Genomic DNA was isolated from fresh leaves of five plants of each cultivar using the SDS (sodium dodecyl sulfate) method . One hundred and seventy-two SSR makers associated with QTLs controlling phenological traits and other agronomic traits were selected according to previous studies (SoyBase (http://www.soybase.org)). SSR primers were from SoyBase (http://www.soybase.org). The PCR reaction mixture contained 100 ng of genomic DNA, 2 μl of 10 × PCR Buffer (+Mg2+), 2 μl of dNTPs (2 mM), 0.5 μl of SSR primer (10 mM), 0.2 μl of Taq polymerase (10 units/μl) and 13.8 μl of ddH2O in a total volume of 20 μl. The amplification program consisted of 94 °C for 5 min, 35 cycles of 94 °C for 30 s, 49 °C for 30 s, 72 °C for 45 s and 72 °C for 5 min. Then, the PCR products were separated on 6% w/v denaturing polyacrylamide gels, and the fragments were visualized by silver staining. The cultivars were also genotyped with Illumina BARCSoySNP6K iSelectBeadChip (Illumina, San Diego, Calif. USA) containing 5,403 SNPs selected from SoySNP50K . After elimination of SNPs with missing allele >24%, or minor allele frequency <0.05 , a total of 5,107 SNPs remained (Additional file 2: Table S2). SSR and SNP data were used for association mapping, and the SNP data was used for QTXNetwork analysis.