pool-GBS of Trifolium pratense cultivar Lea (pools of early versus pools of late elongating plants)
DNA was extracted from leaf tissue of each individual with the DNeasy 96 Plant kit (Qiagen). The 52 individuals in each of the two phenotypic groups (early, late) were randomly divided into three subgroups of 17-18 individuals and equal amounts of DNA from each individual in each subgroup was combined in a pool, creating a total of six DNA pools. Each DNA pool was distributed into 15-16 wells per 96-well plate to create replicate GBS libraries. One plate each was used for PstI and ApeKI single-digest GBS library preparation according to Elshire et al. (2011) and single-end sequenced on a HiSeq2000 instrument by Cornell University, Biotechnology Resource Center. This pool contains the first subgroup (replicate 1) of 17 early elongating individuals, and was used for PstI pool-GBS library construction. All reads of the 15-16 replicate GBS libraries were trimmed to remove adapters, barcodes, and restriction site remnants, and quality filtered. All remaining reads are combined in a single fastq file.
Lea_Early_1_PstI