Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance

Abstract

Background Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use. Results In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR). Conclusions This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

Diverse mechanisms associated with cyhalofop-butyl resistance in Chinese sprangletop (Leptochloa chinensis (L.) Nees): Characterization of target-site mutations and metabolic resistance-related genes in two resistant populations

“…CYP71C4 , GSTF1 , and GSTU6 were also promising cyhalofop-butyl-tolerance genes based on their resistance-associated expression patterns in response to herbicide treatment. Considering three resistance-related P450 genes, namely, one CYP76 and two CYP71A s, were identified in a cyhalofop-butyl-resistant population in Hunan Province ( Chen et al., 2021 ), our findings expand the candidate gene pool implicated in metabolic herbicide resistance and lay the foundation for future investigations clarifying cyhalofop-butyl NTSR in L. chinensis .…”

“…Upregulation of P450- and GST-associated metabolism might contribute to cyhalofop-butyl resistance in this species ( Zhao et al, 2022 ). A whole-transcriptome analysis of L. chinensis indicated six candidate genes associated with cyhalofop-butyl NTSR in L. chinensis ( Chen et al., 2021 ). However, the exact functions of these genes were not clarified.…”

Syntenic analysis of ACCase loci and target‐site‐resistance mutations in cyhalofop‐butyl resistant Echinochloa crus‐galli var. crus‐galli in Japan

“…Although the NTSR mechanisms of cyhalofop-butyl are not well understood, the involvement of cytochrome P450 monooxygenases and glutathione S-transferases, both of which play a central role in herbicide detoxification, 53,54 is often discussed in the study of cyhalofop-butyl-resistant weeds. 39,55,56 In the last 5 years, several molecular players conferring weed resistance to ACCase inhibitors have been identified, although most of them do not seem to be active against cyhalofop-butyl. In E. phyllopogon, a close relative of E. crus-galli, cytochrome P450 genes (CYP81A12, CYP81A15, CYP81A21, and CYP81A24) that detoxify ACCase inhibitors have been identified, 57 although our analysis failed to confirm any cyhalofop-butyl-metabolizing activity of these enzymes (data not shown).…”

First Report on Resistance to HPPD Herbicides Mediated by Nontarget-Site Mechanisms in the Grass Leptochloa chinensis

“…The resistance index (RI) was determined as the ratio of GR 50 for the R population to that of the S population. The fold change in gene expression (as 2 –ΔCt ) was calculated by the comparative CT method relative to the susceptible samples, where ΔCT = [CT target gene CT mean of two internal control genes] …”