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Identification and Validation of Single Nucleotide Polymorphisms in Poplar Using Publicly Expressed Sequence Tags

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Abstract:

By using assembled expressed sequence tags (ESTs) from 14 different cDNA libraries that contain 84 132 sequences reads, 556 Populus candidate single nucleotide polymorphisms (SNPs) were identified. Because traces were not available from dbEST ( http://www.ncbi.nlm.nih.gov/dbEST/index.html), stringent filters were used to identify reliable candidate SNPs. Sequences analysis indicated that the main types of substitutions among candidate SNPs were A/G and T/C transitions, which accounted for 22.0% and 30.8%, respectively. One hundred and ten candidate SNPs were tested. As a result, 38 candidate SNPs were confirmed by directed sequencing of PCR products amplified from six different individuals. Thirteen new SNPs in intron regions were found and multiple SNPs were found to be located in both intron and exon regions of four contigs. Heterozygosis was found in all 47 candidate sites and five SNP sites were heterozygous in all six samples. This is the first report of SNP identification in a tree species which reveals that assembled ESTs from multiple libraries of the public database may provide a rich source of comparative sequences for an SNP search in the poplar genome.

(Managing editor: Li-Hui ZHAO)
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Keywords: expressed sequence tag; poplar; single nucleotide polymorphism

Document Type: Research Article

Affiliations: 1: Forest Genetics and Gene Engineering Laboratory, Nanjing Forestry University, Nanjing 210037, China 2: Genomics and Bioinformatics Institute, Hangzhou 310008, China

Publication date: December 1, 2005

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