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

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 Ala 122 Asn, Pro 197 Ser/Thr/Ile, Trp 574 Leu, and Ser 653 Thr/Asn/Lys substitutions, with Ala 122 Asn, Pro 197 Thr/Ile and Ser 653 Lys 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 .

Genetic variation and structure of complete chloroplast genome in alien monoecious and dioecious Amaranthus weeds

“…The genus is the focus of weed scientific research 13 , because of these amaranth weeds posed a certain threat to agricultural ecology in the new habitat. A. palmeri and A. tuberculatus invade gradually into the new continents out of their origins, and were detected their resistant biotypes 14 . Accurate identification of these species is the basis of weed prevention and control.…”

“…1 ). Xu et al analyzed ITS, ALS (domain C, A and D) and ALS (domain B and E) and constructed topological trees 14 . In Waselkov et al studies, both nuclear and chloroplast sequences support the division of A. pumilus in subgen.…”

Genetic variation and structure of complete chloroplast genome in alien monoecious and dioecious Amaranthus weeds

“…tuberculatus, the two species were almost indistinguishable [14][15] . In this study, it was found that there was only one SNP site difference in matK/trnK-UUU between A. arenicola and A. tuberculatus, while their ITS 14,20 and trnL-UAA sequences showed no difference 20 . In contrast, there are 46 SNPs and 144 InDels between A. arenicola and A. tuberculatus on chloroplast genomes.…”

“…The genus is the focus of weed scienti c research 13 , because of these amaranth weeds posed a certain threat to agricultural ecology in the new habitat. A. palmeri and A. tuberculatus invade gradually into the new continents out of their origins, and were detected their resistant biotypes 14 . Accurate identi cation of these species is the basis of weed prevention and control.…”

“…Stetter and Schmid (2017) inferred the phylogeny of 35 amaranths using genotyping by sequencing (GBS) 16 . Xu et al (2020) analyzed ITS, ALS (domain C, A and D) and ALS (domain B and E) and constructed topological trees 14 . In addition to the part incorrect conclusions drawn by Stetter and Schmid (2017) due to missampling, all of them concluded that the classi cation boundaries between subgenera are not very clear because of some kinds of amaranths, such as A. palmeri and A. spinosus, A. arenicola and subgen.…”