We resequenced 112 glycine soja and 133 glycine max in order to discover their selection signatures.

Modern soybean population (Glycine max) have adapted to diverse environments and improved to various agronomical purposes, since its domestication and geographical dispersion at least 5,000 years ago. The multiple environmental and artificial selections have occurred independently and have generated considerably structured populations resulting in many soybean subpopulations. Their adaptive characteristics developed during the selection processes have abilities enhancing yield and viability or tolerating to biotic and abiotic stresses, so thus it plays a fundamental role as genetic materials in improving other soybean populations. As a step toward this goal, we focused on the subpopulation's selection signature and adaptive characteristics at the population level. We resequenced 112 wild-type, 79 landrace, and 54 improvement cultivars which were a core set selected from 4,234 soybean accessions. We first examined their genetic architectures according to their domestication and subsequent improvement. Then, we subdivided the wild-type, landrace, and improvement into three, two, and two subgroups on the basis of various population analyses, respectively. Through extensive selection analysis and gene-set enrichment analysis, we revealed that two landrace subgroups have selection signals for defense response to soybean cyst nematode type 0 and seed germination and development, respectively, and two improvement subgroups have selection signals for plant growth and viability and development of seed and embryo, respectively. The adaptive characteristics related to seed development were confirmed by our phenotype investigation on one-hundred seed weigh, and the adaptive characteristic for soybean cyst nematode resistance was identified through multiple resistant accessions existing in the subpopulation. Also, these four adaptive characteristics were further confirmed with genomic-based evidence. We uncovered selective sweep regions and unique selection signals in 11 candidate genes that have been reported to be associated with these adaptive characteristics from QTL, genome-wide association, and transcriptome studies. Our research present unique selection signatures and distinct candidate genes of the soybean subpopulations, based on the population and selection analyses. Although the adaptive characteristics require further biological validation, our findings are expected to provide additional information for future marker-assisted breeding strategies and to contribute new options to breeders in seeking donor parents for improvement of soybean population.