sequences. Subgen. Albersia was well supported, but subgen. Amaranthus and subgen. Acnida were not. Amaranthus tuberculatus, A. palmeri and A. spinosus all showed different genetic structuring. Unique SNPs in ALS offered reliable diagnostics for most of the sampled Amaranthus species. Resistant ALS alleles were detected in sixteen A. tuberculatus samples (55.2%), eight A. palmeri (27.6%) and one A. arenicola (100%). These involved Ala122Asn, Pro197Ser/Thr/Ile, Trp574Leu, and Ser653Thr/Asn/Lys substitutions, with Ala122Asn, Pro197Thr/Ile and Ser653Lys being reported in Amaranthus for the first time. Moreover, different resistant mutations were present in different A. tuberculatus populations. In conclusion, the ALS gene is important for species identification, investigating population genetic diversity and understanding resistant evolution within the genus Amaranthus.

Highlights

Amaranthus (Family Amaranthaceae) is a cosmopolitan genus with at least 70 species, including ancient cultivated plants such as the grains Amaranthus cruentus, A. caudatus and A. hypochondriacus, the leafy vegetable and ornamental A. tricolor, and the well-known invasive plant A. retroflexus[1,2]
Riggns et al (2010) classified A. spinosus as a sister group of A. palmeri based on the acetolactate synthase (ALS) gene[17].The sequence homology of EPSP synthase (EPSPS) between glyphosate-resistant A. spinosus and glyphosate-resistant A. palmeri supported the hypothesis that the EPSPS amplicon in A. spinosus originated from A. palmeri[25]
We have observed a similar situation in the ALS gene, namely A. spinosus was grouped into two sections by three stable mutations in ALS and formed parallel branches with A. palmeri

Summary

Introduction

Amaranthus (Family Amaranthaceae) is a cosmopolitan genus with at least 70 species, including ancient cultivated plants such as the grains Amaranthus cruentus, A. caudatus and A. hypochondriacus, the leafy vegetable and ornamental A. tricolor, and the well-known invasive plant A. retroflexus[1,2]. The important agricultural weeds A. palmeri and A. tuberculatus are developing herbicide-resistant biotypes, which in turn can spread globally as seed contaminants in grain[3,4]. Amaranthus palmeri and A. tuberculatus have both evolved herbicide resistant (R) biotypes to at least four herbicide groups: those that target acetolactate synthase (ALS), photosystem II, protoporphyrinogen oxidase (PPO), and 5-enolpyruvylshikimate-3-phosphate (EPSP) s ynthase[8]. This is resulting in considerable losses to agriculture, and the continued evolution of resistance poses a significant threat to global food s ecurity[9,10,11]. The ALS gene has served as a useful molecular marker to study Amaranthus[17]

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Discussion

Conclusion