An Integrated Linkage Map of Loblolly Pine and its Application in QTL Mapping in a Multi-Parent, Pedigree-Structured Population

The genetic linkage map remains a crucial tool for quantitative trait loci (QTL) mapping and marker-aided selection (MAS), particularly in the absence of a physical map or genome sequence.  Although several linkage maps currently exist for loblolly pine (Pinus taeda), including an SSR-based reference map (Echt et al. 2011), additional integration is now possible using recently developed SNP markers.  Such integration and reference map should be highly beneficial for QTL mapping and MAS, comparative genomics, and genome assembly.  Data from the two most recent genetic linkage maps based on SSRs (Echt et al. 2011) and SNPs (Eckert et al. 2010) were combined in JoinMap to construct a new integrated, reference map for loblolly pine.  Constructed from a subset of DNA-based markers (1908 SNPs, 171 SSRs, 65 ESTP and 172 RFLPs) segregating in one common full-sib family (n=162), this map was used to analyze marker genotypes from the multi-parent, pedigreed-structured CCLONEs population (e.g., Resende et al. 2011).  Both association- and map-based methods were used to identify fusiform rust (caused by Cronartium quercuum fsp. fusiforme) resistance QTLs.  Genetic relationships between individuals in the population were inferred from the SSR and SNP marker data using an identity-by-descent (IBD) approach and were then used to correct the pedigree.  Missing progeny genotypes were imputed using Bayesian Analysis of Missing Data (BAMD) and parental genotypes were inferred both by examining the segregation data as well as with a maximum likelihood method implemented in COLONY (Jones and Wang 2010).  Significance of the present results for MAS for rust resistance, including genomic selection, will be presented and discussed.