Molecular Marker Linkage Mapping in Southern Pine (Longleaf Pine and Slash Pine).

Abstract

The goal of this work was to develop molecular markers for use in a backcross breeding program to speed the introgression of genes influencing rapid early height growth (EHG) from slash pine (Pinus elliottii Engelm. var. elliottii) into longleaf pine (Pinus palustris Mill.). The efficacy of molecular markers for genetic mapping in the Pinaceae was determined in segregating haploid and diploid populations. Initial screening for genetic polymorphisms was conducted using the random amplified polymorphic DNA (RAPD) technique. Using DNAs obtained from haploid megagametophytes, a RAPD-based genetic map for longleaf pine clone 3-356 (16 linkage groups and 6 pairs (133 markers) covering 1,635 cM) was constructed. Concern regarding the efficacy of RAPD data lead to a series of computer simulations investigating the effects of missing and mis-scored data on linkage group construction. Given the parameters investigated, levels as high as 15% missing data and 2% mis-scored data still provided accurate low-to medium-density map construction. Individual parental maps were constructed with F$\sb1$ progeny from a slash pine H-28 (X) x longleaf pine 3-356 (X) cross. The longleaf pine 3-356 map consisted of 18 groups and 3 pairs (122 markers) covering 1367.5 cM, and the slash pine H-28 map 13 groups and 6 pairs (91 markers) covering 952.9 cM. Orders and distances of loci in common between the two maps constructed for longleaf pine 3-356 were compared. Orders were found to be conserved for those groups containing three or more loci. However, genetic distance estimates varied considerably, but not in any systematic manner. RAPD and allozyme loci identified as being heterozygous in both parents were utilized to combine the parent-specific maps constructed for the slash pine x longleaf pine cross. Five RAPD loci and one allozyme locus suggested homology between the otherwise parent-specific linkage groups. Substantial phenotypic variation for EHG was observed in the F$\sb1$ population, therefore the parent-specific markers and maps were used to localize putative EHG QTL. Using simultaneous marker models (multiple regression), marker loci were found to be significantly associated with QTL influencing hypocotyl length, total height, brown spot resistance and root collar diameter.