High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

Abstract

The development and application of genomic tools to loblolly pine (Pinus taeda L.) offer promising insights into the organization and structure of conifer genomes. The application of a high-throughput genotyping assay across diverse forest tree species, however, is currently limited taxonomically. This is despite the ongoing development of genome-scale projects aiming at the construction of expressed sequence tag (EST) libraries and the resequencing of EST-derived unigenes for a diverse array of forest tree species. In this paper, we report on the application of Illumina's high-throughput GoldenGate™ SNP genotyping assay to a loblolly pine mapping population. Single nucleotide polymorphisms (SNPs) were identified through resequencing of previously identified wood quality, drought tolerance, and disease resistance candidate genes prior to genotyping. From that effort, a 384 multiplexed SNP assay was developed for high-throughput genotyping. Approximately 67% of the 384 SNPs queried converted into high-quality genotypes for the 48 progeny samples. Of those 257 successfully genotyped SNPs, 70 were segregating within the mapping population. A total of 27 candidate genes were subsequently mapped onto the existing loblolly pine consensus map, which consists of 12 linkage groups spanning a total map distance of 1,227.6 cM. The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics.

Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

“…Given the availability of a large number of single nucleotide polymorphic (SNP) markers for the loblolly pine genome [15], we hypothesized that associations could be detected based on SNP marker linkage to Fr genes. The CCLONES population was already genotyped for SNP markers on each chromosome, so that bulk segregant analysis need not be performed on pools of galled and non-galled progeny to identify Fr-linked markers.…”

Ecological and association genetics in two Mediterranean pine species

“…High-throughput SNP genotyping has been successfully implemented in several conifers (Pavy et al 2008;Eckert et al 2009a;. This approach has generated thousands of markers for genetic mapping, significantly improving our understanding of large and complex conifer genomes (Jermstad et al 2011;Pavy et al 2012;Mart ınez-Garc ıa et al 2013;Neves et al 2014).…”

Application of selected molecular markers in studies on forest trees

“…By use of the Illumina platform, it was possible to create a genotyping chip containing 7252 SNP, the largest of the so far prepared ones for Pinus pinaster (Plomion et al 2016). Analyses with the use of thirdgeneration sequencing technology have been successfully performed also for other coniferous species (Pavy et al 2008;Eckert et al 2009;Chancerel et al 2013;Liu et al 2014). Data obtained by this method have wideranging applications: mapping genomes, identifying seeds with their origins, comparing natural and bred populations, investigating genetic diversity with respect to phenotypic diversity, concluding on historical processes, demographic events as well as selection and adaptation.…”