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.
Highlights
Chickpea (Cicer arietinum L.), known as Bengal Gram is one of the major pulses contributing over 75% of the total production of pulses in the world
After the pre-processing and quality check of data for herbicide susceptible genotype, i.e., ICC5434, 42974090, and 39668970 paired-end reads were obtained for control and treated, respectively
The assembly of unmapped reads resulted in 42 transcripts which were missed in reference-based assembly
Summary
Chickpea (Cicer arietinum L.), known as Bengal Gram is one of the major pulses contributing over 75% of the total production of pulses in the world. It is a major and cheap source of protein as compared to animal protein, important for nutritional security in the developing countries. Weeds are one of the important constraints for chickpea production, as it competes for water, nutrients, light and space. First 6 weeks of crop growth are more critical with respect to weed competition. Weed competes with chickpea resulting into drastic yield reduction and creates problem of harboring fungi, bacterial diseases and insect pests. Transcriptome studies can discover such associated key genes with herbicide tolerance in chickpea
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