← LeaderboardsInvestigatorsiAttributed = a PI's even-split share of each grant — a $1M grant with 2 PIs counts $500K each.
Hudsonalpha Institute For Biotechnology
Huntsville
$35,117,069
Total funding
23
Grants
Funding over time
peak $17.9M · FY2009–25$20M$15M$10M$5M$0
'09
'10
'11
'12
'13
'14
'15
'16
'17
'18
'19
'20
'21
'22
'23
'24
'25
Funding mix
By agency
DOE$17,875,812 · 2
NSF$10,010,861 · 9
DOD$3,651,000 · 3
USDA$2,596,993 · 8
NASA$982,403 · 1
By mechanism
—$35,117,069 · 23
Investigators at Hudsonalpha Institute For Biotechnology
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
GENOME IMPROVEMENT AT JGI-HUDSON ALPHA GSC$17,035,569
· FY2009 · Department of Energy
RII Track-2 FEC: Functional Analysis of Nitrogen Responsive Networks in Sorghum$4,546,896
· FY2018 · O/D
GLOBAL GENOMIC ANALYSIS OF PROSTATE, BREAST AND PANCREATIC CANCER$2,802,000
· FY2010 · Department of the Army
CAREER: Characterizing the repeated evolution of dioecy in plants to engineer artificial chromosomes$1,283,753
· FY2023 · BIO
NSF Engines Development Award: Advancing carbon-neutral crop technologies to develop sustainable consumer goods (AL, GA, NC, TN)$1,000,000
· FY2023 · TIP
Explorations: Building STEM identity through research and career-connected experiential learning$994,224
· FY2024 · TIP
GENETICS AND BIOTECHNOLOGY (COLLECTIVELY CALLED BIOSCIENCE) HAVE MOVED FROM RELATIVELY SPECIALIZED FIELDS TO BROADLY OVERLAPPING RESEARCH ARENAS. AID$982,403
· FY2010 · National Aeronautics and Space Administration
Beginnings: Experiential Learning for Emerging Biotechnology Careers$953,005
· FY2023 · TIP
"APPLYING GENOMIC AND GENETIC TOOLS TO UNDERSTAND AND MITIGATE DAMAGE FROM EXPOSURE TO TOXINS"$849,000
· FY2009 · Department of the Army
GENOME IMPROVEMENT AT JGI-HUDSONALPHA GSC$840,243
· FY2010 · Department of Energy
Collaborative Research: EDGE FGT: Development of Sphagnum (peat) moss as a lab model system for physiological, molecular and functional genomics studies$674,085
· FY2024 · BIO
** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** HEMP IS A CROP SPECIES WITH ENORMOUS POTENTIAL FOR SUSTAINABLY PRODUCING FIBER, OIL, AND PROTEIN IN THE COUNTRY. ONE MAJOR COMPLICATION TO HEMP BREEDING AND PRODUCTION FOR FIBER IS THAT HEMP PLANTS HAVE SEPARATE MALE AND FEMALE SEXES, OFTEN CLOSE TO 50:50, YET FEMALE PLANTS PRODUCE MORE FIBER AND OIL THAN MALE PLANTS DO. A KEY QUESTION IN HEMP BIOLOGY IS THE IDENTIFICATION OF THE GENES THAT CONTROL THE SEX OF HEMP PLANTS (WHETHER IT IS MALE OR FEMALE), WITH THE FUTURE GOAL OF PRODUCING