Research Projects

Chickpea is a major, economically important legume crop grown globally, serving as an excellent source of protein (15-25% content). However, its production faces substantial yield losses due to various combined abiotic and biotic stresses, particularly drought and dry root rot (DRR). DRR, caused by the soil-borne necrotrophic fungus Macrophomina phaseolina (Tassi) Goid, results in worsened yield reduction when combined with drought stress in chickpea. Sustainable crop improvement strategies for combined DRR and drought stress resistance include deploying genome editing technologies that facilitate precise, targeted alterations of key susceptible or resistance genes. However, identifying relevant genes or pathways is crucial for the success of crop improvement programs. Recent advances in ‘omics’ science and high-throughput next-generation technologies, including genomics, transcriptomics, proteomics, metabolomics, and phenomics, have facilitated the understanding of plant-pathogen-microbiome relationships under changing climatic conditions. To understand the biological mechanisms of the combined stress response in chickpea, we propose an integrative multi-omics pipeline that incorporates transcriptomics, whole metagenome sequencing, proteomics, metabolomics, and phenomics to bridge the genome-to-phenome gap. We hypothesize that integrative multi-omics analysis will identify how differential transcript accumulation, hub microbial communities, protein changes, metabolite changes, and phenotypic responses actively facilitate combined drought and DRR tolerance in chickpea. To elucidate tolerance mechanisms, we propose four levels of multi-omics integration (MOI), including sequential integration (level 1), pathway-based integration (level 2), network-based integration (level 3), and machine learning and statistical, or Bayesian-based integration (level 4) approaches. Thus, we will integrate the multi-omics datasets using the proposed four-level MOI approach to identify candidate genes, proteins, metabolites, hub microbial communities, and biological pathways. While previous multi-omics integration studies have detailed methodologies, researchers have limited practical implementation in plants, and no studies have investigated the integration of multi-omics under combined stress in chickpea. This study will provide the first comprehensive integrative view of combined drought and DRR tolerance mechanisms in chickpea. The identification of candidate genes and biological pathways will enable genomics-assisted selection, facilitating precision breeding for climate-resilient chickpea improvement and ultimately contributing to sustainable agriculture and global food security.