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

Abstract

We performed gene and genome targeted SNP discovery towards the development of a genome-wide, multispecies genotyping array for tropical pines. Pooled RNA-seq data from shoots of seedlings from five tropical pine species was used to identify transcript-based SNPs resulting in 1.3million candidate Affymetrix SNP probe sets. In addition, we used a custom 40K probe set to perform capture-seq in pooled DNA from 81 provenances representing the natural ranges of six tropical pine species in Mexico and Central America resulting in 563K candidate SNP probe sets. Altogether, 300K RNA-seq (72%) and 120K capture-seq (28%) derived SNP probe sets were tiled on a 420K screening array that was used to genotype 576 trees representing the 81 provenances and commercial breeding material. Based on the screening array results, 50K SNPs were selected for commercial SNP array production including 20K polymorphic SNPs for P. patula, P. tecunumanii, P. oocarpa and P. caribaea, 15K for P. greggii and P. maximinoi, 13K for P. elliottii and 8K for P. pseudostrobus. We included 9.7K ancestry informative SNPs that will be valuable for species and hybrid discrimination. Of the 50K SNP markers, 25% are polymorphic in only one species, while 75% are shared by two or more species. The Pitro50K SNP chip will be useful for population genomics and molecular breeding in this group of pine species that, together with their hybrids, represent the majority of fast-growing tropical and subtropical pine plantations globally.