International Wheat Genome Sequencing Consortium Inc

TRTECH-PGR: UNLOCKING BREAD WHEAT GENOME DIVERSITY: FOUNDATIONAL GENOME SEQUENCES AND RESOURCES TO ADVANCE BREEDING AND BIOTECHNOLOGICAL IMPROVEMENT OF A GLOBAL FOOD SECURITY CROP -COMMON BREAD WHEAT (TRITICUM AESTIVUM L.) IS A MAJOR FOOD SECURITY CROP, PROVIDING ~20% OF HUMAN DIETARY CALORIES AND PROTEINS WORLDWIDE. GENETIC DIVERSITY UNDERLIES THE PRODUCTIVITY AND ADAPTIVE CAPACITY OF AGRICULTURE; YET, TODAY?S HIGH-YIELDING WHEAT VARIETIES CONTAIN ONLY A SMALL FRACTION OF THE AVAILABLE GENE POOL, RAISING CONCERNS THAT OVERRELIANCE ON EXISTING BREEDING STOCKS COULD LIMIT FUTURE GAINS IN WHEAT PRODUCTION. SIGNIFICANT GENETIC DIVERSITY IS HELD WITHIN LANDRACES THAT WERE TRADITIONALLY FARMED ACROSS EUROPE, NORTHERN AFRICA, AND ASIA FOR THOUSANDS OF YEARS PRIOR TO THEIR DISPLACEMENT BY MODERN AGRICULTURE. THIS PROJECT ADDRESSES A CRITICAL NEED TO PRESERVE, DISCOVER, AND MOBILIZE THESE GENETIC RESOURCES BY GENERATING GENOME SEQUENCES OF EIGHT LANDRACES THAT ARE FOUNDATIONAL TO EARLY REGIONAL GROWING CENTERS AND ENCOMPASS THE WORLDWIDE DIVERSITY OF BREAD WHEAT. IN ADDITION, THIS PROJECT WILL UPDATE THE INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM (IWGSC) CHINESE SPRING REFERENCE GENOME SEQUENCE, AN IMPORTANT COMMUNITY-RESOURCE THAT HAS SERVED AS A SPRINGBOARD FOR ADVANCEMENTS IN WHEAT GENETICS, EVOLUTION, BREEDING AND BIOTECHNOLOGY RESEARCH. WITH RESPECT TO TRAINING AND PUBLIC OUTREACH, THIS PROJECT WILL CONTINUE ESTABLISHED EDUCATION, OUTREACH AND TRAINING ACTIVITIES, INCLUDING SUMMER UNDERGRADUATE RESEARCH INTERNSHIPS, ANNUAL INTERNATIONAL WORKSHOPS, EARLY CAREER SPEAKER AWARDS, AND MONTHLY WEBINAR SERIES. THE PROJECT WILL FURTHER INCREASE SCIENCE, TECHNOLOGY, ENGINEERING AND MATHEMATICS (STEM) EDUCATOR TRAINING, PUBLIC SCIENTIFIC LITERACY, AND CONTRIBUTE TO A DIVERSIFIED WORKFORCE. GENERATION OF GENOME SEQUENCE AND ANNOTATION OF EIGHT STRATEGICALLY SELECTED LANDRACES, ALONG WITH THE UPDATED INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM CHINESE SPRING REFERENCE GENOME SEQUENCE, WILL PROVIDE A CRUCIAL STEP FORWARD IN WORLD-WIDE EFFORTS TO IMPROVE WHEAT BY IDENTIFYING THE EXTENT OF GENOMIC DIVERSITY THAT UNDERLIES ADAPTIVE TRAITS. LANDRACES ARE A PARTICULARLY IMPORTANT RESERVOIR OF PHENOTYPIC TRAITS, HAVING ADAPTED OVER MANY GENERATIONS TO LOCALIZED ENVIRONMENTS AND AGRONOMIC SYSTEMS. THE NINE GENOME ASSEMBLIES WILL BE GENERATED BY APPLYING RECENT ADVANCES IN LONG-READ SEQUENCING, OPTICAL MAPS, AND CHROMOSOME CONFORMATION CAPTURE SEQUENCING, WHICH HAVE BEEN DEMONSTRATED TO PROVIDE LOW-COST, PLATINUM-QUALITY ASSEMBLIES OF EVEN LARGE AND COMPLEX GENOMES SUCH AS HEXAPLOID WHEAT (TRITICUM AESTIVUM L. 2N = 6X = 42, AABBDD). ALL GENOMES WILL BE ANNOTATED USING ESTABLISHED PIPELINES AND ACCESSION-DERIVED TRANSCRIPTOME DATA TO INFORM GENE MODELS ACROSS THE DIVERSITY PANEL. EXISTING ANNOTATIONS IN THE CHINESE SPRING REFERENCE GENOME SEQUENCE, INCLUDING THOUSANDS OF COMMUNITY-CONTRIBUTED AND MANUALLY CURATED GENE MODELS, WILL BE PRESERVED IN THE NEW REFSEQ VERSION, WITH SYNTELOGS IDENTIFIED IN THE EIGHT LANDRACE GENOMES. TO MAKE THIS RESOURCE APPLICABLE TO ADVANCED METHODS OF GENETIC AND BREEDING RESEARCH, THE PROJECT WILL DEVELOP A PRACTICAL HAPLOTYPE GRAPH REPRESENTATION OF THESE AND ADDITIONAL PUBLIC REFERENCE GENOME SEQUENCES DEVELOPED BY THE COMMUNITY AT LARGE. THESE PRODUCTS WILL EXCEED PREVIOUS WHEAT PAN-GENOME EFFORTS AND EMPOWER THE WHEAT COMMUNITY TO STRATEGICALLY INCORPORATE UNDERUTILIZED GERMPLASMS TO MEET CURRENT AND FUTURE CHALLENGES IN CROP RESEARCH AND IMPROVEMENT. PUBLIC ACCESS TO ALL PROJECT OUTCOMES WILL BE PROVIDED THROUGH LONG-TERM REPOSITORIES SUCH AS NCBI (FOR DATA ORIGINATING IN THE UNITED STATES) OR EMBL-EBI (FOR DATA ORIGINATING IN EUROPE) AND FURTHER RELEASED TO THE COMMUNITY VIA THE IWGSC DATA REPOSITORY, GRAINGENES, ENSEMBL PLANTS, AND THROUGH DATA PUBLICATION. 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.- SUBAWARDS ARE PLANNED FOR THIS AWARD.