← LeaderboardsInvestigatorsiAttributed = a PI's even-split share of each grant — a $1M grant with 2 PIs counts $500K each.
Boyce Thompson Institute For Plant Research Inc
$28,515,260
Total funding
45
Grants
Funding over time
peak $13M · FY2008–25$20M$15M$10M$5M$0
'08
'09
'10
'11
'12
'13
'14
'15
'16
'17
'18
'19
'20
'21
'22
'23
'24
'25
Funding mix
By agency
DOD$13,162,402 · 3
USDA$11,483,901 · 35
DOE$3,868,957 · 7
By mechanism
—$28,515,260 · 45
Investigators at Boyce Thompson Institute For Plant Research Inc
InvestigatorsiAttributed = a PI's even-split share of each grant — a $1M grant with 2 PIs counts $500K each.
Exposure= the full size of every grant they're on ($1M each).
Rising Stars
First grant in the last 5 yrs
Not enough data
Emerging Leaders
6–10 yrs in
Not enough data
All-Time
Most funded here, all years
Not enough data
Largest grants
THE PURPOSE OF THIS COOPERATIVE AGREEMENT IS TO FUND RESEARCH IN SUPPORT OF BTO IN THE AMOUNT OF 1,661,679 ON CONTRACT HR0011-17-2-0053.$11,957,069
· FY2017 · Defense Advanced Research Projects Agency
PROBING MECHANISMS OF C4 CARBON CAPTURE$1,221,267
· FY2020 · Department of Energy
FUNCTION AND REGULATION OF CHLOROPLAST-ENCODED ANTISENSE RNAS$1,091,073
· FY2010 · Department of Energy
RAPID$1,080,243
· FY2010 · Department of Defense
DIFFERENTIAL REGULATION OF PLASITD MRNA STABLILITY$915,729
· FY2008 · Department of Energy
** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** PHOSPHOROUS IS ESSENTIAL FOR PLANT GROWTH AND IN MANY AGRICULTURAL SOILS PHOSPHORUS AVAILABILITY LIMITS CROP PRODUCTION. PHOSPHATE-RICH FERTILIZERS CAN TEMPORARILY OFFSETS THESE DEFICIENCIES, BUT HIGH FERTILIZER USEAGE COMES WITH BOTH ECONOMIC AND ENVIRONMENTAL COSTS; LEACHING OF EXCESS PI POLLUTES AQUATIC ECOSYSTEMS, AND ROCK PHOSPHATE RESERVES, FROM WHICH PI-FERTILIZERS ARE DERIVED, ARE BEING DEPLETED. CONSEQUENTLY, INCREASING THE EFFICIENCY OF PHOSPHATE CAPTURE BY CROPS IS IMPORTANT FOR THE ENVIRONMENT AND FOR AGRICULTURAL SUSTAINABILITY. ONE APPROACH IS TO HARNESS THE PLANTS MICROBIAL PARTNERS. MOST PLANT SPECIES, INCLUDING ALL THE MAJOR FOOD CROPS, CAN INCREASE THEIR ACCESS TO PHOSPHATE THROUGH SYMBIOTIC ASSOCIATIONS WITH ARBUSCULAR MYCORRHIZAL (AM) FUNGI. AM FUNGI GROW WITHIN AND AROUND PLANT ROOTS WHERE THEIR HYPHAE CAPTURE AND TRANSFER PHOSPHATE DIRECTLY TO ROOTS. AM FUNGI HAVE CONSERVED MICROBIAL COMMUNITIES ASSOCIATED WITH THEIR HYPHAL SURFACES AND THESE COMMUNITIES HAVE THEPOTENTIAL TO INFLUENCE FUNGAL BIOLOGY AND SUBSEQUENTLY PLANT PERFORMANCE DURING