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W241: The RNA-Seq Based Gene Expression Atlas of a Major Food Legume Chickpea (Cicer arietinum L.)

Kudapa, H., Garg, V., Chitikineni, A. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2018) W241: The RNA-Seq Based Gene Expression Atlas of a Major Food Legume Chickpea (Cicer arietinum L.). In: Plant & Animal Genome Conference XXVI, 13 - 17 January 2018, San Diego, CA.


Chickpea (Cicer arietinum L.) is an important food legume and is an excellent source of protein with wide range of essential amino acids to human diet. In addition, chickpea plants have root nodules with tremendous nitrogen-fixing ability. Plant growth/development are controlled by programmed expression of a suit of genes at the given time, stage and tissue. To understand how underlying genome sequence results in specific plant phenotypes at key developmental stages, information on gene expression patterns and their functions representing multiple tissues at important growth stages of plant is crucial. In this context, a comprehensive Cicer arietinum Gene Expression Atlas (CaGEA) was generated that provides a global view of gene expression in all major organs across the plant developmental stages covering entire life cycle of chickpea. The most drought tolerant and widely used chickpea cultivar, ICC 4958 has been used to generate RNA-Seq data from 27 samples at five important developmental stages (germination, seedling, vegetative, reproductive and senescence) of the plant. From these samples, 27 cDNA libraries were generated and sequenced, resulting in a total of 816 million raw reads. Of these, 794 million filtered reads after QC were subjected for analysis. Gene expression patterns were analyzed to better understand changes during different developmental stages. A total of 25,784 genes were identified to be transcriptionally active in one or more than one tissues representing 91% of 28,269 predicted genes in chickpea genome. CaGEA revealed 15,947 differentially expressed genes (≥2 folds) and among these 4,829 transcription factor genes were identified. In addition, 1,837 novel genes were found to be differentially expressed. In summary, CaGEA is a valuable resource for gene discovery and functional characterization to understand the systematic process of growth/development of chickpea.

Item Type: Conference Item
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Other Information: Workshop: Cool Season Legumes
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