HiPlex amplicon sequencing of candidate genes for haploid induction in chicory and witloof
A single plant was used for extraction of genomic DNA using a CTAB-based method. DNA samples were quantified using Quantus and concentrations were normalized (range 10-20 ng/l). Amplicons for 9 genes putatively involved in haploid induction were amplified in a multiplex PCR with 49 primers (49-plex) per sample, while adding sample-specific indices (Floodlight Genomics, USA). Illumina sequencing adapters were ligated using the KAPA Hyper Prep PCR-free Kit according to manufacturer directions (Kapa Biosystems, USA) and libraries were paired-end sequenced on an Illumina HiSeqX Ten instrument (Admera Health, USA). All read data were demultiplexed, barcodes and adapter sequences were removed, and reads were trimmed and merged.