AM SYMBIOSIS. IN THIS PROJECT, WE WILL EXTEND KNOWLEDGE OF HYPHAE-ASSOCIATED MICROBIAL COMMUNITY COMPOSITION IN A RANGE OF SOIL PHOSPHORUS CONDITIONS THROUGH SEQUENCE-BASED PROFILING APPROACHES. USING HIPR-FISH, A RECENTLY DEVELOPED IMAGING APPROACH THAT HAS BEEN DEPLOYED SUCCESSFULLY IN HUMAN MICROBIOME RESEARCH, THE SPATIAL ORGANIZATION OF THE MICROBIAL COMMUNITIES ON THE HYPHAE WILL BE MAPPED. SPATIAL DATA ARE VALUABLE BECAUSE HIGHER LEVEL FUNCTIONS OF A MICROBIAL COMMUNITY MAY ARISE AS THE RESULT OF MICROBIAL INTERACTIONS. COMMUNITY COMPOSITION, GENOME SEQUENCES AND SPATIAL MAPPING DATA WILL INFORM THE ASSEMBLY OF SYNTHETIC MICROBIAL COMMUNITIES. THESE WILL BE EVALUATED FOR THEIR ABILITY TO ENHANCE PLANT PHOSPHORUS NUTRITION DURING AM SYMBIOSIS, WITH A FOCUS ON ACCESSING RESIDUAL SOIL ORGANIC PHOSPHATE POOLS. THE DATA GENERATED WILL CONTRIBUTE TO A HOLISTIC UNDERSTANDING OF AM SYMBIOSES AND GUIDE PRACTICES TO IMPROVE PHOSPHATE CAPTURE AND ULTIMATELY REDUCE HIGH FERTILIZER INPUTS IN AGRICULTURE.$764,145
· FY2022 · National Institute of Food and Agriculture
** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** FIGHTBLIGHT IS AN INNOVATIVE AND GOAL-ORIENTED PROJECT AIMED AT COMBATING POTATO LATE BLIGHT, THE MOST FORMIDABLE CHALLENGE TO GLOBAL POTATO PRODUCTION. OUR GOAL IS TO INTRODUCE NEW TRAITS FOR DISEASE RESISTANCE THAT WOULD REVOLUTIONIZE HOW WE PROTECT POTATOES FROM THISDEVASTATING DISEASE.THE PROJECT HAS THREE MAIN OBJECTIVES:1. BIOENGINEERING: DEVELOP SOLANACEOUS IMMUNE DECOY RECEPTORS(NLR-ID) SCAFFOLDS TO COMBAT THE HIGHLY VIRULENT STRAINS OF THE POTATO LATE BLIGHT PATHOGEN PHYTOPHTHORA INFESTANS FOUND IN THE FIELD. SOPHIEN KAMOUN LEADS THIS WORK PACKAGE AT THE SAINSBURY LABORATORY(TSL) IN THE UK.2. CISGENICS: UTILIZE EXONUCLEASE-ENDONUCLEASE FUSIONS FOR PRECISE GENETIC ENGINEERING, INCLUDING TARGETED INSERTIONS AND REPLACEMENTS OF CONVENTIONAL INTEGRATED DOMAINS/DECOYS (IDS) WITH INNOVATIVE IDS.THIS PROCESS WILL DELIVER ENGINEERED NLR-IDS CREATED IN OBJECTIVE 1 THROUGH A CISGENIC APPROACH, OVERSEEN BY ALAIN TISSIER AT THE LEIBNIZ INSTITUTE IN GERMANY.3. PATHOLOGY: TEST CISGENIC POTATO VARIETIES EQUIPPED WITH THE NEWLY ENGINEERED NLR-ID RECEPTORS FOR DURABLE RESISTANCE IN BOTH CONTROLLED ENVIRONMENTS AND FIELD TRIALS AGAINST EPIDEMIC STRAINS OF PHYTOPHTHORAINFESTANS. THIS ACTIVITY WILL BE LED BY SILVIA RESTREPO AT THE BOYCE THOMPSON INSTITUTE IN THE US.OUR CENTRAL HYPOTHESIS IS THAT BY ENGINEERING NLR-ID SCAFFOLDS TO INCLUDE EFFECTOR TARGETS OF P. INFESTANS, WE