Genetic models and analytical methods were evaluated to make statistical inferences about the major gene and polygenic effects on quantitative traits for progenies derived from a half-diallel mating design. Using simulated data with different major and polygenic effects, the mixed model could accurately estimate the major and polygenic effects of quantitative traits, and possible genotypes of parents and progenies. Molecular markers of RAPDS were examined for association with phenotypes for tree height and rust infection in a diallel progeny population. A computer program "Mgene" was developed based on this method to screen the progeny test data from the N. C. State University-Industry Cooperative Tree Improvement Program. Superior parents were identified with major genes for growth and disease resistance in loblolly pine populations. Of the over 190 diallels analyzed with this program, nineteen diallels have been found to have the major gene effects in height growth. Some of these superior parents were also found to have high breeding values based on the traditional genetic analysis. With the putative genotypes of superior trees identified, breeders can make effective decisions on management of breeding populations and deployment program.
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