Phantom epistasis in genomic selection: on the predictive ability of epistatic models

• Autores: Schrauf, Matías Florián; Martini, Johannes W.R.; Simianer, Henner; de los Campos, Gustavo; Cantet, Rodolfo Juan Carlos; Freudenthal, Jan; Korte, Arthur; Munilla Leguizamon, Sebastian
• Año de publicación: 2020
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: ADDITIVE EFFECTS; BREEDING; EPISTASIS; GENOMIC; GENOMICS; GENPRED; PREDICTION; RESOURCES; SHARED DATA
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

Genomic selection uses whole-genome marker models to predict phenotypes or genetic values for complex traits. Some of these models fit interaction terms between markers, and are therefore called epistatic. The biological interpretation of the corresponding fitted effects is not straightforward and there is the threat of overinterpreting their functional meaning. Here we show that the predictive ability of epistatic models relative to additive models can change with the density of the marker panel. In more detail, we show that for publicly available Arabidopsis and rice datasets, an initial superiority of epistatic models over additive models, which can be observed at a lower marker density, vanishes when the number of markers increases. We relate these observations to earlier results reported in the context of association studies which showed that detecting statistical epistatic effects may not only be related to interactions in the underlying genetic architecture, but also to incomplete linkage disequilibrium at low marker density (“Phantom Epistasis”). Finally, we illustrate in a simulation study that due to phantom epistasis, epistatic models may also predict the genetic value of an underlying purely additive genetic architecture better than additive models, when the marker density is low. Our observations can encourage the use of genomic epistatic models with low density panels, and discourage their biological over-interpretation.
Fil: Schrauf, Matías Florián. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Cátedra de Mejoramiento Genético Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Martini, Johannes W.R.. Centro Internacional de Mejoramiento de Maíz y Trigo; México
Fil: Simianer, Henner. Universität Göttingen; Alemania
Fil: de los Campos, Gustavo. Michigan State University; Estados Unidos
Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina
Fil: Freudenthal, Jan. Universität Würzburg; Alemania
Fil: Korte, Arthur. Universität Würzburg; Alemania
Fil: Munilla Leguizamon, Sebastian. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Cátedra de Mejoramiento Genético Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina