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Advances in Genomic Selection and GWA
Genomic selection (GS) was applied to all major farm species including dairy, beef, pigs and chicken. Initial methodology was a multi-step procedure consisting of BLUP evaluation, extraction of pseudo-observations for genotyped animals, running genomic predictions via estimation of SNP effects or genomic relationships, and combining genomic and conventional predictions in an index. A newer single-step (SS) procedure works as BLUP with combined pedigree and genomic relationships.
Experiences with GS indicate that:
1) a few thousand genotyped animals are required for a reasonable increase in accuracy over BLUP,
2) SNP effects are not QTLs,
3) SNP selection seem to increase the accuracy of GEBV more with small but almost none with large genotyped population,
4) differences between methods based on estimation of SNP effects and genomic relationships are small,
5) gains with SNP chip > 50k are minimal,
6) gains from genotyping low-accuracy animals are small,
7) across breed/line prediction does not work,
8) genomic predictions decay over time requiring constant phenotyping,
9) single-step procedure is much simpler to use than multi-step and usually more accurate.
Experiences are in agreement with findings that the number of effective SNP is a function of effective population size and equals about 10,000 for cattle and less than 5,000 for pigs and broiler chicken. Gains in accuracy due to genomics for different types of animals can be explained by decomposition of GEBV due to phenotypes, pedigree and genomic information.
Practical applications of GS indicate many potential problems and potentially genomic prediction that is less accurate than the conventional prediction. Problems include genotyping errors, pedigree errors, incorrect imputation, issues with deregression, inaccurate index, etc. Any application of GS requires a proper validation; validation technique used in dairy may be unsuitable for pigs.
For commercial use, the most flexible yet least trouble-prone methodology is a single-step procedure that, with recently developed algorithm for inversion of genomic relationship matrix, can accommodate any number of genotyped animals at low cost.
Keywords: Genomic selection; commercial application; single-step