Transcriptome Profiling to Discover Putative Genes Associated with Paraquat Resistance in Goosegrass (Eleusine indica L.)

Abstract

BackgroundGoosegrass (Eleusine indica L.), a serious annual weed in the world, has evolved resistance to several herbicides including paraquat, a non-selective herbicide. The mechanism of paraquat resistance in weeds is only partially understood. To further study the molecular mechanism underlying paraquat resistance in goosegrass, we performed transcriptome analysis of susceptible and resistant biotypes of goosegrass with or without paraquat treatment.ResultsThe RNA-seq libraries generated 194,716,560 valid reads with an average length of 91.29 bp. De novo assembly analysis produced 158,461 transcripts with an average length of 1153.74 bp and 100,742 unigenes with an average length of 712.79 bp. Among these, 25,926 unigenes were assigned to 65 GO terms that contained three main categories. A total of 13,809 unigenes with 1,208 enzyme commission numbers were assigned to 314 predicted KEGG metabolic pathways, and 12,719 unigenes were categorized into 25 KOG classifications. Furthermore, our results revealed that 53 genes related to reactive oxygen species scavenging, 10 genes related to polyamines and 18 genes related to transport were differentially expressed in paraquat treatment experiments. The genes related to polyamines and transport are likely potential candidate genes that could be further investigated to confirm their roles in paraquat resistance of goosegrass.ConclusionThis is the first large-scale transcriptome sequencing of E. indica using the Illumina platform. Potential genes involved in paraquat resistance were identified from the assembled sequences. The transcriptome data may serve as a reference for further analysis of gene expression and functional genomics studies, and will facilitate the study of paraquat resistance at the molecular level in goosegrass.

Intensive herbicide use has selected for constitutively elevated levels of stress‐responsive mRNAs and proteins in multiple herbicide‐resistant Avena fatua L

“…With one exception ( Echinochloa crus‐galli ), transcriptome analyses of HR to date have been conducted on diploid, allogamous species, such as Eleusine indica L., L. rigidum and A. myosuroides . As such, they reflect the relatively rapid evolution of HR in species with high levels of standing genetic variation, the ability to rapidly spread and create large populations and quickly fix advantageous alleles .…”

Optimizing RNA‐seq studies to investigate herbicide resistance

“…A general review of the literature (Tables and S1) reveals a wide array of RNA‐seq experimental set‐ups employed by weed researchers over the last few years . These initial set‐up decisions can drastically influence the number of transcripts that appear as significantly differentially expressed by the end of the analysis.…”

“…In fact, one of these studies compared only one pooled HR sample with one pooled HS sample and produced 1310 DETs . Other studies with a single replicate returned much longer DET lists, with an average of 44 000 DETs returned in those papers . Controlling for the genetic background was done through either recurrent selection of a single population or by studying a segregating F 2 population …”

Effects of spermidine and salinity stress on growth and biochemical response of paraquat‐susceptibe and ‐resistant goosegrass (Eleusine indica L.)

“…; An et al . ). After paraquat spraying, the decrease of chlorophyll fluorescence (Fv/Fm) in S biotype was irreversible, whereas it was transient in the R biotypes, which recovered gradually afterward.…”

“…Our previous study (An et al . ) indicated that the genes related to PAs could play a vital role in the paraquat resistance of E. indica . Salinity is one of the most severe environmental stresses that affect plant growth and limit crop productivity.…”