ALL-FEMALE POPULATIONS THAT PRODUCE MORE FIBER BIOMASS AND OIL. IN THIS PROPOSAL, WE WILL GENERATE HIGH QUALITY GENOMIC RESOURCES FOR HEMP THAT SPECIFICALLY FOCUS ON IDENTIFYING THESE GENES THAT CONTROL SEX DETERMINATION. WE WILL SEQUENCE AND ASSEMBLE SEVERAL MALE (XY) HEMP GENOMES, AND IDENTIFY GENES IN THOSE GENOMES. FURTHER, WE WILL SEQUENCE THE GENOMES OF PLANTS WITH MUTATIONS IN FLOWER DEVELOPMENT TO NARROW IN ON THE GENES THAT CONTROL SEX. THE IDENTIFICATION OF THESE GENES WILL ALLOW US TO PRODUCEGENETIC MARKERS THAT ARE PERFECTLY LINKED TO SEX, WHICH IS CRUCIAL FOR HEMP BREEDING AND PRODUCTION. IN ADDITION, THE IDENTIFICATION OF THESE GENES SETS THE STAGE FOR PRODUCING ALL-FEMALE POPULATIONS OF HEMP THAT PRODUCE MORE BIOMASS FOR FIBER AND OIL AND PROTEIN. LASTLY, THIS PROJECT WILL DEVELOP A TRAINING PROGRAM FOCUSED SPECIFICALLY ON RECRUITING ALABAMA HBCU UNDERGRADUATES INTO THE AGRICULTURAL INDUSTRY THROUGH A JOINT GENOMICS AND BREEDING TRAINING PROGRAM AT HUDSONALPHA AND NEW WEST GENETICS.$644,082
· FY2023 · 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.** USING GENOMICS TECHNOLOGY TO IDENTIFY MOLECULAR MARKERS THAT CAN BE USED TO SELECT FOR TRAITS OF INTEREST IS STILL NOT AS EFFICIENT AS IT CAN BE. SEQUENCING TECHNOLOGY HAS OUTPACED THE METHODS USED TO CONNECT GENOTYPES TO PHENOTYPES EFFECTIVELY ACROSS A WIDE RANGE OF SPECIES. ONE MAJOR TIME CONSTRAINT IN BREEDING PROGRAMS IS THE BIFURCATION OF THE APPLIED BREEDING PROGRAM WITH THE GENETIC DISCOVERY PROGRAM. USING BREEDING RELEVANT STRUCTURED POPULATIONS IN AN INNOVATIVE WAY HAS THE POTENTIAL TO INCREASE THE RESOLUTION OF GENETIC MAPPING AND DECREASE THE TIME IT TAKES TO DEVELOP IMPORTANT GENOMIC TOOLS. THE ABILITY TO REACT QUICKLY TO EMERGING THREATS IN AGRICULTURE WITH NATIVE GENETIC VARIATION BEING IDENTIFIED, SELECTED FOR, AND DEPLOYED IS AN IMPORTANT GOAL FOR TRANSLATION GENOMICS RESEARCH.WE WILL USE ADVANCED SEQUENCING TECHNOLOGY TO CONSTRUCT A PANGENOME FOR A NEWLY DEVELOPED PEANUT MULTI PARENT ADVANCED GENERATION INTERCROSS POPULATION (MAGIC). WE WILL ASSESS THE ADVANTAGES OF CONSTRUCTING A MAGIC POPULATION IN AN INBRED POLYPLOID CROP THAT HAS MINIMAL GENETIC DIVERSITY. WE WILL MAP TWO VERY IMPORTANT TRAITS IN PEANUT; STEM ROT RESISTANCE AND DROUGHT TOLERANCE. WE WILL USE A MODIFIED STRATEGY TO ATTAIN HIGHER GENETIC RESOLUTION; I.E. INCREASE OUR ABILITY TO DETECT VARIATION THAT IS TIGHTLY LINKED TO OUR TRAIT OF INTEREST. THIS STRATEGY WILL RELY ON THE GENETIC POWER OF THE PANGENOME TO SHIFT THE RESOURCE ALLOCATION FROM POPULATION ADVANCEMENT AND REPLICATION TO ONE YEAR OF INTENSIVE PHENOTYPING AND GENETIC MAPPING. WE ANTICIPATE THAT THE SHIFT IN RESOURCES WILL ALLOW THE IDENTIFICATION OF BENEFICIAL GENOMIC TOOLS QUICKLY, WITHIN BREEDING RELEVANT POPULATIONS, THAT WILL EFFECTIVELY COMBINE BREEDING WITH GENETIC DISCOVERY. AGRONOMICALLY RELEVANT GERMPLASM WILL BE ABLE TO BE SELECTED FOR AND TESTED WITHIN THE GENETIC EXPERIMENT, VASTLY DECREASING THE TIME FROM DISCOVERY TO CROP IMPROVEMENT.THE GOAL OF THIS PROJECT IS TO DEMONSTRATE THIS APPROACH IS VALUABLE AS ANEW TOOL TO MORE QUICKLY DEVELOP GENOMIC RESOURCES AND IMPROVE CROPS MORE EFFECTIVELY TO FEED A GROWING POPULATION IN OUR EVOLVING ENVIRONMENT.$490,000
· FY2023 · National Institute of Food and Agriculture
Increasing Undergraduate Engagement in Bioinformatics$299,927
· FY2021 · EDU
**AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** GENETIC MAPPING LETS BIOLOGISTS DETERMINE THE GENETIC ARCHITECTURE OF LARGE-EFFECT VARIANTS ON TRAITS OF INTEREST (E.G. QTLS). HOWEVER, IT REMAINS A PIECEMEAL PROCESS FOR BREEDERS TO LEVERAGE QTLS TO IDENTIFY ASSAYABLE MARKERS FOR MARKER-ASSISTED SELECTION AND GENERATE CANDIDATE GENES FOR MODIFICATION. WITH THE ADVENT OF MULTIPLE REFERENCE GENOMES, DIVERSITY DATA, AND HIGH-CONFIDENCE GENE ANNOTATIONS, ALL OF THE RAW MATERIALS ARE AVAILABLE TO IDENTIFY HIGH-VALUE MOLECULAR TARGETS FOR BREEDING. HOWEVER, A COMPUTATIONAL FRAMEWORK TO MAKE USE OF THESE DATA DOES NOT EXIST YET FOR COTTON. THE WORK PROPOSED HERE WILL DEVELOP AN EXTENSIBLE AND ACCESSIBLE FRAMEWORK TO LEVERAGE MULTIPLE REFERENCE GENOMES OF COTTON TO EFFECTIVELY FIND TARGETS FOR MOLECULAR BREEDING EFFORTS.HERE, WE WILL BUILD AND VETT TWO RESOURCES TO ACCOMPLISH THIS GOAL. FIRST, MULTIPLE GENOME SEQUENCES WILL BE INTEGRATED INTO A SINGLE SYNTENY-CONSTRAINED 'PAN-GENOME' THAT CORRECTLY HANDLES THE TWO SUBGENOMES OF TETRAPLOID COTTON AND ANCHORS GENES TO THE PHYSICAL COORDINATES OF MULTIPLE REFERENCE GENOMES. SECOND, WE WILL FUNCTIONALLY ANNOTATE THE PAN-GENOME WITH VARIANTS ACROSS THE DIVERSITY OF COTTON AND BUILD A COMPUTATIONAL FRAMEWORK (AND USER-FACING QUERY TOOLS) TO TRANSFORM VARIANTS INTO RANKED SETS OF CANDIDATE GENES. THESE RESOURCES WILL ALLOW RESEARCHERS TO INTERROGATE PHYSICAL REGIONS OF INTEREST (E.G. QTLS), WHICH WILL FORM A STRONG FOUNDATION FOR MOLECULAR BREEDING AND IMPROVEMENT OF COTTON GERMPLASM. THE PROPOSAL IS SUBMITTED TO FY2021 AFRI COMPETITIVE GRANTS PROGRAM: FOUNDATIONAL AND APPLIED SCIENCE PROGRAM PRIORITY AREA: INITIATE INCREMENTAL DEVELOPMENT OF A PANGENOME AND HAPLOTYPE DATABASE FOR GOSSYPIUM HIRSUTUM UPLAND COTTON BREEDING, CO-FUNDED BY THE COTTON BOARD.$294,000
· FY2022 · National Institute of Food and Agriculture
