ddRAD-seq data of the parental p50, Nichi01 and their F2 progenies

We conducted ddRAD-seq on the genomic DNA of the parents, p50 and Nichi01, and 102 of their F2 progenies. The objectives were to construct a linkage map from the genotypes of the F2 progeny and to obtain a scaffolding evidence for improving the genome assembly of Nichi01. The restriction enzyme pairs used in the library construction were PstI and MspI, and EcoRI and MspI. The ddRAD-seq libraries constructed using each restriction enzyme pair were sequenced separately by Hiseq2000. Reads derived from the same sample were merged in a subsequent computational analysis. The re-distribution of reads based on the barcode sequences was performed by the script "process_radtags" in stacks v1.48.