Chickpea transcriptomics: insights into stress responses and future applications
Zeba Shahnaz A , Muhammad Abu Bakar Zia

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Abstract
Transcriptomics, a cornerstone of modern genomics, plays a pivotal role in deciphering gene expression patterns and understanding complex biological processes. Among legume crops, Cicer arietinum (chickpea) ranks as the third most important globally, following soybean and lentil, and serves as a vital source of dietary protein and essential nutrients. Over the past two decades, transcriptomic research on chickpea has advanced remarkably, transitioning from earlier methods such as expressed sequence tags (ESTs) and serial analysis of gene expression (SAGE) to cutting-edge technologies such as next-generation sequencing (NGS). NGS has revolutionized chickpea genomics research, enabling the identification of key genes, regulatory pathways, and adaptive mechanisms in response to biotic and abiotic stresses, including drought, salinity, and extreme temperatures. Recent studies have also highlighted the pivotal roles of small RNAs, such as microRNAs (miRNAs) and long intergenic non-coding RNAs (lincRNAs), in stress signaling and adaptation. This review synthesizes the progress in chickpea transcriptomics, showcasing its potential in unravelling genetic mechanisms underlying stress resilience and agronomic improvement. Emerging tools, including single-cell RNA sequencing and integrative multi-omics approaches, hold promise for accelerating the development of climate-resilient and high-yielding chickpea varieties. Such advancements are essential for addressing global food security challenges and ensuring sustainable agricultural practices in the face of climate change.
Keywords: abiotic stresses, biotic stresses, chickpea, genomics, transcriptomics.
References
Afonso-Grunz F, Molina C, Hoffmeier K, Rycak L, Kudapa H, Varshney RK, Drevon J-J, Winter P, Kahl G (2014) Genome-based analysis of the transcriptome from mature chickpea root nodules. Frontiers in Plant Science 5, 325.
| Crossref | Google Scholar |
Afzal M, Alghamdi SS, Khan MA, Al-Faifi SA, Rahman MHu (2023) Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2. Scientific Reports 13, 21223.
| Crossref | Google Scholar | PubMed |
Bandekar PA, Putman B, Thoma G, Matlock M (2022) Cradle-to-grave life cycle assessment of production and consumption of pulses in the United States. Journal of Environmental Management 302, 114062.
| Crossref | Google Scholar | PubMed |
Basu U, Hegde VS, Daware A, Jha UC, Parida SK (2022) Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea. Plant Molecular Biology 108(6), 565-583.
| Crossref | Google Scholar | PubMed |
Bhaskarla V, Zinta G, Ford R, Jain M, Varshney RK, Mantri N (2020) Comparative root transcriptomics provide insights into drought adaptation strategies in chickpea (Cicer arietinum L.). International Journal of Molecular Sciences 21, 1781.
| Crossref | Google Scholar | PubMed |
Channale S, Kalavikatte D, Thompson JP, Kudapa H, Bajaj P, Varshney RK, Zwart RS, Thudi M (2021) Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea. Scientific Reports 11, 17491.
| Crossref | Google Scholar | PubMed |
Dubey S, Bhattacharjee A, Pradhan S, Kumar A, Sharma S (2023) Composition of fungal communities upon multiple passaging of rhizosphere microbiome for salinity stress mitigation in Vigna radiata. FEMS Microbiology Ecology 99(11), fiad132.
| Crossref | Google Scholar |
El-Esawi MA, Al-Ghamdi AA, Ali HM, Alayafi AA (2019) Azospirillum lipoferum FK1 confers improved salt tolerance in chickpea (Cicer arietinum L.) by modulating osmolytes, antioxidant machinery and stress-related genes expression. Environmental and Experimental Botany 159, 55-65.
| Crossref | Google Scholar |
Garg R, Patel RK, Jhanwar S, Priya P, Bhattacharjee A, Yadav G, Bhatia S, Chattopadhyay D, Tyagi AK, Jain M (2011) Gene discovery and tissue-specific transcriptome analysis in chickpea with massively parallel pyrosequencing and web resource development. Plant Physiology 156(4), 1661-1678.
| Crossref | Google Scholar | PubMed |
Garg R, Bhattacharjee A, Jain M (2015) Genome-scale transcriptomic insights into molecular aspects of abiotic stress responses in chickpea. Plant Molecular Biology Reporter 33, 388-400.
| Crossref | Google Scholar |
Gupta K, Garg R (2023) Unravelling differential DNA methylation patterns in genotype dependent manner under salinity stress response in chickpea. International Journal of Molecular Sciences 24(3), 1863.
| Crossref | Google Scholar | PubMed |
Gupta S, Garg V, Kant C, Bhatia S (2015) Genome-wide survey and expression analysis of F-box genes in chickpea. BMC Genomics 16(1), 67.
| Crossref | Google Scholar |
Hickey LT, Hafeez AN, Robinson H, Jackson SA, Leal-Bertioli SCM, Tester M, Gao C, Godwin ID, Hayes BJ, Wulff BBH (2019) Breeding crops to feed 10 billion. Nature Biotechnology 37, 744-754.
| Crossref | Google Scholar | PubMed |
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, BhanuPrakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, KaviKishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal 9, 922-931.
| Crossref | Google Scholar | PubMed |
Jain M, Pole AK, Singh VK, Ravikumar RL, Garg R (2015) Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars. Molecular Breeding 35, 98.
