Soil microbes shape the future of crop breeding

In a new review article in Trends in Plant Science, SLU researchers and international colleagues have summarized how soil microbes that live around the roots of crops plays a critical role in plant protection.

– A better understanding of the plant-microbe partnerships can lead to more resilient and sustainable agriculture. We have been breeding crops for thousands of years, but often overlooked the microbial partners that live alongside them, says Sangam L. Dwivedi, lead author of the study.

Breeding for the ability to assemble and work with beneficial microbes

The research community is now identifying key genes that regulate the assembly and composition of the rhizosphere microbiome in plant genomes.

– Our review brings together mounting evidence showing how microbes impact plant health, stress tolerance, nutrition, and productivity. It is time we make them part of the breeding equation, says SLU researcher Ramesh Vetukuri, another author of the study.

New technologies such as genome-wide association studies (GWAS) and microbial GWAS, metagenomics, and synthetic microbial communities (SynComs) are important tools investigate the genetic and functional connections between plants and their root microbiomes.

– What excites me most is the idea of breeding crops not just for their genetic traits, but for their ability to assemble and work with beneficial microbes. Especially under climate stress, these partnerships can be the difference between crop failure and success, says Ramesh.

Conserving microbial resources

To develop more resilient cropping systems, we need to conserve the microbial genetic resources of both wild and domesticated plants. This is vital as these microbes harbor unique traits that support plant growth, resilience, nutrient acquisition, and disease resistance. Wild plants often maintain associations with a more diverse and resilient microbiome than domesticated ones, due to millennia of co-evolution in diverse and often harsher environments. In contrast, domesticated crops have gone through genetic bottlenecks and selection pressures that may have unintentionally led to the loss of beneficial plant-microbe associations, especially since traditional breeding rarely considered the microbiome.

– Feeding the world sustainably means rethinking how we improve crops. We must consider the plant holobiont—the plant and its microbial partners—as a single unit and a new target for breeding. This is especially critical for smallholder agriculture in the Global South, where low-input farming systems dominate and farmers often rely on natural soil fertility and microbial interactions rather than external agrochemicals, says SLU Professor Rodomiro Ortiz and last author of the study.