Transcriptomic Analysis Reveals Responses Of Rice To Two Pesticides Abamectin And Thiamethoxam

Agricultural insect pests(IPs)are one of the significant constraints to crop yield.Crop protection intents to prevent and avoid losses as a consequence of IPs.Since ages,plant breeders and crop protection scientists are in search of a better way to cope IPs restraints.For this purpose,many techniques have been used,and each of them added their contribution to overcome the obstruction.Furthermore,each method has its impacts and limitations,but the most effective and simplest method to control IPs is the use of pesticide application.It is a known fact that pesticide application is an extensive approach to eliminate IPs,and has severe adverse effects on the environment and ecosystem.Although,studies have been reported measuring the inauspicious effects of pesticides on living organisms including plants and animals,however,there is lack of knowledge,whether it could influence the physiological and metabolic processes of plants.Therefore,we systemically analyzed the continuous transcriptomic changes in rice through Illumina RNA-sequencing to reveal the quantity of RNA in a biological sample after a spray of two commercial pesticides,Abamectin(ABM)and Thiamethoxam(TXM).A total of 470 Differentially Expressed Genes(DEGs)were annotated in rice under ABM treatments involvedin several vital processes,including response to stimuli,signaling transport and protein.Since we didn’t observe any severe alterations in the gene expressions in rice under ABM treatments,we endeavored TXM,another commercial pesticide to check whether it can influence rice transcriptome.It is worthwhile to study the influence of TXM on the endogenous metabolic processes in plants as it has a little more impact on GE level compared to ABM.A total of 670 DEGs were detected in TXM treated rice.TXM-specific DEGs,by contrast,involved in different localization-related GO terms and cellular processes may be due to the broad spectrum characteristics of TXM.We also scrutinized the co-expressed DEGs,and found 166 shared DEGs expressed differentially under both pesticides treatments.Also,it is noteworthy that DEGs were abundant under Id treatments compared 3h and 3d treatments indicating no long lasting effects of pesticides on gene expressions.These limited alterations in DEGs in response to two pesticides application indicated that pesticides could not dramatically affect the performance of ice.As a plant development hormone,auxins play critical roles in plant growth and reproduction.Here,we found that ABM regulates many genes with potential functions in the auxin response,including one auxin efflux carrier gene Os01g69070,three auxin-repressed genes Os03g22270,Os11g44810,and Os08g35190,and two auxin response SAUR genes Os06g45970,Os02g07110,suggesting that ABM may influence the aux:in signaling in rice.Also,to be used for DEGs,RNA-seq dataset is an excellent resource for alternatively spliced(AS)genes analysis.Thus,we examined the AS changes in response to pesticides and acquired approximately 270 genes experiencing 274 DE AS activity under both pesticide treatments.Altogether,178 DE AS events under ABM and 167 DE AS events under TXM were observed,consisting of special and shared events among treatments.We classified DE AS into four types;i.e.,Exon skipping(ES),the most abundant(67.15%)of AS events,followed by Alternative 3’splice site(A3SS)(20.44%),Intron retention(IR)(6.93%)and Alternative 5’splice site(A5SS)(5.47%).Subsequently,we carried out the distribution of DEGs by DE AS into different pathways using MapMan analysis and found them enriched in RNA and protein metabolic processes.Alternative splicing was accompanied with alterations in host gene expressions,illustrating its potential role in controlling gene transcription during pesticide spraying.Consequently,long non-coding RNAs(1ncRNAs),another significant contributor to coding gene expressions were also detected impacted by the two pesticides.Approximately,83 differentially expressed 1ncRNAs(DELs)were observed among ABM and TXM treatments.LncRNAs act:as a miRNA"sponge"to trigger the expression of protein-coding genes.Thus,we predict miRNA-1ncRNA-PCG interaction indicating IncRNA TU9050A and TU38959 induces the expressions of their neighboring coding genes through the sponge activity of miRNAs.TE insertion is another significant contributor of gene expressions in plants other than 1ncRNAs.Therefore,we identified 193 and 387 DE TEs under ABM and TXM treatments with 92 co-expressed DE TEs,respectively.DE TEs were abundant near to genes compared to random TEs,indicating DE TEs involvement in GE regulations under farm chemicals.Thus,our results suggested that TEs led to a variation in adjacent coding or non-coding transcripts.Altogether,our results provide valuable insights into pest management through appropriate timing and balanced mixture over sustainable application of field drugs.