Date Published: June 24, 2019
Publisher: Public Library of Science
Author(s): Diógenes Ferreira Filho, Júlio Sílvio de Sousa Bueno Filho, Luciana Correia de Almeida Regitano, Maurício Mello de Alencar, Rosiana Rodrigues Alves, Sarah Laguna Conceição Meirelles, Tiratha Raj Singh.
Analysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (p≫n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg, the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the p≫n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotypes in validation groups of a cross-validation scheme; and when we selected a larger number of markers (more than 100), the correlations exceeded 0.90, showing the efficiency in identifying relevant SNPs (or segregations) for both GWAS and GWS. In the simulation study, we obtained similar results.
Technological advances in the genotyping process have allowed the development of new molecular marker classes, among which single nucleotide polymorphism (SNP) stands out. One of the main advantages of this type of marker is the possibility of simultaneous genotyping of thousands of SNPs, widely distributed throughout the genome, such that some of these markers will probably be in linkage disequilibrium with quantitative trait loci (QTLs).
The tournament method tends to consistently select the same markers in repeated analyses, whereas Bayesian Lasso tends to select different markers.