Maize Genetics Cooperation Newsletter vol
81 2007
University of Minnesota
Kansas State University
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.
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