Methods for mapping a phenotypic trait to a corresponding chromosomal location are provided. Statistical methods which correlate pedigrees with multiple genetic markers, the haplotype, to determine identical-by-descent (IBD) data are employed to map phenotypic traits. The statistical models provided are a HAPLO-IM+ model, a HAPLO-MQM model, and a HAPLO-MQM+ model. These statistical methods are applied to map traits determined alternatively by single genes or by quantitative trait loci. Methods of marker assisted selection (MAS) using a variety of genetic markers are provided. Plants selected by MAS using the methods are provided. Additionally, methods for cloning nucleic acids corresponding to phenotypic traits that are in linkage disequilibrium with genetic markers are provided, and for transducing them into plant cells are provided. Transgenic plants transduced with the cloned nucleic acids corresponding to phenotypic traits, e.g. QTL, are provided.
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