CAN ACTIVATE SPECIFIC IMMUNE RECEPTORS AND ACHIEVE DISEASE RESISTANCE. THIS PROPOSAL BUILDS ON PRIOR RESEARCH DEMONSTRATING THE POTENTIAL FOR SHUFFLING NLR-ID WITH UNCONVENTIONAL EFFECTOR TARGETS, PLANT-DERIVED DOMAINS, AND ANTIBODIES, INTRODUCING UNPRECEDENTED FUNCTIONALITIES INTO THE PLANT IMMUNE SYSTEM.THE TIMING FOR FIGHTBLIGHT COULD NOT BE BETTER. ADVANCES IN GENE-EDITING TECHNOLOGY NOW PERMIT EFFICIENT, SCAR-FREE TARGETED INSERTIONS AND GENETIC MODIFICATIONS OVER EXTENSIVE SEQUENCES. BY THE END OF THIS GRANT, WE WILL HAVE DEVELOPED NOVEL CISGENIC TRAITS AND GATHERED FIELD DATA DEMONSTRATING ROBUST RESISTANCE TO P. INFESTANS.FIGHTBLIGHT ALIGNS PERFECTLY WITH THE RESEARCH THEME OF PROGRAMMABLE PLANTS, AS WE SEEK TO BIOENGINEER POTATOES WITH NEW CHARACTERISTICS THAT ENABLE THEM TO WITHSTAND BLIGHT. THIS PROJECT STANDS AS A PIONEERING EXAMPLE OF HOW GENE EDITING (GE) AND CISGENIC APPROACHES CAN OFFER SOLUTIONS TO CROP DISEASES, POTENTIALLY SETTING A NEW STANDARD FOR AGRICULTURAL BIOTECHNOLOGY.$760,506
· FY2025 · National Institute of Food and Agriculture
** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** WITH AN EVER-INCREASING WORLD POPULATION, IT WILL BE NECESSARY TO PRODUCE MORE FOOD WITH FEWER INPUTS FROM THE AGRICULTURAL LAND THAT IS CURRENTLY IN CULTIVATION. TO CONTINUE IMPROVING CROP PLANT PRODUCTIVITY IN THE UNITED STATES, MEET GOALS OF THE USDA REEU PROGRAM, AND ADDRESS THE AFRI FARM BILL PRIORITY AREAS AGRICULTURE SYSTEMS AND TECHNOLOGY AND PLANT HEALTH AND PRODUCTION AND PLANT PRODUCTS, IT IS IMPERATIVE TO TRAIN FUTURE SCIENTISTS WHO CAN DEVELOP AND APPLY INNOVATIVE AGRICULTURAL TECHNOLOGIES USING A COMBINATION OF PLANT BIOLOGY AND ENGINEERING RESEARCH APPROACHES. A FIVE-YEAR UNDERGRADUATE INTERNSHIP PROGRAM WILL BE IMPLEMENTED AT THE BOYCE THOMPSON INSTITUTE AND CORNELL UNIVERSITY. EACH SUMMER, TWELVE UNDERGRADUATES FROM THROUGHOUT THE UNITED STATES WILL CONDUCT INTERDISCIPLINARY RESEARCH FOR TEN WEEKS IN THE LABORATORIES OF TWELVE PLANT BIOLOGY AND ENGINEERING FACULTY MENTORS. EARLY-CAREER UNDERGRADUATE PARTICIPANTS WILL BE CHOSEN BASED ON ACADEMIC EXCELLENCE, AS WELL AS CULTURAL AND ETHNIC DIVERSITY. UNDERGRADUATE RESEARCHERS WILL RECEIVE TRAINING IN THE APPLICATION OF NEW TECHNOLOGIES TO BOTH BASIC AND APPLIED AGRICULTURAL RESEARCH. STUDENT PROJECTS WILL INCLUDE HIGH-THROUGHPUT AUTOMATED PHENOTYPING, ROBOTIC SCOUTING IN AGRICULTURAL FIELDS, DEVELOPMENT OF NETWORKED MICROSENSORS THAT REPORT PLANT WATER STATUS, IMPLEMENTATION OF NEW PLANT TRANSFORMATION METHODS, AND CONSTRUCTION OF SYNTHETIC BIOSENSORS. IN ADDITION TO CONDUCTING HANDS-ON AGRICULTURAL ENGINEERING RESEARCH, STUDENTS WILL RECEIVE TRAINING IN BIOINFORMATICS, PROJECT PLANNING, SCIENTIFIC ETHICS, RESEARCH PRESENTATIONS, AND WRITING GRADUATE SCHOOL APPLICATIONS.$747,485
· FY2022 · National Institute of Food and Agriculture
** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** OVER 72% OF FLOWERING PLANT SPECIES ARE CAPABLE OF MUTUALISTIC SYMBIOSES WITH ARBUSCULAR MYCORRHIZAL (AM) FUNGI. IN THIS NUTRITIONALLY-BASED MUTUALISM, THE FUNGI LIVE WITHIN AND AROUND THE ROOT AND TRANSFER PHOSPHATE AND NITROGEN FROM THE SOIL TO THE ROOT. IN RETURN, THE PLANT CELL PROVIDES THE FUNGI WITH CARBON, IN THE FORM OF LIPID AND SUGARS. THE SYMBIOSIS HAS A HUGE IMPACT ON PLANT MINERAL NUTRITION AND ON THE LEVEL OF CARBON DIRECTED UNDERGROUND, BOTH OF WHICH INFLUENCE MANY ASPECTS OF ECOSYSTEM FUNCTIONING. PHOSPHATE TRANSPORT PROTEINS MOVE PHOSPHATE ACROSS THE FUNGAL AND PLANT MEMBRANES. PREVIOUS WORK HAS IDENTIFIED PHOSPHATE TRANSPORT PROTEINS ACTIVE DURING SYMBIOSIS AND HAS REVEALED THAT PHOSPHATE TRANSPORT IS A KEY REGULATOR OF THE ASSOCIATION. THIS PROJECT SEEKS A MECHANISTIC UNDERSTANDING OF THE REGULATORY PROCESS AND AIMS TO IDENTIFY HOW THE PLANT ROOT CELLS SENSE PHOSPHATE AND REGULATE THEIR CELL BIOLOGY TO MAINTAIN THE SYMBIOSIS. THE FUNCTION OF A FUNGAL PHOSPHATE TRANSPORTER WILL ALSO BE ASSESSED. A MECHANISTIC UNDERSTANDING OF PI TRANSPORT AND ITS ROLE IN REGULATING THE SYMBIOSIS COULD PROVIDE KEY TARGETS FOR BREEDING CROPS THAT ARE OPTIMIZED FOR PI ACQUISITION THROUGH AM SYMBIOSIS. THIS COULDIMPROVE PHOSPHATE CAPTURE BY CROPS AND ULTIMATELY REDUCE HIGH FERTILIZER INPUTS IN AGRICULTURE AND ASSOCIATED ENVIRONMENTAL DAMAGE ARISING FROM EXCESS FERTILIZER RUN-OFF. THE PROJECT WILL PROVIDE TRAINING OPPORTUNITIES FOR SCIENTISTS AT ALL LEVELS OF THEIR CAREERS, FROM HIGH SCHOOL STUDENTS TO POSTDOCS. LECTURES ANDENGAGEMENT ACTIVITIES WITH THE PUBLIC WILL INCREASE AWARENESS OF AM SYMBIOSIS.$500,000
· FY2024 · National Institute of Food and Agriculture
INCREASING POTATO YIELD THROUGH GENETIC AND BIOCHEMICAL ANALYSIS OF COMPENSATORY GROWTH RESPONSES DURING TUBER MOTH INFESTATION$498,000
· FY2014 · National Institute of Food and Agriculture
FUNCTIONAL GENOMICS APPROACHES TO DISSECT THE MECHANISMS USED BY ARBUSCULAR MYCORRHIZAL FUNGI TO DEVELOP SYMBIOTIC ASSOCIATIONS WITH PLANTS$496,957
· FY2014 · National Institute of Food and Agriculture