COTTON BREEDING HAS MADE SIGNIFICANT STRIDES DUE TO THE RAPID ACCUMULATION OF UPLAND COTTON REFERENCE GENOMES, WHICH HAVE IDENTIFIED CRUCIAL GENOMIC REGIONS LINKED TO SUPERIOR FIBER QUALITY, ROBUST STRESS RESILIENCE, AND VALUABLE PIMA COTTON INTROGRESSIONS. HOWEVER, FULLY LEVERAGING THESE GENETIC INSIGHTS IN PRACTICAL BREEDING PIPELINES IS CHALLENGING DUE TO TWO PRIMARY GAPS: 1) LACK OF INTEGRATED AND STANDARDIZED GENOMIC RESOURCES: EXISTING GENETIC DATA IS OFTEN FRAGMENTED, HINDERING COMPREHENSIVE COMPARISONS ACROSS CULTIVARS, AND 2) ABSENCE OF USER-FRIENDLY TOOLS: BREEDERS LACK INTUITIVE PLATFORMS TO EXPLORE AND UTILIZE REGIONS OF INTEREST IDENTIFIED THROUGH GENETIC MAPPING STUDIES.THIS PROJECT AIMS TO SOLVE THOSE PROBLEMS BY CREATING A COMPREHENSIVE, WELL-ORGANIZED COLLECTION OF COTTON GENOMES, CALLED A PAN-GENOME--THAT BRINGS TOGETHER AND IMPROVES EXISTING GENOME DATA. THIS RESOURCE WILL HELP SCIENTISTS AND BREEDERS BETTER UNDERSTAND HOW COTTON VARIETIES DIFFER AT THE GENETIC LEVEL. WE WILL ALSO PINPOINT KEY GENETIC REGIONS LINKED TO TRAITS BREEDERS CARE ABOUT MOST. TO MAKE THIS WORK ACCESSIBLE AND USEFUL, WE WILL DEVELOP A USER-FRIENDLY ONLINE PLATFORM CALLED THE BREEDER RESOURCE HUB. THIS TOOL WILL ALLOW COTTON BREEDERS TO EASILY EXPLORE GENETIC REGIONS OF INTEREST, SHARE DATA, AND APPLY NEW DISCOVERIES TO SPEED UP THE DEVELOPMENT OF BETTER COTTON VARIETIES THROUGH BOTH TRADITIONAL AND MODERN BREEDING METHODS. ULTIMATELY, THIS RESEARCH CAN LEAD TO MORE SUSTAINABLE COTTON FARMING, STRONGER RURAL ECONOMIES, AND BETTER CONSUMER COTTON PRODUCTS, ALL WHILE HELPING AMERICAN AGRICULTURE REMAIN COMPETITIVE GLOBALLY.$294,000
· 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.** IN THE U.S. INDUSTRIAL HEMP (I.E. CANNABIS SATIVA VARIETIES PRODUCING <0.3% TOTAL THC AS OPPOSED TO DRUG-TYPE OR 'MARIJUANA' VARIETIES) HAS DEEP ROOTS AS AN INTEGRAL PART OF THE EARLY ECONOMY SUPPORTING THE PRODUCTION OF TEXTILES ROPE PAPER ETC. HOWEVER U.S. HEMP RESEARCH AND PRODUCTION WERE VIRTUALLY ERADICATED IN THE EARLY 20TH CENTURY BUT HAVE SINCE BEEN REINVIGORATED FOLLOWING ITS LEGALIZATION BY THE 2014 AND 2018 FARM BILLS. DUE TO PROLONGED PROHIBITION HEMP HAS LOST NEARLY 100 YEARS OF SCIENTIFIC AND AGRICULTURAL DEVELOPMENT COMPARED TO OTHER MAJOR CROPS. STILL THERE IS STRONG POTENTIAL FOR A GROWING HEMP INDUSTRY TO MAKE SIGNIFICANT CONTRIBUTIONS TO THE U.S. BIOECONOMY