Development of a single nucleotide polymorphism array for population genomic studies in four European pine species.

Annika Perry,Stephen Cavers,Witold Wachowiak,Alison Downing,Richard Talbot

doi:10.1111/1755-0998.13223

Abstract

Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N=20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.

Highlights

Due to their high ecological and economic value, tree species have been intensively studied to evaluate their genetic diversity, evolutionary and population history as well as applied areas including conservation and tree breeding (De La Torre et al, 2014; Pyhäjärvi, Kujala, & Savolainen, 2019)
We considered all available genomic resources for these species, including single nucleotide polymorphism (SNP) derived from transcriptomes and resequencing of candidate genes from previous population genetic studies
Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array with an average of 3.47 SNPs per unigene

Summary

| INTRODUCTION

Due to their high ecological and economic value, tree species have been intensively studied to evaluate their genetic diversity, evolutionary and population history as well as applied areas including conservation and tree breeding (De La Torre et al, 2014; Pyhäjärvi, Kujala, & Savolainen, 2019). Arrays containing thousands of loci provide much higher coverage and resolution of the genome compared with traditional sequencing and PCR-based genotyping methods Their usefulness is dependent on the inclusion of markers, which have been carefully chosen to avoid ascertainment bias, either via their distribution across the genome or their frequency within and among populations. We describe the design and testing of a 49,829 SNP chip (Axiom_PineGAP array) for population genetic and molecular breeding studies in pines, with a focus on Scots pine (Pinus sylvestris L.), dwarf mountain pine (P. mugo T.), mountain pine (P. uncinata R.) and peat-bog pine (P. uliginosa N.) These taxa form a monophyletic group within Pinaceae, but differ strongly in phenotype, geographical distribution and ecology (Wachowiak, Perry, Donnelly, & Cavers, 2018). The aim was to develop a new large scale molecular tool for population genomic analysis of pines and to test its ability to differentiate species by genotyping a sample collection from each of the focal species

| Design of the array

Findings

| DISCUSSION