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

Author: Chagne, D.; Chaumeil, P.; Ramboer, A.; Collada, C.; Guevara, A.; Cervera, M. T.; Vendramin, G. G.; Garcia, V.; Frigerio, J-M.; Echt, Craig; Richardson, T.; Plomion, Christophe;

Date: 2004

Source: Theor. Appl. Genet. (2004) 109: 1204-1214

Publication Series: Miscellaneous Publication

Description: 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 the coding sequence were predicted using FrameD. Trinucleotides appeared to be the most abundant repeated motif (63 and 5 1% in P. taedu 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). Fiky-three primer pairs amplifying a single PCR fragment in the source species (mainly P. tuedu), 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 cDNASSRs 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.

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Chagne, D.; Chaumeil, P.; Ramboer, A.; Collada, C.; Guevara, A.; Cervera, M. T.; Vendramin, G. G.; Garcia, V.; Frigerio, J-M.; Echt, Craig; Richardson, T.; Plomion, Christophe 2004. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor. Appl. Genet. (2004) 109: 1204-1214

 


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