AND GDP PER CAPITA. THIS IS BECAUSE OF THE VARIETY OF INDUSTRIES HEMP CAN SUPPORT: CONSTRUCTION LIVESTOCK FEED/BEDDING NUTRITION SUPPLEMENTS ESSENTIAL OIL MEDICINE FOOD PLASTIC ALTERNATIVES AND BODY CARE. THE LIMITED UNDERSTANDING AND DEVELOPMENT OF INDUSTRIAL HEMP THAT PERSISTS GLOBALLY HIGHLIGHTS AN OPPORTUNITY FOR THE GROWTH OF THE U.S. BIOECONOMY AND TO BECOME A GLOBAL LEADER IN HEMP PRODUCTION AND RESEARCH.HOWEVER MUCH OF THE GENETIC DIVERSITY IN HEMP REMAINS UNSAMPLED LIMITING OUR UNDERSTANDING OF THE GENETIC VARIATION AVAILABLE FOR CROP IMPROVEMENT. HEMP IS A DIOECIOUS (I.E. SEPARATE MALE AND FEMALE PLANTS) CROP EXHIBITING EXTREME GENETIC VARIABILITY AND COMPLEX (X/Y) SEX CHROMOSOMES WHICH PRESENTS CHALLENGES IN COMPUTATIONAL ANALYSES AND HINDERS THE DEVELOPMENT OF EFFICIENT MOLECULAR MARKERS THAT COULD BE USED FOR GENETIC SELECTION AND CROP IMPROVEMENT. KNOWLEDGE OF AGRICULTURALLY IMPORTANT GENES IN HEMP IS GENERALLY LACKING. STILL IT IS ESPECIALLY THE CASE FOR PLANT TRAITS LINKED TO SEX CHROMOSOMES WHICH ARE IMPORTANT BECAUSE DIFFERENT SEX-SPECIFIC TRAITS ARE PREFERRED BY GROWERS: MALES (XY) PRODUCE FIBER BETTER FOR TEXTILES WHEREAS FEMALES (XX) PRODUCE 'GRAIN' (FOR FOOD/OIL) AND FLOWERS ENRICHED WITH MEDICINAL COMPOUNDS.THIS PROJECT AIMS TO ACCELERATE THE ESTABLISHMENT OF HEMP AS A USEFUL SUSTAINABLE CROP AND AN IMPORTANT U.S. COMMODITY BY LEVERAGING THE USDA HEMP GERMPLASM COLLECTION AND CUTTING-EDGE DNA-SEQUENCING TECHNIQUES TO ADDRESS THE ABOVEMENTIONED ISSUES. GERMPLASMS ARE IMPORTANT SOURCES OF GENETIC VARIATION BUT THE USDA HEMP GERMPLASM COLLECTION IS LARGELY UNCHARACTERIZED PRESENTING LIMITED VALUE FOR PLANT BREEDING. THE USDA HEMP GERMPLASM COLLECTION CONTAINS HUNDREDS OF UNIQUE HEMP LINES INCLUDING SOME FROM U.S. FERAL POPULATIONS AND ITS DIVERSITY HOTSPOT IN ASIA BOTH OF WHICH ARE UNDERREPRESENTED IN PREVIOUS GENOMIC SAMPLING EFFORTS DESPITE THEIR POTENTIAL CONTRIBUTIONS TO CROP IMPROVEMENT. THROUGH THIS PROJECT I WILL GENERATE AND ANALYZE A MASSIVE GENOMIC DATASET COMPOSED OF THE FULL ARRAY OF GENETIC DIVERSITY AVAILABLE IN THE USDA HEMP GERMPLASM COLLECTION RESULTING IN INVALUABLE DATA/RESULTS THAT WILL BE MADE AVAILABLE TO BREEDING PROGRAMS AND OTHER HEMP STAKEHOLDERS. I WILL ALSO LEVERAGE THESE RESULTING DATA TO DISCOVER GENE VARIANTS TIED TO AGRICULTURALLY IMPORTANT PLANT TRAITS WHICH WILL BENEFIT MOLECULAR MARKER DEVELOPMENT FOR GENETIC SELECTION AND CROP IMPROVEMENT.$225,000
