A genome-wide SNP genotyping resource for tropical pine tree species

Area of Science:

• Genetics
• Forestry
• Bioinformatics

Background:

• Tropical pines are crucial for global timber production.
• Developing molecular tools is essential for their genetic improvement and conservation.
• Existing genetic resources for multispecies tropical pine genotyping are limited.

Purpose of the Study:

• To discover and develop a genome-wide, multispecies SNP genotyping array for tropical pines.
• To facilitate population genomics and molecular breeding in tropical pine species and their hybrids.

Main Methods:

• Gene and genome-targeted SNP discovery using pooled RNA-seq and capture-seq data.
• Development of a 420K SNP screening array from RNA-seq and capture-seq data.
• Selection of 50K SNPs for a commercial array, including ancestry-informative markers.

Main Results:

• Identified 1.3 million candidate transcript-based SNPs and 563K candidate capture-seq SNPs.
• Tiled 300K RNA-seq and 120K capture-seq SNPs onto a 420K screening array.
• Selected 50K SNPs for the Pitro50K chip, with 75% shared across multiple species, and 9.7K ancestry informative SNPs.

Conclusions:

• The Pitro50K SNP chip is a valuable resource for population genomics and molecular breeding in tropical pines.
• This array will support research and breeding efforts for major fast-growing tropical and subtropical pine plantations worldwide.
• The developed SNP markers will aid in species and hybrid discrimination, enhancing breeding strategies.