Genotyping Populus deltoides By Exome Resequencing

Poplars have emerged as model trees to study the biology and genetics of woody, perennial plants. We are using an association genetics approach to identify the genes that regulate wood formation and biomass growth, taking advantage of the availability of a reference genome to design assays for exome resequencing and genotyping. In this study we genotyped 579 individuals of a Populus deltoides (eastern cottonwood) association population. Barcoded genomic DNA libraries were generated and multiplexed exome capture was performed using a total of 204,108 probes to capture 18,153 genes. The captured DNA was sequenced using the Illumina HiSeq 2000 platform and aligned to the reference genome with MOSAIK. Single nucleotide polymorphisms (SNPs) were identified using FREEBAYES and GATK software. A total of 99.3% of the target genes were captured and one million SNPs were identified in the population, which will now be tested for association with biomass productivity measured in greenhouse and field conditions, and wood quality traits. Because population genetic structure can generate spurious associations in association studies, a subset of 10,000 SNPs was used to verify if this confounding effect was significant. The analysis with the software STRUCTURE revealed the presence of three main subpopulations, indicating that the future association genetics study needs to account for this structure in our population.