Establishment of Chinese soybean Glycine max core collections with agronomic traits and SSR markers

It is very important to efficiently study and use genetic diversity resources in crop breeding and sustainable agriculture. In this study, different sampling methods and sample sizes were compared in order to optimize the strategies for building a rationally sized core collection of Chinese soybean (Glycine max). The diversity in the core collection captured more than 70% of that in the pre-core collection, no matter what sampling methods were used, at a sampling proportion of 1%. Core collections established with both simple sequence repeat (SSR) marker data and agronomic traits were more representative than those chosen on an independent basis. An optimal sampling method for a soybean core collection was determined, in which strategy ‘S’ (allocating accessions to clusters according to the proportion of square root of the original sample size within each ecotype) was used based on SSR and agronomic data. Curve estimation was used to estimate the allelic richness of the entire Chinese soybean germplasm and a minimum sample size for a core collection, on which a sampling proportion of about 2% was determined to be optimal for a core collection. Further analysis on the core collection with fourteen agronomic traits and allelic constitution at 60 SSR loci suggested that it highly represented the entire collections both on genetic structure and diversity distribution. This core collection would provide an effective platform in proper exploitation of soybean germplasm resources for the study of complex traits and discovering important novel traits for crop genetic development.