Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species

We estimated average genetic diversity of two Glycine annual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11 G. canescens accessions. Among the perennials, G. canescens showed the highest nucleotide diversity and the other perennials except G. tomentella had higher nucleotide diversity than the two annuals. Phylogenetic analysis of the Glycine showed a similar genome grouping with the previous report except G. cyrtoloba and G. stenophita formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships, G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens. Neutrality selection tests within species showed that most genes were subjected to a recent directional selection due to a selective sweep or rapid population expansion. Although most gene sequence had negative and significant Tajimas D, the sequences were homogeneous in the levels of polymorphism and divergence between G. max and other Glycine species based on the HKA test, thus, Glycine perennials may have experienced very similar evolutionary selection as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennial Glycine species and their origins from the warmer and drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of climate change.