· 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.** SOYBEAN IS A MAJOR CROP IN US AGRICULTURE, AND PRODUCING HIGHER-QUALITY SOYBEAN LINES IS IMPERATIVE TO GROWING THE SOYBEAN INDUSTRY. HYBRID CROPS BENEFIT FROM HYBRID VIGOR, A PHENOMENON IN WHICH THE OFFSPRING OF GENETICALLY UNIQUE PARENTS EXHIBIT INCREASED GROWTH. THE CREATION OF THESE HYBRIDS IS DIFFICULT IN SOYBEAN SINCE IT IS A HERMAPHRODITIC PLANT THAT SELF-POLLINATES BEFORE IT CAN BE POLLINATED BY A DIFFERENT INDIVIDUAL PLANT. THE MAJOR GOAL OF THIS PROJECT IS TO IMPROVE THE EASE WITH WHICH HYBRID SOYBEAN CROSSES CAN BE MADE BY SOYBEAN BREEDERS.SEX CHROMOSOMES HAVE EVOLVED IN PLANTS REPEATEDLY, CONFERRING FEMALENESS OR MALENESS TO INDIVIDUAL PLANTS WITHIN A SPECIES. SUCH PLANTS MUST CROSS-POLLINATE, WHICH LEADS TO THE CREATION OF MORE VIGOROUS HYBRID OFFSPRING. IN THIS PROJECT, I PROPOSE TO ENGINEER SEX CHROMOSOMES IN SOYBEAN, THUS CREATING UNIQUE MALE AND FEMALE SOYBEAN PLANTS. I WILL ACCOMPLISH THIS BY USING MOLECULAR CLONING AND TRANSFORMATION TECHNIQUES TO GENETICALLY MANIPULATE SOYBEAN PLANTS BASED ON OUR KNOWLEDGE OF WHAT CONSTITUTES SEX CHROMOSOMES IN PLANTS. AGAIN USING MOLECULAR CLONING AND TRANSFORMATION TECHNIQUES, I WILL ALSO CREATE A SOYBEAN LINE IN WHICH SEX DETERMINATION WILL BE CONTROLLABLE BY SHINING A RED LIGHT ON THE PLANTS DURING A PARTICULAR DEVELOPMENTAL PHASE--THIS IS A TOOL CALLED OPTOGENETICS. THIS WILL YIELD PLANTS THAT REMAIN HERMAPHRODITES BY DEFAULT, MAKING IT POSSIBLE FOR THEM TO BE DEPLOYED IN FIELDS WITHOUT THE NEED TO BE MONITORED. THIS PROJECT WILL THUS PRODUCE SOYBEAN LINES THAT WILL ENABLE SOYBEAN BREEDERS TO CREATE STRONGER HYBRID LINES, THUS BOLSTERING THE SOYBEAN INDUSTRY.$225,000
· FY2024 · 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.** MANY IMPORTANT CROPS ARE DIFFICULT TO BREED NEW TRAITS, SUCH AS DISEASE RESISTANCE, INTO PROMPTLY. FOR EXAMPLE, BLUEBERRIES ARE A PERENNIAL CROP THAT TAKES MANY YEARS TO BECOME PRODUCTIVE. WITHOUT GENETIC TECHNOLOGY, WE HAVE TO WAIT UNTIL THE BLUEBERRY IS AT A PRODUCTIVE AGE AND TAKE EXTENSIVE DATA IN THE FIELD TO EVALUATE ITS SET OF TRAITS. THIS MEANS WHEN NEW CROSSES ARE MADE WE MAY NOT KNOW FOR YEARS IF THEY ADDRESS THE ISSUES WE NEED THEM TO ADDRESS. IN FACT, WITH CONVENTIONAL BREEDING, IT CAN TAKE UP TO 20 YEARS TO DEVELOP A NEW BLUEBERRY LINE. THIS CAN HAVE DEVASTATING EFFECTS ON THE AGRICULTURAL INDUSTRY AS A NEW STRESSOR (DROUGHT, DISEASE, PEST, ETC...)COULD WIPE OUT A CROP YIELD FOR THAT YEAR DUE TO THE SUSCEPTIBILITY OF THE PLANT. HOWEVER, NEW GENETIC TECHNOLOGIES ALLOW US TO MOVE MUCH FASTER IN TERMS OF BREEDING BETTER CROPS. WE CAN DO THIS BY EVALUATING