Major gene detection for fusiform rust resistance using segregation analysis and linkage analysis in loblolly pine

This research explored a new analytical approach to detect major gene(s) for fusiform rust resistance using complex segregation analysis in a diallel progeny population of loblolly pine (Pinus taeda L.). Time trends and genetic differences for infection were analyzed with a polygenic model using a Bayesian logistic approach for a progeny population from a six-parent half-diallel. Large genetic differences among parents were found. Among the six parents, parent A showed consistently low infection over time and across sites. This genetic difference could be due to strong polygenic effects and/or major gene effects. A Bayesian analysis of a threshold model with Gibbs sampler was developed and used to make inferences about a mixed inheritance model (MIM) of major genes and polygenes. Results showed that the MIM was a better model to explain the inheritance of rust-resistance than the pure polygenic model. A large major gene variance (above 40% of total variance) indicated the existence of major genes for rust resistance in this population. Estimates of parental genotypes and probabilities of carrying favorable alleles showed that parent A might carry two favorable alleles. Bulk segregant and marker/trait co-segregation analyses were used to search for major resistance genes. An improved map of the Fr2 resistance linkage group was developed with additional RAPD markers found in this study. An effort to define another resistance locus in parent A using progeny of cross A x F inoculated with an intermediate spore density using mixed gall inoculum was not successful, perhaps because of the complexity of suspected multiple gene interaction effects in tree A and unknown pathogen virulence composition. With high inoculum density and mixed inocula, a proposed two-gene model as an explanation for observed rust infection in the current diallel progeny population could not be confirmed by molecular evidence. Results of this study provided molecular and statistical evidence to support that the parent A may carry multiple rust resistance genes.