Abstract

Genomics Approaches for Divulging Gene/Genome Regulation and Translational Research for Crop Improvement

Mukesh Jain, Associate Professor, Jawaharlal Nehru University

Next-generation sequencing (NGS) technologies have accelerated the whole genome/transcriptome sequencing efforts for gene discovery and understanding the molecular basis of important agronomic traits via deployment of various genomics tools. I shall illustrate the use of NGS technologies in generation of genomic resources and connecting genes and genomic variations to agronomic traits giving examples from a non-model (chickpea) crop plant, which can provide blueprint for their genetic enhancement via biotechnological and/or breeding approaches. We sequenced the genome/transcriptome of chickpea to reveal the gene space. Several genetic variations among the cultivated and wild chickpea were identified. Many of these variations were found to be associated with important agronomic traits. Global transcriptome dynamics was analyzed using RNA-seq to identify novel genes/pathways involved in flower development and abiotic stress responses in chickpea. Further, to understand the molecular mechanisms governing seed size, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size in chickpea, using high-throughput RNA sequencing. We identified stage- and cultivar-specific expression patterns for a significant proportion of the genes. The transcriptional changes in pathways of cell cycle, endoreduplication, carbohydrate metabolism and hormone signal transduction were found to determine seed size in the chickpea cultivars. Via weighted gene co-expression network analysis, we revealed that majority of stage-specific modules are preserved in the two chickpeas cultivars, but developmental specificity and timing of some modules differ between them. We found that different stages of seed development can be delineated by functional modules of co-expressed genes. Our studies provide insights into the molecular signatures and regulatory mechanisms underlying agronomic traits and will surely facilitate research in various areas of functional and translational genomics in crop plants.