*4.3. Genetic Map and DNA Marker Analysis*

To compare the detection power of GPC QTL, high-density and low-density linkage maps of the RIL population were both used to map QTL, respectively. The high-density linkage map constructed by one of the GBR method, specific length amplified fragment, was composed of 18,194 SNP markers and spanned 2132.56 cM with an average genetic distance of 0.12 cM. In our previous study, we constructed the SLAF library for each RIL and the products were further sequenced using Illumina HiSeq 2500 system (Illumina, Inc.; San Diego, CA, USA) [29]. Polymorphism loci between the parents were identified for the selection of high-quality SNP markers after filtering out the low-quality raw reads. SNP markers with more than 20% missing data and the segregation distortion were further filtered out. A total of 18,194 high quality SNP markers were used to genotype the 280 RILs. The low-density linkage map constructed by the gel-based method consisted of 121 SSR and 87 InDel markers and spanned 1399.40 cM with an average distance of 7.61 cM.

For the three RH-derived populations, leaf samples of each individual were extracted for genomic DNA through the modified CTAB method [31]. To genotype the three RH-derived populations, a total of six InDel markers (Table S2) in the mapping interval of *qGPC1-1* were designed with Primer3.0 (http://primer3.ut.ee/) based on the 30-fold genome resequencing of the parents, HHZ and JZ1560. According to our previous study [32], the PCR was performed in 10-μL reactions containing 2 × *Taq* MasterMix (CW0682, CWBIO) 5-μL, 0.4 μM of each primer and 50 ng DNA template. The PCR program was set as an initial denaturation at 94 ◦C for 2 min, then followed by 30 cycles of 30 s at 94 ◦C, 30 s at 55 ◦C and 30 s at 72 ◦C, and finally 2 min at 72 ◦C. The PCR products were analyzed on 2.5% agarose gels.
