SNP marker development in Pinus sylvestris L. in stress-responsive genes characterized from Pinus cembra L....

Area of Science:

• Plant genetics
• Molecular ecology
• Forestry

Background:

• Massively parallel sequencing of cDNA generates valuable sequence data for expressed genes.
• Molecular markers like single nucleotide polymorphisms (SNPs) are crucial for detecting adaptive signals in populations.
• Stress-responsive genes are key targets for understanding environmental adaptation.

Purpose of the Study:

• To design novel PCR markers from the Swiss stone pine (Pinus cembra L.) transcriptome.
• To test these markers for SNPs in the Scots pine (Pinus sylvestris L.).
• To evaluate the utility of de novo markers for studying adaptive genetic variation in pines.

Main Methods:

• Designing PCR markers based on stress-responsive genes from Pinus cembra L. transcriptome.
• Testing 84 primers on Pinus sylvestris L. DNA from diverse habitats.
• Sequencing amplified products and performing BLAST searches.
• Analyzing polymorphic sites, including SNPs and indels, in 19 candidate genes.

Main Results:

• Identified 8 synonymous and 11 non-synonymous SNPs across 3735 analyzed sites in Pinus sylvestris L.
• No insertions/deletions (indels) were detected.
• Demonstrated the transferability of de novo markers from Pinus cembra L. to Pinus sylvestris L.

Conclusions:

• De novo molecular markers targeting conserved regions are effective across different pine species.
• The detected SNPs provide valuable tools for investigating adaptive genetic variation.
• These findings support the study of genes critical for the long-term adaptation of pine species.