A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy

Table 1 GBS library data for the three populations analyzed in this study

	Population 1	Population 2	Population 3
Description	F2 from cross between Prize and mutagenized Williams 82	F2 from cross between two breeding lines	81 unrelated lines
Number of samples	378	391	200
Sequencer	Illumina HiSeq2500	Illumina HiSeq4000	Illumina HiSeq2500
Read length	100 bp	100 bp	100 bp
Number of reads	234,574,472 (single-end)	392,001,642 (single-end)	247,063,538 (single-end)
Average depth per sequenced base	1.87 reads	3.63 reads	4.47 reads
Average percent of genome covered by at least 1 read	2.29	2.02	2.35
Average percent of genome covered by at least 2 reads	1.08	1.42	1.71

DNA was extracted using the CTAB method [19] except for the Prize x NMU-mutagenized Williams 82 population (Population 1), which used the E-Z 96 Plant DNA kit (Omega Bio-Tek, Norcross, GA). All libraries were sequenced at low coverage typical of plant breeding experiments, with coverage varying from 1.87× to 4.47×

ISSN: 1471-2105