THE GENETICS OR GENOTYPE OF A NEWLY BRED YOUNG PLANT TO SEE IF HAS THE SET OF TRAITS WE ARE LOOKING FOR WITHOUT WAITING FOR IT TO GROW AND TAKING EXTENSIVE DATA. THIS ALLOWS PLANT BREEDERS TO MAKE DECISIONS ON WHICH PLANTS TO CONTINUE TO GROW AND WHICH TO CULL. IT ALSO INFORMS BREEDERS AS TO WHICH PLANTS TO CROSS FOR THE BEST POSSIBLE OUTCOME. THESE TECHNOLOGIES ARE ALREADY BEING WIDELY USED TO IMPROVE THE EFFICIENCY OF CROP BREEDING FOR MANY SPECIES AND HAVE BEEN SHOWN TO DRASTICALLY DECREASE THE AMOUNT OF TIME IT TAKES TO RELEASE A NEW LINE. HOWEVER, SOME MORE GENOMICALLY COMPLICATED SPECIES DON'T HAVE THE SAME TOOLS AVAILABLE YET. MANY FRUIT AND NUT CROPS TAKE MANY YEARS TO BE PRODUCTIVE, TAKE MUCH LONGER TO BREED NEW VARIETIES, AND HAVE GENOMES THAT ARE DIFFICULT TO WORK WITH TO FIND TRAITS OF INTEREST. THESE CROPS MUSTN'T GET LEFT BEHIND IN THIS NEW ERA OF GENETIC-BASED BREEDING. BLUEBERRIES SERVE AS A GREAT MODEL FOR HOW TO CONSTRUCT AND IMPLEMENT NEW GENOMIC TOOLS FOR THESE CROPS. BLUEBERRIES ARE A VERY HEALTHY AND DELICIOUS CROP THAT ARE NATIVE TO THE UNITED STATES THAT HAVE A LARGE ECONOMIC VALUE FOR THE AGRICULTURAL INDUSTRY. THERE ARE A FEW SPECIES OF CULTIVATED BLUEBERRY THAT HAVE DIFFERENT PLOIDY LEVELS. PLOIDY REFERS TO THE NUMBER OF GENOMES PRESENT IN AN ORGANISM. HUMANS ARE DIPLOID AS THEY HAVE TWO GENOME SETS- ONE FROM THEIR MOTHER AND ONE FROM THEIR FATHER. BLUEBERRIES ARE MORE COMPLICATED AS THEY ARE TETRAPLOID, HAVING FOUR GENOMIC SETS, OR HEXAPLOID, HAVING SIX GENOMIC SETS. IN ADDITION, THEY ARE HIGHLY HETEROZYGOUS MEANING EACH GENOMIC SET MIGHT DIFFER FROM THE OTHERS GREATLY. THIS MAKES DEVELOPING GENOMIC TOOLS FOR BLUEBERRIES MORE DIFFICULT. WITH THIS PROJECT, WE WILL USE BLUEBERRIES AS A MODEL TO SHOW HOW WE CAN IMPLEMENT STATE-OF-THE-ART GENOMIC TOOLS TO IDENTIFY GENETIC REGIONS THAT CORRELATE TO AGRICULTURALLY IMPORTANT TRAITS AND DEVELOP MARKERS FOR THESE TRAITS THAT BREEDERS CAN THEN USE IN THEIR BREEDING LABS. SPECIFICALLY, WE WILL GENERATE NEW GENOME ASSEMBLIES FOR BLUEBERRY LINES THAT ARE BEING USED FOR BREEDING AT THE UNIVERSITY OF GEORGIA (UGA),AND CREATE A PANGENOME- A REFERENCE MAP CONSISTING OF MULTIPLE BLUEBERRY GENOMES. THIS PANGENOME WILL CONTAIN MOST OF THE GENETIC DIVERSITY FOUND WITHIN UGA'S BREEDING PROGRAM. WE WILL THEN USE THE PANGENOME REFERENCE TO MAP THE GENETICS OF ALARGE POPULATION OF (>800 LINES) OF BLUEBERRIES. USING THE GENETIC INFORMATION FROM THIS BLUEBERRY POPULATION MAPPED TO THE PANGENOME ALONG WITH DATA TAKEN IN THE FIELD, WE WILL BE ABLE TO