The identification of genomic regions affected by selection during breeding of soybean (Glycine max (L.) Merr.) may indicate the positions of important agronomic traits genes or genes underlying adaptation to a specific target environment. This study investigated the effects of breeding in Central-East European environments by a hitchhiking mapping approach and pedigree analysis. Population genetic principles were applied to microsatellite markers using multiple outlier detection tests. The analysed populations comprised ancestral genotypes and elite varieties, developed at the Institute of Field and Vegetable Crops, Novi Sad. The pedigree analysis confirmed narrow genetic base of elite genotypes. As a result of long-term breeding, all analysed parameters showed significant reduction in genetic diversity in the elite population, compared to the ancestral. Specific population structure of analysed varieties, which has been largely influenced by the pedigree, probably caused a low level of genetic differentiation between the populations. Using at least two approaches, nine markers were considered as strong positive selection candidates, indicating regions involved in the adaptation to Central-East Europe environments. Also, an excess of linkage disequilibrium was confirmed in the elite population, probably caused by selection. Bottleneck tests provided evidence of population bottlenecks only for the candidate positive selection loci in the elite population, suggesting that selection might shaped the pattern of genetic diversity in these regions. The co-localisation analysis of the candidate positive selection loci and previously mapped quantitative trait loci (QTLs), identified in total 264 QTLs in selectively important genomic regions. The highest number of identified QTLs had impact on the reproductive period. In silico analysis revealed a high level of agreement between the identified QTLs and the traits expected to be under selection during soybean breeding, indicating that selection was mostly directed towards increasing the yield of elite varieties in a specific environmental conditions. Furthermore, E1 gene that controls flowering time and maturity in soybean, or its surrounding region, seems to be a major contributor for adaptation to environmental conditions of Central-East Europe. It is assumed that most of the selectively important genes had regulatory role, acting as transcription factors, as well as a role in the processes of transport. The identified selectively important genomic regions in a specific breeding program could have practical importance for future breeding and yield improvement.

Keywords: Glycine max, hitchhiking mapping, microsatellites, selection, adaptation, breeding