Genomic dissection of widely planted soybean cultivars leads to a new breeding strategy of crops in the post-genomic era

Abstract Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding. Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding. We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China. Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations: Northeast China (NE) versus the Huang-Huai-Hai River Valley and South China (HS). A total of 309 selective regions were identified as being impacted by geographical origins. The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population. To study the association between phenotypic differences and geographical origins, we recorded the vegetative period under different growing conditions for two years, and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin. By iteratively calculating accumulated genetic diversity, we established a platform panel of cultivars and have proposed a novel breeding strategy named “Potalaization” for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the “plateau” for accumulating elite loci and traits, breeding novel widely adapted cultivars, and upgrading breeding technology. In addition to providing new genomic information for the soybean research community, the “Potalaization” strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.