Breeding and Genetics

摘要

Accurate and complete pedigrees are, even in the post genomics era,fundamental to plant and animal breeding because accurate genetic andgenomic evaluations often rely on making genomic and pedigree relationshipsconsistent. Program Fixped uses haplotypes to accurately confirmor discover distant relatives, such as maternal grandsires (MGS) andmaternal great-grandsires (MGGS), with improved efficiency comparedwith individual SNP methods. In the US dairy cattle database, around300,000 animals with no dam ID can be linked to their discovered MGSand MGGS by creating a constructed dam or maternal granddam (MGD)ID to fill in the missing pedigree information. Program Finddam createsthe constructed dam and/or MGD ID to link calves to MGS and MGGS inthe pedigree. This ID consists of 3 parts: 1) as currently, a 3-letter countrycode 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 maternalgranddam respectively, and 3) the numeric portion of the calf ID(animal key) to ensure stability of data processing that can be expandedto 9 digits in the next few years. Program Finddam also allows linkingcalves to ~60,000 discovered MGS and MGGS not previously added becausetheir dam and MGD ID were already reported. Recently expandedfeatures of Fixped are discovery and confirmation of close relativessuch as sires, dams, full and half sibs, clones, and paternal grandsires.Implementation of Fixped will increase the speed of genotype loading andavoid processing delays near deadlines because the current uploading programcan then only confirm if the reported ancestors are correct and avoidsearching the whole database for genotypes of relatives. Finally, whena real dam ID is found outside the database, those IDs will be preferredover constructed IDs unless the reported dam or MGD do not match thegenotypes of the calf and grandsire. Pedigree providers will have an optionto remove discovered relationships that they believe to be incorrect.