Cross-species transferability and mapping of genomic and cDNA SSRs in pines

• Published in: Theoretical and applied genetics 2004-10, Vol.109 (6), p.1204-1214
• Main Authors: Chagne, D, Chaumeil, P, Ramboer, A, Collada, C, Guevara, A, Cervera, M.T, Vendramin, G.G, Garcia, V, Frigerio, J.M, Echt, C
• Format: Article
• Language: English
• Subjects: Base Sequence; Biological and medical sciences; Chromosome Mapping; Chromosomes; Classical genetics, quantitative genetics, hybrids; complementary DNA; computer analysis; computer software; Crosses, Genetic; DNA Primers; DNA, Complementary - genetics; DNA, Plant - genetics; Fundamental and applied biological sciences. Psychology; genes; Genetic Markers; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Life Sciences; Methods, theories and miscellaneous; Microsatellite Repeats; Phylogeny; Pinus; Pinus - genetics; Pinus pinaster; Pinus taeda; Pinus taeda - genetics; Polymerase Chain Reaction; Pteridophyta, spermatophyta; Repetitive Sequences, Nucleic Acid; SSRIT software; Trinucleotide Repeats; Vegetals
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-004-1683-z

Two unigene datasets of Pinus taeda and Pinus pinaster were screened to detect di-, tri- and tetranucleotide repeated motifs using the SSRIT script. A total of 419 simple sequence repeats (SSRs) were identified, from which only 12.8% overlapped between the two sets. The position of the SSRs within their coding sequences were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 51% in P. taeda and P. pinaster, respectively) and tended to be found within translated regions (76% in both species), whereas dinucleotide repeats were preferentially found within the 5'-and 3'-untranslated regions (75 and 65%, respectively). Fifty-three primer pairs amplifying a single PCR fragment in the source species (mainly P. taeda), were tested for amplification in six other pine species. The amplification rate with other pine species was high and corresponded with the phylogenetic distance between species, varying from 64.6% in P. canariensis to 94.2% in P. radiata. Genomic SSRs were found to be less transferable; 58 of the 107 primer pairs (i.e., 54%) derived from P. radiata amplified a single fragment in P. pinaster. Nine cDNA-SSRs were located to their chromosomes in two P. pinaster linkage maps. The level of polymorphism of these cDNA-SSRs was compared to that of previously and newly developed genomic-SSRs. Overall, genomic SSRs tend to perform better in terms of heterozygosity and number of alleles. This study suggests that useful SSR markers can be developed from pine ESTs.