Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies

Abstract

"No plant is an island too…" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.

Keywords: artificial ecosystem selection; holobiont; microbiome; plant breeding; synthetic microbiota.

FIGURE 1

The ‘Plant Microbiome’ can be described as the sum total of the genomic contribution made by the diverse microbial communities that inhabit the surface and internal tissues of the plant parts. The rhizosphere, endosphere, phyllosphere constitute the major compartments in which the microbial communities reside in the plant. The soil microbiome is the main source from which the plant selects and builds its microbiome profile. The plant genotype (e.g., dicot bean plant and a monocot rice plant), its root exudates (indicated by blue shade for bean and green for rice), the soil types and properties, and the environmental factors influence the plant microbiome makeup (indicated by different colored microbes inhabiting the plant compartments in bean and rice plant). Mycorrhizal association in both plants is indicated by thin lines extending from the roots into the surrounding soil.

FIGURE 2

This represents the direct (keystone microbiota and soil transplant) and the indirect methods (microRNA transfer) of co-propagating the microbiome with planting material from selected situations for raising next-generation crops.