Apeltes female grandparent resequenced from QTL cross
Genomic DNA was converted into nextRAD genotyping-by-sequencing libraries (SNPsaurus, LLC). Genomic DNA was first fragmented with Nextera reagent (Illumina, Inc), which also ligates short adapter sequences to the ends of the fragments. The Nextera reaction was scaled for fragmenting 5 ng of genomic DNA, although 7.5 ng of genomic DNA was used for input to compensate for the amount of degraded DNA in the samples and to increase fragment sizes. Fragmented DNA was then amplified by polymerase chain reaction (PCR) for 26 cycles at 73 C, with one of the primers matching the adapter and extending 9 nucleotides into the genomic DNA with the selective sequence GTGTAGAGG. The nextRAD libraries were sequenced on an Illumina HiSeq 4000 with one lane of 150 bp reads.