9 - Genomic insights of plant endophyte interaction: prospective and impact on plant fitness

Abstract

In the current scenario of burgeoning population, climate change, and increasing burden on crop production, it is very much essential to implement several strategies for sustainable climate-resilient “smart” crop production. Microorganisms are abundantly present in nature and commonly associated with plants. The microorganisms commonly known as endophytes can establish a mutualistic relationship with host plants while living within them and yet remain asymptomatic. Endophytic communities have profound effects on the physiology and overall performance of host plants by promoting its growth, development, and alleviating abiotic/biotic stresses. At the same time and being sessile organisms, plants are also in contact with different class of microorganism. Thus, identification of functional microbial entities and understanding the mechanism of plant–endophytes association are very much essential in terms of imparting plant fitness. In context of identification and characterization of any organism, genomics, transcriptomics, proteomics, and metabolomics (commonly termed as omics) play significant role, which are nowadays standing in the row of first preference of research experimentation. In this era of omics technologies, there is a growing need to interpret the genomic aspect of plant–endophyte and endophyte-endophyte in the rhizosphere for developing strategies in relation with green sustainable agriculture. With the advent of high-throughput next-generation sequencing platforms, the omics techniques have become a very effective for identification of genes, protein families, metabolic pathways and its regulon for endophytic species in a specific environmental niche or ecosystem. Moreover, the endophytes improve nutrient use efficiency and have potential use in agriculture as biofertilizers and biocontrol agents. The beneficial endophytes are thus an alternative green solution for chemical fertilizers and insecticides thus contributing to smart climate-resilient technologies for sustainable agriculture. In this chapter, we highlight the deployment of genomic approaches to unravel the molecular mechanism of beneficial plant–endophyte relationship. This understanding is expected to shed light on the commercialization of potential endophytes for climate resilience agriculture.