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 fail 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 ® 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.

Quantitative trait loci mapping for vegetative propagation in pedunculate oak

“…These authors identified 9 QTLs explaining between 2.79 and 8.11% of the phenotypic variance of rooting ability, with 5 being detected in two consecutive years and 4 being specific to only one year. In maritime pine (C. Plomion, unpublished data), only one strong QTL was detected on linkage group 6 of the map described by Plomion et al [25,26], explaining a high percentage (18.7%) of the phenotypic variance.…”

Establishment and optimization of ISSR and SAMPL molecular markers as a tool for breeding programs of Pinus radiata

“…The 22.3 % of segregation distortion detected can be due to band co-migration, on which two or more different loci generate bands of a similar or same size (Plomion et al 1995). Studies in the same species have detected up to 34 % of segregation distortion (Kuang et al 1999), however the smaller number of offspring compared to earlier studies (Wilcox et al 2001, Devey et al 2004 could be responsible for the low representativeness of the expected allelic proportions.…”

Contribution of two-dimensional electrophoresis of proteins to maritime pine genetics

“…The gels were simultaneously run and silverstained according to Damerval et al (1987) in the apparatus described by Granier and de Vienne (1986 (fig 1). In a haploid progeny we observed the 1:1 segregation ratio for presence and absence of a spot (Plomion et al, 1995b).…”

“…Although RFLPs are almost unlimited in number, they require elaborate laboratory techniques, which makes them labor intensive, timeconsuming and costly (Kesseli et al, 1994). In addition, DNA content is so high in Pinaceae (Ohri and Khoshoo, 1986;Wakamiya et al, 1993) Menozzi, 1993, 1995) and for genetic mapping (Plomion et al, 1995b (Tulsieram et al, 1992;Nelson et al, 1993;Binelli and Bucci, 1994;Plomion et al, 1995a), or when RAPD primers are screened for informative markers segregating 1:1 in diploid tissues (Carlson et al, 1991;Kubisiak et al, 1995). However, the conifer genome is characterized by a high proportion of repetitive DNA (Miksche and Hotta, 1973;Rake et al, 1980;Kriebel, 1985).…”

“…However, the conifer genome is characterized by a high proportion of repetitive DNA (Miksche and Hotta, 1973;Rake et al, 1980;Kriebel, 1985). Thus, RAPD markers tend to amplify from highly repetitive DNA (ie, mostly noncoding DNA) (Plomion et al, 1995b).…”