Comparison of genetic map construction and quantitative trait locus (QTL) mapping on the linkage groups (LGs) A07 and C01 of the HJ-DH population with the Map B and Map C. Only a sub-set of molecular markers are presented for each genetic LG. The single nucleotide polymorphism (SNP) markers with underlined (red color) are the mHemi-SNPs and Pseudo-simple SNPs. The detailed information about the LGs of the Map B is described in Additional file 3: Table S3, and the data of the Map C comes from Cai et al. . The sub-set same molecular markers between the two LGs depicted are aligned with black lines. PC: protein content; SD: silique density. Significance thresholds for QTLs at the level P = 0.05 are estimated based on 1000 permutation.