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Methods to implement ancestor discovery in the US dairy cattle database.

J. Nani




Methods to implement ancestor discovery in the US dairy cattle database.
J. Nani*1,2, J. Cole2, P. VanRaden2. 1Instituto Nacional de Tecnologia Agropecuaria EEA Rafaela Rafaela, SantaFe, Argentina, 2Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA Beltsville, MD.

Accurate and complete pedigrees are, even in the post genomics era, fundamental to plant and animal breeding because accurate genetic and genomic evaluations often rely on making genomic and pedigree relationships consistent. Program Fixped uses haplotypes to accurately confirm or discover distant relatives, such as maternal grandsires (MGS) and maternal great-grandsires (MGGS), with improved efficiency compared with individual SNP methods. In the US dairy cattle database, around 300,000 animals with no dam ID can be linked to their discovered MGS and MGGS by creating a constructed dam or maternal granddam (MGD) ID to fill in the missing pedigree information. Program Finddam creates the constructed dam and/or MGD ID to link calves to MGS and MGGS in the pedigree. This ID consists of 3 parts: 1) as currently, a 3-letter country code so that each country can construct their own IDs (i.e., USA), 2) DAM or MGD following the country code for the calf dam and maternal granddam respectively, and 3) the numeric portion of the calf ID (animal key) to ensure stability of data processing that can be expanded to 9 digits in the next few years. Program Finddam also allows linking calves to ~60,000 discovered MGS and MGGS not previously added because their dam and MGD ID were already reported. Recently expanded features of Fixped are discovery and confirmation of close relatives such as sires, dams, full and half sibs, clones, and paternal grandsires. Implementation of Fixped will increase the speed of genotype loading and avoid processing delays near deadlines because the current uploading program can then only confirm if the reported ancestors are correct and avoid searching the whole database for genotypes of relatives. Finally, when a real dam ID is found outside the database, those IDs will be preferred over constructed IDs unless the reported dam or MGD do not match the genotypes of the calf and grandsire. Pedigree providers will have an option to remove discovered relationships that they believe to be incorrect.

Keywords: ancestry discovery, pedigree, genomics.