Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing

Abstract

Background: Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable. Since large variability in tolerance limit of herbicide already exists in chickpea varieties, thus the genes offering herbicide tolerance can be introgressed in variety improvement programme. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea.Results: This is first transcriptomic studies of chickpea or even any legume crop using two herbicide susceptible and tolerant genotypes exposed to imidazoline (Imazethapyr). Approximately 90 million paired-end reads generated from four samples were processed and assembled into 30,803 contigs using reference based assembly. We report 6,310 differentially expressed genes (DEGs), of which 3,037 were regulated by 980 miRNAs, 1,528 transcription factors associated with 897 DEGs, 47 Hub proteins, 3,540 putative Simple Sequence Repeat-Functional Domain Marker (SSR-FDM), 13,778 genic Single Nucleotide Polymorphism (SNP) putative markers and 1,174 Indels. Randomly selected 20 DEGs were validated using qPCR. Pathway analysis suggested that xenobiotic degradation related gene, glutathione S-transferase (GST) were only up-regulated in presence of herbicide. Down-regulation of DNA replication genes and up-regulation of abscisic acid pathway genes were observed. Study further reveals the role of cytochrome P450, xyloglucan endotransglucosylase/hydrolase, glutamate dehydrogenase, methyl crotonoyl carboxylase and of thaumatin-like genes in herbicide resistance.Conclusion: Reported DEGs can be used as genomic resource for future discovery of candidate genes associated with herbicide tolerance. Reported markers can be used for future association studies in order to develop marker assisted selection (MAS) for refinement. In endeavor of chickpea variety development programme, these findings can be of immense use in improving productivity of chickpea germplasm.

Overexpression of Chickpea Defensin Gene Confers Tolerance to Water-Deficit Stress in Arabidopsis thaliana

“…Chickpea is one of the most important pulse crops cultivated worldwide and forms a rich source of dietary protein. Studies over the past decade have revealed a huge amount of information related to chickpea genome ( Jain et al, 2013 ; Varshney et al, 2013 ; Gupta et al, 2016 ) and transcriptome analyses of this plant under stress conditions have been reported ( Hiremath et al, 2011 ; Agarwal et al, 2012 ; Jhanwar et al, 2012 ; Singh et al, 2013 ; Pradhan et al, 2014 ; Garg et al, 2016 ; Iquebal et al, 2017 ). Herein, we report the cloning and characterization of Ca-AFP and its Agrobacterium -mediated genetic transformation in A. thaliana .…”

Stacked genetically modified soybean harboring herbicide resistance and insecticide rCry1Ac shows strong defense and redox homeostasis disturbance after glyphosate-based herbicide application

“…The amount of ferridoxin is also decreased in tobacco under various stresses, including those from herbicide treatment [70]. Iquebal et al [71] observed that genes involved in the photosynthetic pathway were deregulated after exposure to herbicides in resistant chickpea variety [71]. In Lolium perenne sensitive plants, chlorophyll fluorescence was also affected by glyphosate [72].…”

Identification, Characterization, and Evaluation of Polymorphic Microsatellite Markers for Parentage Assignment in Pinctada fucata

“…Genomic DNA was extracted using a standard phenol/chloroform protocol (Sambrook and Russell ). The 31 microsatellite primers were designed based on transcriptome data for P. fucata (unpublished) and tested with 32 wild individuals (Rice ; Iquebal et al ). The total volume of the polymerase chain reaction (PCR) was 12.5 μL, including approximately 50 ng of DNA template, 0.25 mM of each deoxy‐ribonucleoside triphosphate (dNTP), 0.25 μM of forward (labeled with FAM/HEX/TAMRA) and reverse primers, 5 U/μL of Taq polymerase, and 2.5 μL of 10 × PCR buffer (TaKaRa, Tokyo, Japan).…”