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**AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** MOST ECONOMICALLY IMPORTANT CHARACTERS IN FOOD ANIMALS AND PLANTS ARE COMPLEX QUANTITATIVE TRAITS. LARGE-SCALE CYBER-INFORMATICS AND DATA ANALYTICS HAVE GREATLY FACILITATED GENETIC MAPPING AND GENOMIC PREDICTION OF ECONOMIC TRAITS. GENOTYPE IMPUTATION, THE PROCESS BY WHICH A SMALL SUBSET OF GENOMIC LOCATIONS ARE GENOTYPED TO INFER WHOLE GENOME GENOTYPES BASED ON EXISITING WHOLE GENOME SEQUENCES,IS A PROVEN, ACCURATE, AND COST-EFFECTIVE ALTERNATIVE TO DIRECT SEQUENCING OF GENETIC SELECTION CANDIDATES. HOWEVER, SCALABLE AND ACCESSIBLE GENOTYPE IMPUTATION TOOLS ARE LACKING IN PIGS AND OTHER LIVESTOCK ANIMALS. OUR PROJECT IS DRIVEN BY CRITICAL NEED, HIGH POTENTIAL IMPACT, AND CLEARLY DEFINED GOALS. OUR MULTI-PD TEAM WITH COMPLIMENTARY EXPERTISE WILL DEVELOP A NOVEL CYBER-INFORMATICS TOOL TO DIRECTLY ADDRESS THE FACT PROGRAM PRIORITY. THE LONG-TERM GOALS OF THIS PROJECT ARE TO DEVELOP, DEPLOY, AND MAINTAIN A SWINE IMPUTATION (SWIM) SERVER TO SERVE THE U.S. AND INTERNATIONAL SWINE GENETICS RESEARCH COMMUNITY. THIS SERVER WILL ALLOWUSERS TO UPLOAD SNP CHIP GENOTYPES AND RECEIVE IMPUTED WHOLE GENOME SEQUENCES. OUR INFORMATICS AND DATA SCIENCE APPROACH WILL ENABLE THE SWINE GENETICS COMMUNITY TO EFFECTIVELY UTILIZE EXISTING DNA SEQUENCE DATA, SIGNIFICANTLY REDUCE THE NEED TO ALLOCATE RESOURCES TO SEQUENCE NEW ANIMALS, AND ACCELERATE THE RATE OF GENETIC IMPROVEMENT.

$499,900FY2021National Institute of Food and AgricultureUSDA

Michigan State University, East Lansing MI

Investigators

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