R. J. Goos

Marker-assisted versus phenotypic selection for iron-deficiency chlorosis in soybean

Iron-deficiency chlorosis (IDC) is an important agronomic trait when soybean (Glycine max (L.) Merr.) is planted on calcareous soil. Breeders need confirmation that marker-QTL (quantitative trait loci) associations developed using association mapping, will be effective in a different set of genotypes than the ones used to identify those markers. Marker-QTL associations that had previously been identified in separate mapping experiments were evaluated. Marker-assisted selection (MAS) was compared to phenotypic selection (PS) to evaluate the association mapping approach to identifying markers. The PS or MAS criteria were used to select the 20 most IDC-tolerant and IDC-susceptible lines, based on three 2009 selection sites. Three sites in 2010 were used as validation to compare the effectiveness of the different selection criteria. A random sample (RS) was generated as a control. When validation was conducted averaged across three 2010 sites, PS was the best method to select for IDC with a mean of 1.78, compared to MAS with a mean of 2.05. Since PS was so effective the process of genotyping, which is required for MAS, was unnecessary. The additive effects of QTL that had been estimated from the original mapping experiments were biased upward when compared to QTL effects estimated from the 2009 data. Also, many markers in the target population of experimental lines did not have a gene frequency of 0.5, which greatly reduced the effectiveness of MAS.