SAINT PAUL, MINNESOTA

University of Minnesota

MANHATTAN, KANSAS

Kansas State University

Marker-assisted selection without QTL mapping: prospects for genome-wide selection for quantitative traits in maize

-- Bernardo, R., Yu, J.

The availability of cheap and abundant molecular markers in maize has allowed breeders to ask “How can molecular markers best be used to achieve breeding progress?” without conditioning this question on how breeding has traditionally been done. Exploiting molecular markers in breeding has involved finding a subset of markers associated with one or more traits, i.e., QTL mapping. In contrast, genome-wide selection refers to marker-based selection without first identifying a subset of markers with significant effects. Our objectives were to assess, in simulation studies, the response due to genome-wide selection compared with marker-assisted recurrent selection (MARS), and to determine the extent to which phenotyping can be minimized and genotyping maximized in genome-wide selection. We simulated genome-wide selection that comprised evaluating doubled haploids for testcross performance in cycle 0, followed by two cycles of selection based on markers. Individuals were genotyped for a set of 128, 256, 512, or 768 markers, and breeding values associated with each of the markers were predicted and were all used in genome-wide selection. We found that across different numbers of QTL (20, 40, and 100) and levels of heritability, the response to genome-wide selection was 18 to 43% larger than the response to MARS. Responses to selection were maintained when the number of doubled haploids phenotyped and genotyped in cycle 0 was reduced and the number of plants genotyped in cycles 1 and 2 was increased. Such schemes that minimize phenotyping and maximize genotyping would be feasible only if the cost per marker data point is reduced to about 2 cents. The convenient but incorrect assumption of equal marker variances led to only a minimal loss in the response to genome-wide selection. We conclude that genome-wide selection, as a brute-force and black-box procedure that exploits cheap and abundant molecular markers, is superior to MARS in maize.