Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

Abstract

A detailed genomic map was constructed for one F1 individual of maritime pine, using randomly amplified polymorphic DNA (RAPD) and protein markers scored on megagametophytes of germinated seeds. Proteins allowed the localization of exclusively coding DNA in the large genome of this Pinus species, mapped with RAPD markers that essentially fall within repetitive (i.e. mostly noncoding) DNA. Dot blots experiments of 53 RAPD fragments showed that 89 per cent amplified from highly repetitive chromosomal regions. The map comprised 463 loci, including 436 RAPDs amplified from 142 10-mer oligonucleotide primers and 27 protein loci. Twelve major and one minor linkage groups were identified using a LOD score ⩽ 5 and a recombination fraction Θ ≤ 0.30. A framework map was ordered with an interval support ≥4, covering 1860 cM which provided almost complete coverage of the maritime pine genome. The average distance between two framework markers was 8.3 cM; only one interval was larger than 30 cM. Protein loci were well distributed throughout the map. Their potential use as anchor points to join RAPD-based maps is discussed. Finally, the genomic maps of Arabidopsis and maritime pine were compared. Linkage groups were shown to have similar total map lengths on a chromosomal basis, despite a 57-fold difference in DNA content.