An Axiom SNP genotyping array for Douglas-fir

Area of Science:

• Forestry
• Genetics
• Plant Science

Background:

• Genetic markers are crucial for understanding forest tree populations, quantitative trait loci, gene function, and breeding.
• Advancements in genotyping technologies now allow for large-scale SNP analysis.
• Douglas-fir is a globally significant tree species economically and ecologically.

Purpose of the Study:

• To design and validate SNP assays for Douglas-fir (Pseudotsuga menziesii).
• To assess the utility of these SNPs for population genomics and genomic selection.
• To improve genome coverage and increase the number of reliably genotyped SNPs.

Main Methods:

• Designed SNP assays for over 55,000 potential SNPs based on transcriptome sequencing.
• Tested SNP assays on approximately 2,300 coastal and 13 interior Douglas-fir trees.
• Developed protocols to 'rescue' SNPs failing quality control by lowering call rate thresholds.

Main Results:

• As many as 28,000 SNPs were reliably genotyped and polymorphic.
• Lowering the SNP call rate threshold increased successful SNPs from 20,669 to 28,094.
• SNPs demonstrated good performance in Hardy-Weinberg equilibrium and minor allele frequency, and worked well on interior Douglas-fir.

Conclusions:

• The developed SNP assays can genotype 10,000-15,000 loci.
• The Axiom genotyping array provides a foundation for Douglas-fir population genomics and genomic selection.
• The array is currently being used to construct a linkage map and test genomic selection.