LEPIDOPTERAN INSECTS ARE AMONG THE MOST IMPORTANT AGRICULTURAL PESTS, AND STRATEGIES FOR CONTROL IN SUSTAINABLE AGRICULTURAL SYSTEMS WILL REQUIRE INTEGRATED BIOLOGICAL APPROACHES. CRITICAL TO SUCH APPROACHES IS AN UNDERSTANDING OF THE INITIAL INTERACTIONS BETWEEN PATHOGENIC MICROBES AND INSECT GUT CELLS. BACULOVIRUSES ARE VIRULENT PATHOGENS OF SOME LEPIDOPTERAN INSECTS BUT THEIR INFECTIONS ARE LIMITED IN THE MIDGUT OF CERTAIN HOST SPECIES, WHICH LIMITS THEIR EFFECTIVENESS AS BIOCONTROL AGENTS. WE AIM TO PERFORM COMPARATIVE TRANSCRIPTOMIC STUDIES OF THESE CRITICAL VIRUS-MIDGUT INTERACTIONS, IN BOTH HIGHLY-PERMISSIVE AND SEMI-PERMISSIVE HOST SPECIES. WE WILL COMPARE INFECTION BY THE BACULOVIRUS ACMNPV IN THE MIDGUT OF A SEMI-PERMISSIVE HOST (HELICOVERPA ZEA) WITH OUR PRIOR STUDIES IN THE PERMISSIVE HOST (TRICHOPLUSIA NI). FOR THESE STUDIES, WE AIM TO: 1) CHARACTERIZE ACMNPV GENE EXPRESSION AND H. ZEA RESPONSES TO INFECTION IN THE MIDGUT; 2) PERFORM A COMPARATIVE ANALYSIS TO IDENTIFY VIRAL GENES AND HOST GENES THAT ARE DIFFERENTIALLY EXPRESSED IN THE FULLY- AND SEMI-PERMISSIVE HOST MIDGUTS; AND 3) EXPERIMENTALLY MODIFY VIRAL AND HOST GENE EXPRESSION TO A) ENHANCE VIRAL REPLICATION IN THE MIDGUT AND SYSTEMIC INFECTION, AND B) NEUTRALIZE HOST GENES THAT MAY RESTRICT ACMNPV INFECTION IN THE SEMI-PERMISSIVE HOST. BY IDENTIFYING VIRAL FACTORS AND HOST RESPONSES INFLUENCING MIDGUT INFECTION, IT WILL BE POSSIBLE TO USE MODIFIED PATHOGENS AND TRANSGENIC PLANTS TO MANIPULATE THIS INTERACTION AND LIMIT THE SEVERITY OF INSECT PESTS USING SUSTAINABLE AGRICULTURAL PRACTICES.$490,597
· FY2021 · National Institute of Food and Agriculture
MAIZE IS A MAJOR CROP IN THE U.S., AND WORLDWIDE, AND SERVES AS A CRITICAL SOURCE OF FOOD AND MANY OTHER PRODUCTS. AS AN INTENSIVELY GROWN CROP, HOWEVER, IT HAS SUBSTANTIAL IMPACT ON LAND, WATER AND ENERGY RESOURCES. OUR WORK TARGETS THE PRODUCTIVITY OF MAIZE PLANTS, REASONING THAT INCREASING PRODUCTIVITY WILL RESULT IN GREATER EFFICIENCY OF USE FOR THESE RESOURCES.OUR MAIN TARGET FOR IMPROVING PRODUCTIVITY IS PHOTOSYNTHESIS, I.E. THE CAPTURE OF LIGHT ENERGY BY LEAVES AND ITS CONVERSION TO CHEMICAL ENERGY AND ULTIMATELY PLANT GROWTH. WE INTEND TO INCREASE THE RATE AT WHICH MAIZE PLANTS ABSORB CARBON DIOXIDE BY CREATING NOVEL GENETIC BACKGROUNDS AND TESTING THEM FOR PHOTOSYNTHESIS RATES, METABOLISM OF SUGARS, AND GROWTH AND YIELD. THIS WILL BE DONE MAINLY IN THE LABORATORY, BUT ALSO IN SPECIALIZED FIELD SITES. IF WE ARE SUCCESSFUL, COMMERCIAL SEED PRODUCERS WILL BE ABLE TO ACCESS OUR TECHNOLOGY AND PLACE IT IN SEED VARIETIES COMMONLY USED BY U.S. AND FOREIGN FARMERS.$475,000
