Exome Resequencing in a Populus deltoides Association Population

Populus deltoides (eastern cottonwood) is a model species to study the biology and genetics of wood formation and biomass growth in woody, perennial plants. The availability of a reference genome and ease of genetic transformation and vegetative propagation make poplars especially suited to conduct association genetics studies to identify the genes determining bioenergy traits. In this study we are resequencing the coding fraction of the genome in 579 individuals of a P. deltoides association population. This “whole-genome” genotyping approach is based on the generation of barcoded genomic DNA libraries, multiplexed exome capture and sequencing of the captured DNA. A total of 204,108 oligonucleotide probes were designed to capture 18,153 genes. This highly multiplexed genome complexity reduction by sequence capture allows high-throughput characterization of a large number of individuals, and reduces the sequencing cost significantly. The information generated will be analyzed to identify polymorphisms such as single nucleotide polymorphisms (SNPs) and copy number variants (CNVs), which will be used for population genetics and association studies. The final goal is the identification of polymorphisms responsible for biomass productivity and wood quality traits.