A High-Density, Consensus Linkage Map for Loblolly Pine

Loblolly pine (Pinus taeda) is the most widely cultivated and fastest growing pine species in the southeastern United States.  A high-density consensus genetic linkage map for loblolly pine is needed for comparing the locations of genotype-phenotype associations between populations, for accelerated breeding with genomic selection, and for comparisons of genome structure between species and populations.  A linear programming approach (MergeMap, Wu et al 2011) was used to merge the maps of Echt et al., (2011) and Martínez-García et al., (2013) with an unpublished map constructed from two unrelated mapping populations - BC1, a pseudo-backcross ([P. elliottii x P. taeda] x P. elliottii]) and 10-5, a sample of megagametophytes from a single tree.  The Martínez-García map contains 2466 SNP, SSR and other markers genotyped in 689 individuals from BASE and QTL populations whereas, the Echt et al. (2011) reference map contains 492 SSR, RFLP and ESTP markers genotyped in 270 individuals from the BASE population.  The BC1_10-5 composite map was constructed using segregation data from the two populations (BC1, 772 SNPs and 490 full-sib progeny; 10-5, 2841 SNPs and 72 haploid megagametophyte samples) for 173 shared markers.  The Martínez-García and Echt maps were merged using MergeMap with the BC1_10-5 map using 796 SNPs common to the three maps. The final consensus map includes 4744 markers with 346 to 481 markers per linkage group with mean and maximum distances of 0.45 cM and 4.0 cM between adjacent markers, respectively.  The resulting consensus map was used to estimate linkage disequilibrium (LD) extent in three experimental populations with contrasting genetic designs (i.e., a full-sib QTL mapping population, a multi-family pedigree, and an unrelated association mapping population).  Estimates of LD extent were used to estimate the density of markers required to represent all segregating haplotype blocks in each population for the purposes of comprehensively discovering causal variants controlling quantitative traits and accurately predicting phenotype from genotype.  This high-density consensus map provides an important new resource for the conifer genetics community allowing for powerful comparative analyses of genome-wide genetic properties between individuals, populations and species.  The enhanced understanding will promote progress on developing maker-assisted and genomic selection applications in loblolly pine and other important pine species world-wide.