Genotypic and phenotypic characterization of a Populus deltoides association population - poplar

Poplars are the fastest growing commercial forest species cultivated in North America. Their wood is used for furniture, pulpwood and, recently, biofuel production. The high levels of genetic and phenotypic variation, wide distribution across the continent, and sequenced genome make poplar an excellent choice for studying genetic polymorphisms underlying economically important traits. We genotyped a Populus deltoides association population of 579 individuals using a sequence capture technique targeting 18,153 genes previously identified to be expressed in poplar xylem (Quesada et al. 2008), together with part of their upstream and downstream regulatory regions, and intergenic regions located every 15 kbp throughout the genome. We designed 227,943 RNA-based 120 nucleotide long probes targeting 27 Mbp (5%) of the poplar genome. The libraries were sequenced on 48 lanes of Illumina HiSeq 2000 platform yielding an average of 27.3 million reads per genotype and mean on-target depth of 26.1 X. All targeted genes and 96.3% of the intergenic regions were captured. SNPs were identified with three different software (GATK HaplotypeCaller, FREEBAYES and SAMTOOLS) and a consensus set of 529,628 SNPs was generated by selecting the SNPs identified by all three programs. These will be used in GWAS to find markers for wood quality traits and eQTLs, as well as to build prediction models of phenotypes. A subset of 10,000 randomly selected SNPs was chosen to study population structure. Our analysis with STRUCTURE software shows existence of 2 separate subpopulations. This population structure needs to be accounted for in association studies to avoid false positives.