Genotyping-by-Sequencing for SNP Discovery

Genotyping‐by‐sequencing libraries were prepared by restricting genomic DNA with HindIII‐HF (NEB) with Ampure XP bead (Beckman‐Coulter) cleanup. Sequence data were obtained on an Illumina Hiseq 4000 instrument at the UC Davis Genome Center. Single nucleotide polymorphism (SNP) calling was performed using the TASSEL GBS pipeline (Glaubitz et al., 2014 (link)) with alignment to the Chandler genome (Marrano et al., 2020 (link)), resulting in 13,320 polymorphic SNPs. The phangorn package in R (R Core Team, 2017 ; Schliep et al., 2017 ) was used to construct a neighbour‐joining tree from the distance matrix.