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Title: Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.)

Author
item ARRUDA, MARCIO - University Of Illinois
item LIPKA, ALEX - University Of Illinois
item BROWN, P - University Of Illinois
item KRILL, A - University Of Illinois
item THURBER, C - Abraham Baldwin Agricultural College
item Brown-Guedira, Gina
item DONG, YANHONG - University Of Minnesota
item FORESMAN, B - University Of Illinois
item KOLB, FREDRICK - University Of Illinois

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2016
Publication Date: 6/16/2016
Citation: Arruda, M., Lipka, A., Brown, P.J., Krill, A.M., Thurber, C., Brown Guedira, G.L., Dong, Y., Foresman, B.J., Kolb, F. 2016. Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.). Molecular Breeding. 36(7):1-11.

Interpretive Summary: Genomic selection (GS) and marker-assisted selection (MAS) are two molecular breeding approaches that can be used for development of improved varieties of crops. Although similar, these approaches differ in their applications and how DNA markers are used to estimate the breeding values of different lines. In this study, GS and MAS were compared in their ability to predict resistance to a destructive wheat disease, Fusarium head blight (FHB). A panel consisting of 273 soft red winter wheat lines from the US Midwestern and Eastern regions was used in this study. The statistical models for MAS were built using markers for Fhb-1, the best-studied gene for FHB resistance, and two additional sets of markers: one independently identified by other groups and a newer set identified “in house”. In contrast, genomic selection models relied on 19,992 single nucleotide polymorphisms (SNPs) distributed throughout the genome. Intermediate to high values of prediction accuracy (0.4 – 0.9) were observed for most GS models, with lower values (< 0.3) found for MAS models. Our results indicate that GS is a more appropriate strategy than MAS for FHB resistance.

Technical Abstract: Genomic selection (GS) and marker-assisted selection (MAS) rely on marker-trait associations and are both routinely used for breeding purposes. Although similar, these two approaches differ in their applications and how markers are used to estimate breeding values. In this study, GS and MAS were compared in their ability to predict six traits associated with resistance to a destructive wheat disease, Fusarium head blight (FHB). A panel consisting of 273 soft red winter wheat lines from the US Midwestern and Eastern regions was used in this study. The statistical models for MAS were built using Fhb-1, the best-studied quantitative trait loci (QTL) for FHB resistance, and two sets of QTL: one independently identified by other groups and a newer set identified “in house”. In contrast, genomic selection models relied on 19,992 SNPs distributed throughout the genome. For the MAS and GS models, marker effects were respectively estimated with ordinary least square and ridge regression best unbiased linear prediction. Intermediate to high values of prediction accuracy (0.4 – 0.9) were observed for most GS models, with lower values (< 0.3) found for MAS models. Treating QTL as fixed effects in GS models resulted in higher prediction accuracy when compared with a GS model with only random effects, but overestimated accuracies were obtained with in house QTL. For the same selection intensity, GS resulted in higher selection differentials than MAS for all traits. Our results indicate that GS is a more appropriate strategy than MAS for FHB resistance.