· FY2020 · National Institute of Food and Agriculture
CHARACTERIZATION & UTILIZATION OF NEMATODE ASCAROSIDE(NA)-INDUCED PLANT IMMUNITY$473,795
· FY2017 · National Institute of Food and Agriculture
COMMON MILKWEED IS A PERENNIAL PLANT WITH A WIDE DISTRIBUTION IN THE CENTRAL AND EASTERN UNITED STATES. POTENTIAL USES OF MILKWEED INCLUDE THE HARVEST OF FIBER, HYPOALLERGENIC FLOSS, AND MEDICALLY RELEVANT METABOLITES. CARDENOLIDES, A CLASS OF COMPOUNDS THAT IS ABUNDANT IN MILKWEED, HAVE BEEN USED FOR CENTURIES TO TREAT HEART FAILURE, ARRHYTHMIAS, AND OTHER HUMAN DISEASES. CARDENOLIDE PRODUCTION FOR PHARMACEUTICAL APPLICATIONS AND CLINICAL RESEARCH HAS BEEN LIMITED BY THEIR UNKNOWN BIOSYNTHETIC PATHWAYS AND SOMETIMES LIMITED ABUNDANCE IN A COMPLEX MIXTURE OF PLANT METABOLITES. BASED ON PRELIMINARY RESULTS THAT INCLUDE A MILKWEED GENOME SEQUENCE, GENE EXPRESSION DATA, AND METABOLITE PROFILING DATA, FURTHER EXPERIMENTS WILL BE CONDUCTED TO IDENTIFY PATHWAYS FOR THE BIOSYNTHESIS OF CARDENOLIDES IN MILKWEED. TOGETHER, THESE EXPERIMENTS WILL PROVIDE NEW INSIGHT INTO AN IMPORTANT METABOLIC PATHWAY WHOSE ENZYMATIC STEPS HAVE NOT BEEN DETERMINED IN ANY PLANT SPECIES. PRIOR WORK HAS DEMONSTRATED THAT MILKWEED CAN BE GROWN IN CONVENTIONAL AGRICULTURAL ENVIRONMENTS, AND THEREFORE HAS POTENTIAL AN AGRICULTURAL CROP. BY ELUCIDATING BIOSYNTHETIC PATHWAYS FOR THE PRODUCTION OF PLANT-BASED CHEMICALS, IT WILL BE POSSIBLE TO USE SELECTIVE BREEDING TO IMPROVE THE ECONOMIC VALUE OF MILKWEED. RESOURCES DEVELOPED THROUGH THIS PROJECT WILL LEAD TO THE MORE TARGETED PRODUCTION OF PHARMACEUTICAL COMPOUNDS IN MILKWEED AND CAN BE USED TO IMPROVE THE AGRONOMIC PROPERTIES THIS SPECIES AS A NEW PERENNIAL FIELD CROP FOR AMERICAN FARMERS.$460,000
· FY2020 · National Institute of Food and Agriculture
INCREASING RUBISCO ABUNDANCE IN MAIZE TO MODIFY PLANT PERFORMANCE$459,950
· FY2016 · National Institute of Food and Agriculture
MODIFYING INSECT MIDGUT RESPONSES TO PATHOGEN ATTACK$455,000
· FY2015 · National Institute of Food and Agriculture
OSMOREGULATORY COLLAPSE TO CONTROL PHLOEM-FEEDING INSECT PESTS$452,000
· FY2012 · National Institute of Food and Agriculture
DOMESTICATION AND INTENSIVE BREEDING HAS MADE TOMATO (SOLANUM LYCOPERSICUM) ONE OF THE WORLD MOST IMPORTANT AGRICULTURAL CROPS. TRAITS SUCH AS FRUIT SIZE, PLANT HABIT AND EASE OF GERMINATION, MAKE MODERN CULTIVARS PARTICULARLY AMENABLE TO COMMERCIAL CULTIVATION AND DISTINGUISH DOMESTICATED CULTIVATED TOMATO FROM ITS WILD RELATIVES. SINCE DOMESTICATION HAS RESULTED IN LIMITED GENETIC DIVERSITY WITHIN THE CULTIVATED GERMPLASM, UTILIZING WILD SPECIES IS A COMMON FEATURE OF MODERN BREEDING PROGRAMS. THE WILD RELATIVES OF TOMATO REPRESENT A RICH SOURCE OF PHENOTYPIC VARIATION, INCLUDING VALUABLE METABOLIC DIVERSITY, WITH GREAT POTENTIAL TO IMPROVE CULTIVATED VARIETIES. HOWEVER, THE MOLECULAR BASIS FOR PHENOTYPIC DIFFERENCES BETWEEN CULTIVATED AND WILD SPECIES OF TOMATO IS STILL LARGELY UNKNOWN AND FINDING THE GENES THAT INFLUENCE TRAITS SUCH AS FRUIT SHAPE, SIZE AND METABOLITE CONTENT, IS OFTEN LENGTHY AND TECHNICALLY CHALLENGING. INTERESTINGLY, MANY SUCH GENES CAUSE PHENOTYPIC DIFFERENCES AS A RESULT OF CHANGES IN GENE REGULATION RATHER THAN CHANGES IN PROTEIN FUNCTION. ONE METHOD TO IDENTIFY SUCH GENES IS TO COMPARE GENE EXPRESSION BETWEEN SPECIES. HOWEVER, SIMPLE COMPARISONS CANNOT DISTINGUISH GENES DIFFERENTIALLY REGULATED BY INDIRECT FACTORS SUCH AS DIFFERENCES IN GROWTH HABIT, PLANT ANATOMY OR CELLULAR ENVIRONMENT AS OPPOSED TO TRUE REGULATORY VARIANTS.THIS PROJECTS APPLIES A NEW APPROACH BASED ON THE ANALYSIS OF HYBRIDS OF WILD AND CULTIVATED TOMATO SPECIES TO IDENTIFY CANDIDATE GENES AFFECTING PHENOTYPIC VARIATION, PARTICULARLY TRAITS RELATED TO FRUIT QUALITY. BY SIMULTANEOUSLY ANALYZING THE EXPRESSION OF WILD AND CULTIVATED ALLELES IN A HYBRID PLANT, IT IS POSSIBLE TO ELIMINATE BACKGROUND EFFECTS ON GENE EXPRESSION AND UNCOVER GENES SHOWING CIS-REGULATION (E.G. CHANGES IN EXPRESSION DUE TO PROMOTER VARIATION) WHICH CONSTITUTE INTERESTING TARGETS FOR CROP IMPROVEMENT. WE WILL APPLY THIS APPROACH TO HYBRIDS OF A RANGE OF CULTIVATED TOMATO SPECIES AND TOMATO WILDSPECIES AT DIFFERENT DEVELOPMENTAL STAGES, AND ANALYZE DISTINCT FRUIT TISSUES, TO GENERATE A COMPREHENSIVE DATASET OF CIS-REGULATED GENES AND A LIST OF VERIFIED HIGH PRIORITY CANDIDATE GENES TO IMPROVE FRUIT QUALITY. TOMATO IS AN ECONOMICALLY IMPORTANT VEGETABLE CROP WORLDWIDE AND AN IMPORTANT SOURCE OF NUTRIENTS BENEFICIAL TO HUMAN HEALTH. DEVELOPING TOMATO VARIETIES THAT ACHIEVE OPTIMAL FRUIT YIELD WHILE MAINTAINING FRUIT QUALITY (FLAVOR, AROMA, HEALTH-RELATED METABOLITES) IS OF HIGH ECONOMIC IMPORTANCE BUT PRESENTS COMPLEX CHALLENGES. BY GENERATING A DATASET OF CANDIDATE GENES CONTROLLING PHENOTYPIC VARIATION, THIS RESEARCH WILL PROVIDE NEW TOOLS FOR DESIGNING STRATEGIES TO ENHANCE VALUED FRUIT TRAITS. IN ADDITION, THIS STUDY WILL OFFER INSIGHTS INTO THE REGULATORY EVENTS THAT ACCOMPANIED TOMATO DOMESTICATION.$440,417
