RESEARCH-PGR: Genetics and Mechanisms of Microbe-dependent Heterosis

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In corn and many other crop and wild plants, hybrid cultivars are larger, more resilient, and more productive than their inbred parent cultivars. This phenomenon, called hybrid vigor, is a cornerstone of modern crop breeding efforts and has immense value for global food security. Despite over a century of intensive research, the causes of hybrid vigor are still poorly understood. Recently, the first evidence has arisen that microbes in the soil play an important role in hybrid vigor. This project will investigate the microbial contribution to hybrid vigor in more detail, combining classic and cutting-edge scientific approaches, including field experiments, microbial culture, DNA sequencing, and advanced molecular techniques such as metaproteomics. Specifically, this study will (1) test a wide range of microbial strains and soil microbiomes for the ability to induce hybrid vigor in corn; (2) identify genetic variants and regions of the corn genome that are associated with responsiveness to soil microbes; and (3) characterize the behavior of microbes within the roots of inbred and hybrid corn at the molecular level. Together, the results will advance knowledge of how, when, and why soil microbes affect hybrid vigor which could potentially lead to applications in agriculture and ecological conservation. This project will also grow the American scientific workforce by supporting the training of two post-doctoral researchers, one Ph.D. student, and two undergraduate student researchers. It will also support four high-school teachers to attend researcher-led workshops to learn about soil microbes and agricultural ecosystems.This project was motivated by preliminary data showing that hybrid vigor (i.e., heterosis) of maize root mass was eliminated or greatly reduced in sterile conditions or diminished soil microbial communities in the field. The overarching goals are to determine the generality of this phenomenon with respect to the microbes and host genotypes; to investigate the genetic architecture of microbe-dependent heterosis; and to characterize molecular mechanisms of microbial interactions with inbred and hybrid hosts. An existing collection of maize root endophytes will be screened for the ability to induce maize heterosis, in monoculture and in simplified communities. Metaproteomics will be used to quantify in planta protein expression by heterosis-inducing and non-inducing bacterial strains while colonizing roots of inbred vs. hybrid hosts, while RNA-seq will be used to quantify host gene expression aboveground. The generality of microbe-induced heterosis will be assessed by measuring better-parent heterosis in a genetically diverse panel of maize hybrids and their parent lines, under sterile and inoculated conditions. Finally, a high-resolution mapping population (“IBM”) will be backcrossed to each parent line, generating a test population that will be used to map genomic loci that interact with microbes to affect phenotype when in the heterozygotic state. The same test population will be scored for disease resistance in the field to investigate the interplay with plant immunity. Together, these experiments will help clarify how inbred and hybrid maize plants interact with their microbial neighbors, and how these interactions relate to the expression of phenotypic heterosis. All data and genetic resources will be made available to the general public through long-term repositories.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.