IDENTIFY THE GENETIC REGIONS CORRELATED TO FRUIT WEIGHT, FLOWERING TIME, AND FRUIT DEVELOPMENT TIME.WE WILL THEN BUILD MARKERS FOR THAT WILL INDICATE IF THESE GENETICREGIONS ARE PRESENT THAT CAN CHEAPLY AND QUICKLY BE USED IN A STANDARD BREEDING LAB SO BREEDERS CAN SCREEN THEIR LINES EARLY FOR THESE TRAITS. WHILE WE WILL RELEASE ALL NEW GENETIC AND GENOMIC DATA FOR PUBLIC USE THAT WILL BE GREATLY VALUABLE TO BLUEBERRY BREEDERS IN THE SOUTHEAST, WE WILL ALSO DEVELOP AND RELEASEAN ANALYTICAL PIPELINE THAT EFFICIENTLY DEALS WITH COMPLICATED GENOMES. THESE TOOLS WILL GREATLY AID BREEDERS WORKING ON CROPS WITH COMPLICATED GENOMES WORLDWIDE.$225,000
· FY2024 · 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.** HOPS ARE PERENNIAL BINES, BEST KNOWN FOR THEIR ROLE IN BEER PRODUCTION. THE GOAL OF BREEDING PROGRAMS IS TO DEBUT NEW VARIETIES WITH DISTINCT FLAVOR PROFILES, DISEASE RESISTANCE, AND/OR SUITABILITY TO A NEW ENVIRONMENT. WHAT IS LACKING IN HOPS, THAT HAS ACCELERATED RESEARCH FOR OTHER CROPS, IS QUALITY GENOME REFERENCES. IMPORTANTLY, IN THE HOP GENUS, HUMULUS, ONLY FEMALES DEVELOP THE VALUABLE HOP CONES THAT ARE ENRICHED IN THE BITTER ACIDS AND OTHER ESSENTIAL OILS USED IN BEER PRODUCTION. THIS SUGGESTS THERE ARE GENOMIC DIFFERENCES BETWEEN FEMALES AND MALES THAT CONTROL HOP CONE DEVELOPMENT. IDENTIFYING THE GENES INVOLVED IN INITIATING FEMALE HOP CONE DEVELOPMENT VERSUS MALE POLLEN DEVELOPMENT IN HUMULUS WOULD REDUCE LABOR AND CROP LOSS FROM UNINTENDED CROSSES. ADDITIONALLY, SUPERIOR MARKERS FOR EARLY IDENTIFICATION OF FEMALES AND MALES ACROSS ALL CULTIVARS AND VARIETIES IN BREEDING PROGRAMS WOULD REDUCE RESOURCE USAGE BY EARLY IDENTIFICATION OF THE MALES THAT HAVE NO ECONOMIC VALUE. WITH THIS RESEARCH, I WILL USE CUTTING-EDGE TECHNOLOGIES TO GENERATE A GENOMIC TOOLKIT TO HELP SUSTAINABLE ACCELERATE HOP BREEDING PROGRAMS. TO ACCOMPLISH THIS, I WILL FIRST GENERATE HIGH-QUALITY GENOME REFERENCES FOR THE FIVE VARIETIES OF HUMULUS LUPULUS AND ITS SISTER SPECIES H. JAPONICUS THAT I WILL MAKE PUBLICALLY AVAILABLE. I WILL ALSO EXAMINE DIFFERENCES IN GENES EXPRESSED IN HOP CONES AND OTHER TISSUES TO DETERMINE THOSE INVOLVED IN HOP CONE DEVELOPMENT. I WILL ALSO DEVELOP MARKERS FOR EARLY IDENTIFICATION OF FEMALES, AS WELL AS VARIETY AND ISOLATE-SPECIFIC MARKERS ACROSS HUMULUS. FINALLY, I WILL ESTABLISH THE SOUTHEASTERN HOP ALLIANCE, WHERE OUR COMMUNITY OF HOP SCIENTISTS CAN ORGANIZE GERMPLASM, KEEP TRACK OF CROSSES, AND COMMUNICATE RESEARCH FINDINGS.$199,911
· FY2023 · National Institute of Food and Agriculture