J. Y. Gai, L. Chen, Y. H. Zhang, T. J. Zhao, G. N. Xing, H. Xing
Soybean Research Institute, Nanjing Agricultural University
National Center for Soybean Improvement
National Key Laboratory of Crop Genetics and Germplasm Enhancement

“Breeding by Design” as a concept described by Peleman and van der Voort aims to converge elite alleles for all genes of agronomic importance from potential genetic resources, that could be achieved through high-resolution allele detection based on precise QTL (quantitative trait locus/loci) mapping of potential parental resources. The present paper reviews the works at the Chinese National Center for Soybean Improvement (NCSI) on exploration of QTL and their elite alleles of agronomic traits for genetic dissection of germplasm resources in soybeans towards practicing “Breeding by Design”. Among the major germplasm resources, the released commercial cultivars (RC), farmers’ landraces (LD) and annual wild soybean accessions (WS), RC was recognized as the potential adapted parental sources with a great number of new alleles (45.9%) emerged and accumulated during the 90 years’ scientific breeding processes. A mapping strategy, i.e. a full model procedure scanning (including additive (A), epistasis (AA), A × environment (E) and AA × E effects) with QTLNetwork2.0 followed by verification with other procedures, was suggested and used for the experimental data with their genetic model usually unknown. Total 110 traits/times were analyzed for their QTL, with 14.5% of the traits/times showing major QTL (contribution rate more than 10.0 % for each QTL), 55.5% showing a few major QTL but more small effect QTL, and 30.0% having only small QTL. In addition to the detected QTL, there showed a collection of unmapped minor QTL sometimes accounting for even more than 50% of the genetic variation in a number of traits. Integrated with linkage mapping, association mappings were conducted on germplasm populations and validated to be able to provide complete information on multiple QTL and their multiple alleles. Accordingly, the QTL and their alleles of agronomic traits for large samples of RC, LD and WS were identified and then the QTL-allele matrices were established. Based on which the parental materials can be chosen for complementary recombination among loci and alleles and the cross plan can be optimized genetically. It has provided a way towards breeding by design, but the accuracy will depend on the precision of the loci and allele matrices.