Whole Genome Re-Sequencing and Mutation Screening In Hundreds Of North-American Poplar Trees

The genus Populus is phenotypically diverse and naturally adapted to a wide range of environments. Under ideal environmental conditions, poplar trees are fast growing and hardy with excellent wood traits. Poplar has been identified as a key species in the search for a renewable source of liquid biofuels, and possesses traits favorable to the extraction of lignocellulosic biomass for biofuel production. With the ultimate aim to identify molecular markers for the improvement of poplar as a biofuels feedstock, we embarked on a genome wide association (GWAS) study that will deepen our understanding of the genetic architecture of complex growth, wood fiber quality, adaptive and disease resistance traits. For the phase of genomic marker selection, we performed Illumina whole genome resequencing (100bp paired end reads) for over 500 mainly P. balsamifera and P. trichocarpa accessions from different natural populations grown in common gardens. Here we present our variant detection analysis pipeline, software packages and parameters used for the detection of SNPs and short insertions and deletions on a whole genome level. We also discuss the effect of coverage (30X vs. 15X sequence depth) on the number and quality of identified variants. We classified these polymorphisms based on location in the genome, and identified many polymorphic sites with putative non-synonymous amino acid changing effects. Together with phenotypic traits currently being measured, we will generate a large genomic dataset suitable for the dissection of complex polygenic traits in Populus.