Mapping of genetic host compatibility loci that promote the colonization of bacterial endophytes in maize

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PLAIN LANGUAGE SUMMARY (GENERAL PUBLIC) Humans, animals and plants have thriving ecosystems of bacteria that live inside them without causing disease. Remarkably, humans possess more genes from their microbial inhabits than from the human genome itself, and the situation is likely similar in plants. Microbes that inhabit plants without causing disease are called endophytes. We recently conducted the most comprehensive geographic and evolutionary study of bacterial endophytes of diverse types of corn (maize) spanning Central America to Canada. Corn is one of the world’s important crops, supplying 15% of human calories, yet there is limited knowledge about the microbes that inhabit this crop, even though some of these microbes, for example, may be producing toxins. Thus it is important to understand factors that cause particular endophytes to thrive or not within a plant. In our previous study, we discovered that some bacterial endophytes persisted in corn across thousands of years of crop breeding and migration across the Americas, whereas other endophytes colonized only a single corn variety. These results suggested that corn is able to recognize, and either accept or reject, specific strains of endophytes. Unfortunately, scientists have very little knowledge as to how specific plants accept or reject specific endophytes. Endophytes may be recognized, then accepted or rejected, by different genetic factors in the host plant and/or may be more or less compatible with the host’s internal environment (e.g. some plants may have the appropriate nutrients to feed an endophytic strain). This proposal attempts to understand how corn accepts or rejects specific endophytes at the genetic level. We will measure which endophytes are present or absent in two types of corn used by corn geneticists (B73 and Mo17), then use these differences to map the corn genes (QTLs) responsible for accepting or rejecting a selected endophyte. Why is this proposal important? It is important to understand how crops are able to distinguish between microbial enemies that cause important crop diseases, compared to neutral or friendly microbes such as endophytes – such information may help scientists better understand crop disease outbreaks and how to prevent them. The second reason, is that for decades, there has been interest in using endophytes to coat onto seeds (termed inoculants) or spray onto crops, since some microbes can suppress crop disease or reduce the need for fertilizers. Whether safe or not, organic farmers already promote the use of microbes as natural alternatives to synthetic pesticides and fertilizers. Now major agbiotech companies have staked part of their future growth on the sale of “biologicals” including endophytes. Unfortunately, in the past, endophytes have often not succeeded because they fail to persist in the plant after inoculation; one reason for these failures may be competition from other microbes in the field, but another major reason appears to be poor compatibility of a specific endophyte with a specific crop variety. If researchers can map the endophyte compatibility genes in crops, they can use traditional breeding to breed crops that will accept beneficial endophytes. In fact, one reason why corn was selected for this basic research proposal, as opposed to a simpler plant, is that the information gained can immediately translate into real world applications for corn farmers. My lab is in an excellent position globally to conduct this research. First, we have a unique collection of endophytes, and we have already characterized their colonization across 13 types of corn. Second, my Lab has expertise in both endophyte biology and corn genetics, which is an unusual combination.