**Transcriptome Analysis in Chickpea (***Cicer arietinum* **L.): Applications in Study of Gene Expression, Non-Coding RNA Prediction, and Molecular Marker Development**

Chandra Kant, Vimal Pandey, Subodh Verma, Manish Tiwari, Santosh Kumar and Sabhyata Bhatia

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/intechopen.69884

#### **Abstract**

Extensive analyses of transcriptome have been carried out in chickpea, which is the third most important legume valued as a source of dietary protein and micronutrients. Over the last two decades, several laboratories have used a wide range of techniques encompassing expressed sequence tag (EST) analysis, serial analysis of gene expression (SAGE), microarray and next-generation sequencing (NGS) technologies for analysing the chickpea transcriptomes. However, chickpea transcriptome analysis witnessed significant progress with the advent of the NGS platforms. Gene expression analyses using NGS platforms were carried out in the vegetative and reproductive tissues such as shoot, root, mature leaf, flower bud, young pod, seed and nodule by various groups which resulted in identification of several tissue-specific transcripts. Some laboratories have utilized transcriptomics to explore the response of chickpea to abiotic and biotic stresses such as drought, salinity, heat, cold, *Fusarium oxysporum* and *Ascochyta rabiei* differentially expressed genes and also established crosstalk between biotic and abiotic stress responses. Transcriptome analysis has been utilized extensively to identify non-coding RNAs such as miRNAs and long intergenic non-coding (LINC) RNAs. Transcriptome analysis has facilitated the development of molecular markers such as simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs) and potential intron polymorphisms (PIPs) that are being used to expedite the chickpea breeding programmes. The available chickpea transcriptomes will continue to serve as the foundation for devising strategies for chickpea improvement.

**Keywords:** transcriptome, chickpea, next-generation sequencing (NGS), gene expression, molecular markers

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