Gene Prediction of Major QTL Intervals

The ‘Williams 82.a2.v1’ genome has enough common genetic information to be defined as the reference genome for predicting the candidate genes. Soybase¹ and the previously constructed high-density genetic map provided the genetic distances and physical positions that were used to determine the physical positions of the major QTL intervals. Using the genomic information provided by Phytozome², and referring to the ‘Williams 82.a2.v1’ genome sequence, the soybean genes in the major QTL intervals were identified and the corresponding gene annotations were performed. Candidate genes involved in the growth and development of soybean were selected from the gene annotation data, which came mainly from the databases listed in Supplementary Table S1.