Genotyping-by-sequencing (GBS) was conducted following the protocol of Elshire et al. (2011) (link) and as described for carrot (Arbizu et al., 2016 (link); Iorizzo et al., 2016 (link); Ellison et al., 2017 (link)). Library construction and sequencing were performed by the University of Wisconsin-Madison Biotechnology Center (WI, United States) using half-sized reactions. Genomic DNA was digested with ApeK1, barcoded, and pooled for sequencing with 85–95 pooled samples per Illumina HiSeq 2000 lane. Samples were sequenced using single end, 100 nt reads and v3 SBS reagents (Illumina, San Diego, CA, United States).
SNPs were called using the TASSEL-GBS pipeline version 5.2.31 (Bradbury et al., 2007 (link); Glaubitz et al., 2014 (link)). Filtering was conducted in VCFtools version 0.1.14 (Danecek et al., 2011 (link)) with the following parameters: a minimum minor allele frequency of 0.1 and maximum missing data of 10% for both genotype and marker.
SNPs were called using the TASSEL-GBS pipeline version 5.2.31 (Bradbury et al., 2007 (link); Glaubitz et al., 2014 (link)). Filtering was conducted in VCFtools version 0.1.14 (Danecek et al., 2011 (link)) with the following parameters: a minimum minor allele frequency of 0.1 and maximum missing data of 10% for both genotype and marker.
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