· FY2019 · National Institute of Food and Agriculture
GREEN PEACH APHIDS (MYZUS PERSICAE) ARE WIDELY PREVALENT AGRICULTURAL PESTS THAT REDUCE YIELD BY CONSUMING PLANT NUTRIENTS AND TRANSMITTING VIRUSES TO NUMEROUS FRUITS, VEGETABLES, AND FIELD CROPS. APHIDS FEED PRIMARILY FROM THE PHLOEM SIEVE ELEMENTS OF THEIR HOST PLANTS. IN THE COURSE OF PHLOEM FEEDING, APHIDS ALTERNATE BETWEEN SECRETING PROTEIN-CONTAINING SALIVA INTO SIEVE ELEMENTS AND INGESTING PHLOEM SAP. SEVERAL STUDIES HAVE DEMONSTRATED THAT SPECIFIC APHID SALIVARY PROTEINS, ALSO CALLED EFFECTORS, PLAY A CRITICAL ROLE IN SUCCESSFUL APHID FEEDING. CONVERSELY, SOME SALIVARY PROTEINS ELICIT VISIBLE RESPONSES IN PLANT LEAVES, SUGGESTING THAT PLANTS RECOGNIZE THESE INDIVIDUAL APHID PROTEINS AND INITIATE DEFENSES. HOWEVER, ONLY A FEW OF THE LIKELY DOZENS OF PROTEINS IN APHID SALIVA HAVE BEEN CHARACTERIZED, AND THE FUNCTIONS OF MOST APHID SALIVARY PROTEINS REMAIN COMPLETELY UNKNOWN. THE WIDE HOST RANGE OF GREEN PEACH APHIDS SUGGESTS THAT THIS SPECIES HAS A PARTICULARLY EFFECTIVE COMPLEMENT OF SALIVARY PROTEINS THAT FUNCTION BOTH IN SUPPRESSING PLANT DEFENSES AND IN PROMOTING NUTRIENT FLOW TO APHID FEEDING SITES.IN THE COURSE OF THIS PROJECT, THE FUNCTIONS OF SIX GREEN PEACH APHID SALIVARY PROTEINS WILL BE CHARACTERIZED. TWO OF THESE PROTEINS APPEAR TO ELICIT PLANT DEFENSE RESPONSES. FOUR OTHERS MOVE TO SPECIFIC LOCATIONS WITHIN THE PLANT CELLS FROM WHICH THE APHIDS ARE FEEDING, SUGGESTING THAT THEY HAVE A ROLE IN MANIPULATING PLANT METABOLISM FOR THE BENEFIT OF THE APHIDS. THE EFFECTS OF APHID SALIVARY PROTEINS WILL BE CHARACTERIZED WITH PLANT GENE EXPRESSION AND METABOLITE PROFILING ASSAYS. PROTEIN INTERACTION STUDIES WILL IDENTIFY PLANT PROTEINS THAT CONTRIBUTE TO THE RECOGNITION OF APHID FEEDING, AS WELL AS PLANT PROTEINS THAT ARE TARGETED BY THE APHIDS TO SUPPRESS PLANT DEFENSES AND PROMOTE NUTRIENT FLOW TO THE SITE OF APHID FEEDING. APHID GENE EXPRESSION SILENCING WILL DETERMINE THE EXTENT TO WHICH INDIVIDUAL SALIVARY PROTEINS ARE REQUIRED FOR SUCCESSFUL HOST PLANT UTILIZATION. CHARACTERIZATION OF ESSENTIAL APHID SALIVARY PROTEINS, AS WELL AS INTERACTIONS WITH ENDOGENOUS PLANT PROTEINS, WILL NOT ONLY PROVIDE A BETTER UNDERSTANDING OF FACTORS THAT CONTRIBUTE TO THE INVASIVENESS OF GREEN PEACH APHIDS, BUT ALSO WILL ENABLE THE IMPLEMENTATION OF NEW RESISTANCE MECHANISMS IN CROP PLANTS THROUGH BREEDING OR BIOTECHNOLOGY APPROACHES.$440,334
· FY2021 · National Institute of Food and Agriculture