title: Experiences with a single-step genome evaluation.
abstract: Genomic selection can be implemented based on the genomic relationship matrix (GBLUP) and can be combined with phenotypes from nongenotyped animals through the use of best linear unbiased prediction (BLUP). A common method to combine both sources of information involves multiple steps, but is difficult to use with complicated models and is nonoptimal. A simpler method, termed single-step GBLUP, or ssGBLUP, integrates the genomically derived relationships (G) with population-based pedigree relationships (A) into a combined relationship matrix (H) and allows for genomic selection in a single step. The ssGBLUP method is easy to implement and uses standard BLUP-based programs. Experiences with field data in chickens, pigs, and dairy indicate that ssGBLUP is more accurate yet much simpler than multi-step methods. The current limits of ssGBLUP are approximately 100,000 genotypes and 18 traits. Models involving 10 million animals have been run successfully. The inverse of H can also be used in existing programs for parameter estimationm, but a properly scaled G is needed for unbiased estimation. Also, as genomic predictions can be converted to SNP effects, ssGBLUP is useful for genomic-wide association studies. The single-step method for genomic selection translates the use of genomic information into standard BLUP, and variance-component estimation programs become a routine.
authors: Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA. ignacy@uga.edu
authors: Ignacy
authors: I
authors: Misztal
authors: Samuel E
authors: SE
authors: Aggrey
authors: William M
authors: WM
authors: Muir
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D003198:Computer Simulation; D016678:Genome; D023281:Genomics / Q000379:methods*; D058751:Livestock / Q000235:genetics*; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D012044:Regression Analysis; D034421:Sus scrofa / Q000235:genetics*