| Crossref | Google Scholar |
Jha UC, Bohra A, Singh NP (2014) Heat stress in crop plants: its nature, impacts and integrated breeding strategies to improve heat tolerance. Plant Breeding 133(6), 679-701.
| Crossref | Google Scholar |
Kaashyap M, Ford R, Kudapa H, Jain M, Edwards D, Varshney R, Mantri N (2018) Differential regulation of genes involved in root morphogenesis and cell wall modification is associated with salinity tolerance in chickpea. Scientific Reports 8, 4855.
| Crossref | Google Scholar | PubMed |
Kaashyap M, Ford R, Mann A, Varshney RK, Siddique KHM, Mantri N (2022) Comparative flower transcriptome network analysis reveals DEGs involved in chickpea reproductive success during salinity. Plants 11(3), 434.
| Crossref | Google Scholar | PubMed |
Krieg CP, Smith DD, Adams MA, Berger J, Layegh Nikravesh N, von Wettberg EJ (2024) Greater ecophysiological stress tolerance in the core environment than in extreme environments of wild chickpea (Cicer reticulatum). Scientific Reports 14, 5744.
| Crossref | Google Scholar | PubMed |
Kumar K, Srivastava V, Purayannur S, Kaladhar VC, Cheruvu PJ, Verma PK (2016) WRKY domain-encoding genes of a crop legume chickpea (Cicer arietinum): comparative analysis with Medicago truncatula WRKY family and characterization of group-III gene(s). DNA Research 23(3), 225-239.
| Crossref | Google Scholar | PubMed |
Kumar M, Chauhan AS, Kumar M, Yusuf MA, Sanyal I, Chauhan PS (2019) Transcriptome sequencing of chickpea (Cicer arietinum L.) genotypes for identification of drought-responsive genes under drought stress condition. Plant Molecular Biology Reporter 37, 186-203.
| Crossref | Google Scholar |
Leo AE, Linde CC, Ford R (2016) Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea. Theoretical and Applied Genetics 129, 1333-1345.
| Crossref | Google Scholar | PubMed |
Li Y, Ruperao P, Batley J, Edwards D, Davidson J, Hobson K, Sutton T (2017) Genome analysis identified novel candidate genes for ascochyta blight resistance in chickpea using whole genome re-sequencing data. Frontiers in Plant Science 8, 359.
| Crossref | Google Scholar |
Madrid E, Seoane P, Claros MG, Barro F, Rubio J, Gil J, Millán T (2014) Genetic and physical mapping of the QTLAR3 controlling blight resistance in chickpea (Cicer arietinum L). Euphytica 198, 69-78.
| Crossref | Google Scholar |
Merga B, Haji J (2019) Economic importance of chickpea: production, value, and world trade. Cogent Food & Agriculture 5(1), 1615718.
| Crossref | Google Scholar |
Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR (2020) Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. The Plant Journal 104(5), 1195-1214.
| Crossref | Google Scholar | PubMed |
Parween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D (2015) An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Scientific Reports 5, 12806.
| Crossref | Google Scholar | PubMed |
Sagi MS, Deokar AA, Tar’an B (2017) Genetic analysis of NBS-LRR gene family in chickpea and their expression profiles in response to Ascochyta blight infection. Frontiers in Plant Science 8, 838.
| Crossref | Google Scholar |
Sharma R, Rawat V, Suresh C (2017) Genome-wide identification and tissue-specific expression analysis of nucleotide binding site–leucine rich repeat gene family in Cicer arietinum (kabuli chickpea). Genomics Data 14, 24-31.
| Crossref | Google Scholar | PubMed |
Srivastava R, Bajaj D, Malik A, Singh M, Parida SK (2016) Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea. Scientific Reports 6, 33616.
| Crossref | Google Scholar | PubMed |
Upasani ML, Limaye BM, Gurjar GS, Kasibhatla SM, Joshi RR, Kadoo NY, Gupta VS (2017) Chickpea–Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies. Scientific Reports 7, 7746.
| Crossref | Google Scholar | PubMed |
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar’an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J, Cook DR (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31(3), 240-246.
| Crossref | Google Scholar | PubMed |
Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS, Viswanatha KP (2014) Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 127, 445-462.
| Crossref | Google Scholar | PubMed |
Varshney RK, Thudi M, Roorkiwal M, He W, Upadhyaya HD, Yang W, Bajaj P, Cubry P, Rathore A, Jian J, Doddamani D, Khan AW, Garg V, Chitikineni A, Xu D, Gaur PM, Singh NP, Chaturvedi SK, Nadigatla GVPR, Krishnamurthy L, Dixit GP, Fikre A, Kimurto PK, Sreeman SM, Bharadwaj C, Tripathi S, Wang J, Lee S-H, Edwards D, Polavarapu KKB, Penmetsa RV, Crossa J, Nguyen HT, Siddique KHM, Colmer TD, Sutton T, von Wettberg E, Vigouroux Y, Xu X, Liu X (2019) Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics 51(5), 857-864.
| Crossref | Google Scholar | PubMed |
Verma M, Kumar V, Patel RK, Garg R, Jain M (2015) CTDB: an integrated chickpea transcriptome database for functional and applied genomics. PLoS ONE 10, e0136880.
| Crossref | Google Scholar | PubMed |