Project Grant 20236701339158

**AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** WHEAT IS AN IMPORTANT GLOBAL STAPLE CROP, WITH THE U.S. AS ONE OF THE TOP 5 COUNTRIES IN WHEAT PRODUCTION. ONE OF THE MOST CRITICAL PLANT PATHOGENS REGULARLY AFFECTING WHEAT IN THE U.S. IS THE FUNGUS FUSARIUM GRAMINEARUM (FG) WHICH CAUSES A DISEASE COMMONLY REFERRED TO AS FUSARIUM HEAD BLIGHT (FHB), HEAD SCAB, OR JUST SCAB. INFECTION OF WHEAT WITH FG CAUSES GREAT ECONOMIC LOSSES DUE TO REDUCTIONS IN BOTH GRAIN YIELD AND QUALITY, AND TO THE ACCUMULATION OF SIGNIFICANT LEVELS OF FUNGAL TOXINS. THE U.S. F.D.A. HAS SET STRICT GUIDELINES FOR THE AMOUNTS OF THESE TOXINS ALLOWABLE IN WHEAT PRODUCTS INTENDED FOR HUMAN FOOD OR ANIMAL FEED. FG HAS BEEN REPORTED IN AT LEAST 18 STATES THAT PRODUCE WHEAT. SERIOUS FHB EPIDEMICS HAVE OCCURRED IN KANSAS IN 1982, 1990, 1993, 1995, 2008, 2009, 2015 AND 2019 WITH ANNUAL LOSSES AVERAGING $6.5 MILLION. HISTORICALLY, IN MANAGEMENT DECISIONS AND CROP RESISTANCE BREEDING, ALL POPULATIONS OF FG HAVE BEEN TREATED AS IDENTICAL. THIS CLASHES WITH DOCUMENTED VARIATION IN POPULATIONS IN TERMS OF TOXIN PRODUCTION, FUNGICIDE SENSITIVITY, AND AGGRESSIVENESS. IDENTIFICATION OF THE GENETIC BASIS OF TRAIT VARIATION IN A LARGE SAMPLE OF NATURAL FG ISOLATES IS A CRITICAL FIRST STEP IN LEVERAGING THIS VARIATION FOR DISEASE MITIGATION.MOST FUSARIUM RESEARCH HAS FOCUSED ON BREEDING FOR RESISTANCE IN CROPS, ASSESSMENT OF FUNGICIDE APPLICATIONS, OR PREDICTION OF OUTBREAKS WHILE ASSUMING THAT ALL FG ISOLATES ARE EQUIVALENT. THIS PROPOSAL PRESENTS AN EFFICIENT WAY TO CONNECT THE VARIATION PRESENT AMONG THE GENOMES OF DIFFERENT FG ISOLATES WITH IMPORTANT TRAIT VARIATION RELATED TO PATHOGEN AGGRESSIVENESS, FUNGAL TOXIN CONTAMINATION, AND FUNGICIDE SENSITIVITY. THROUGH ADVANCES IN DNA SEQUENCING TECHNOLOGIES, WE CAN EFFICIENTLY SURVEY GENOMIC DIFFERENCES AMONG FG ISOLATES, DEVELOPING THOUSANDS OF GENETIC MARKERS ACROSS HUNDREDS OF DIFFERENT ISOLATES IN THE SCOPE OF ONLY A FEW EXPERIMENTS. EXPERIMENTS TO CHARACTERIZE THE TRAIT VARIATION OF ORGANISMS ARE MORE DIFFICULT AND TIME CONSUMING. TO MAKE THIS PROCESS MORE EFFICIENT, WE WILL PERFORM MOST EXPERIMENTS IN HIGHLY CONTROLLED LABORATORY ENVIRONMENTS. WE WILL CARRY OUT SOME EXPERIMENTS, SUCH AS THOSE TO TEST LEVELS OF FUNGICIDE SENSITIVITY, ON A MINIATURIZED SCALE IN ORDER TO MEASURE LARGE ISOLATE SAMPLES AND MULTIPLE FUNGICIDES SIMULTANEOUSLY, INCREASING THROUGHPUT. OTHERS WILL USE STANDARDIZED ENVIRONMENTS AND GROWTH MEDIA, TO REDUCE NOISE IN THE MEASUREMENTS DUE TO ENVIRONMENTAL VARIATION. THESE TRAIT MEASUREMENTS WILL BE PAIRED WITH MEASUREMENTS OF THE PATHOGEN IN A MORE NATURAL SETTING, DURING ITS INFECTION OF WHEAT, TO LINK THE LABORATORY MEASURES WITH THE MORE CLEARLY RELEVANT TRAITS THAT CAPTURE PATHOGEN-PLANT INTERACTIONS. WE WILL USE TWO DISTINCT GENETIC METHODS TO IDENTIFY THE GENETIC MARKERS THAT CORRESPOND TO DIFFERENCES IN THE PATHOGEN TRAITS - A METHOD THAT CORRELATES TRAIT VALUES WITH GENETIC MARKER STATE IN A SAMPLE OF UNRELATED ISOLATES TO IDENTIFY CANDIDATE MARKERS AT HIGH RE,SOLUTION; AND A MORE TRADITIONAL METHOD BASED ON THE DIRECT OBSERVATION OF CO-INHERITANCE OF MARKERS WITH TRAIT VALUES IN PROGENY FROM A CONTROLLED GENETIC CROSS, THAT ALTHOUGH PROVIDING RESULTS AT LOWER RESOLUTION, SERVES AS STRONG CONFIRMATION OF THE PREVIOUS METHOD. BY IDENTIFYING GENETIC MARKERS THAT MAY CAUSE EXTREME VALUES IN PATHOGEN TRAITS, SUCH AS AGGRESSIVENESS, TOXIN PRODUCTION, AND FUNGICIDE RESISTANCE, WE CAN USE THESE MARKERS IN EFFORTS TO MONITOR PATHOGENS OVER TIME AND PROVIDE EARLY WARNING ABOUT ESPECIALLY SEVERE DISEASE OUTBREAKS. WE CAN ALSO TARGET THE BIOLOGICAL PROCESSES THESE MARKERS ARE INVOLVED IN FOR IMPROVEMENTS IN DISEASE MANAGEMENT. THESE IMPROVEMENTS IN PATHOGEN MANAGEMENT WILL ULTIMATELY CONTRIBUTE TO REDUCED CROP LOSS AND A SAFER FOOD SUPPLY DUE TO THE REDUCTION OF CONTAMINATING TOXINS IN SMALL GRAINS.