Single-step genomic evaluations with 570K genotyped animals in US Holsteins
Keywords:APY, ssGBLUP, validation
The objectives of this study were to implement and evaluate the “Algorithm for proven and Young” (APY) for inversion of the genomic relationship matrix (G) in single-step genomic BLUP (ssGBLUP). Phenotypic data included 11,626,576 final scores on 7,093,380 US Holsteins and genotypes were available for 569,404 animals. Daughter deviations for young genotyped bulls with no classified daughters in 2009 but with at least 30 classified daughters in 2014 were computed using BLUP with all the phenotypes and pedigrees. Genomic predictions (GEBV) were obtained by ssGBLUP using phenotypes up to 2009. We calculated the G inverse with APY based on genomic recursions on a subset of “base” animals. We tested several subsets including 9,406 bulls with at least 1 daughter, 9,046 bulls and 1052 dams, 9,046 bulls and 7,422 classified cows, and random samples of 5,000, 10,000, 15,000, 20,000, and 30,000 animals. Validation reliability was calculated as R2 with a linear regression of daughter deviations on GEBV for young genotyped bulls. The reliabilities were 0.39 with 5,000 randomly chosen base-animals, 0.45 with base-animals including bulls and cows, and 0.44 with the remaining subsets. Setting up the G inverse for all the genotypes with 10,000 base-animals took 1.3 hours and 57GB of memory. Genomic predictions with G inverse are accurate when the number of base animals is at least 10,000. Single-step genomic BLUP using the G inverse via APY is applicable to populations with a large number of genotyped animals.
LicenseAuthors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).