Related Experiment Video
Updated: May 31, 2026
07:01
Processing the Loblolly Pine PtGen2 cDNA Microarray
Published on: March 20, 2009
Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative
Emilie Chancerel1, Camille Lepoittevin, Grégoire Le Provost
1INRA, UMR1202 BIOGECO, F-33610 Cestas, France.
BMC Genomics
|July 20, 2011
Summary
High-throughput single nucleotide polymorphism (SNP) genotyping using the GoldenGate assay is effective for genetic mapping in maritime pine. This approach enables robust genetic map construction and comparative genomics in conifers.
Area of Science:
- Genetics
- Bioinformatics
- Forestry
Background:
- Single nucleotide polymorphisms (SNPs) are key genetic variations.
- Advanced genotyping technologies enable large-scale SNP analysis for diverse applications.
- Maritime pine (Pinus pinaster Ait.) is a crucial conifer for European plantations.
Purpose of the Study:
- Evaluate the efficacy of high-throughput SNP genotyping for genetic mapping in maritime pine.
- Develop a custom SNP assay for maritime pine.
- Construct genetic maps and facilitate comparative genomics.
Main Methods:
- Designed a custom GoldenGate assay for 1,536 SNPs (in vitro and in silico).
- Genotyped offspring from outbred (G2) and inbred (F2) pedigrees.
- Integrated mapped SNPs with existing markers and constructed consensus maps.
Main Results:
- Achieved assay success rates of 63.6% (in silico) and 74.8% (in vitro) with a 0.4% error rate.
- Mapped 394 SNPs, integrating 287 into G2 maps and 179 into F2 maps.
- Generated a consensus map of 357 SNPs and aligned linkage groups with Pinus taeda.
Conclusions:
- The GoldenGate assay is successful for high-throughput SNP genotyping in maritime pine.
- The SNP array will be expanded using new sequencing technologies for broader comparative genomics.
- This work provides anchor points for comparative genomics across conifer species.
