Genetic Diversity and Phylogenetic Relationships of Annual and Perennial Glycine Species

Abstract

We have estimated the 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. The other perennials, except for 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 for G. cyrtoloba and G. stenophita which formed a sister clade in the study. Divergence analysis supported the phylogenetic relationships that G. falcata was the most divergent from G. max, followed by G. cyrtoloba, G. syndetika, G. tomentella D3, G. stenophita and G. canescens Most genic 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 a very similar evolution 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 suggests the perennials maybe a potential source of heat and drought resistance that will be of value in the face of climate change.

Keywords: divergence; nucleotide diversity; perennial crop relatives; phylogenetic analysis; soybean; trans-specific polymorphism.

Figure 1

Geographical origin of the accessions. The origin of 98 accessions of the two annual and the six perennial Glycine species and the average annual precipitation in the corresponding regions.

Figure 2

The locations of 76 orthologous genes on the 20 G. max chromosomes (Gm1- Gm20). The bars indicate the positions of the 76 genes used for the genetic diversity analysis.

Figure 3

Phylogenetic trees of the Glycine species. The phylogenic tree of the 77 accessions of the eight Glycine species is based upon 52 orthologous gene sets. The letter next to each species indicates its nuclear genome designation as defined by Singh and Hymowitz (1985a), Hymowitz et al. (1998), and Doyle et al. (2004). The designation following the PI numbers of the G. canescens accessions indicates the subgroup designation (G1 through G3 and U = unassigned to a subgroup) assigned by Brown et al. (1990). G. canescens accessions followed by “ND” were not included in the Brown et al. (1990) study and thus, their subgroup was not determined. Nodes are based on 100 bootstrap replicates. The bootstrap values lower than 50 were eliminated. Phaseolus vulgaris L. and Vigna unguiculata (L.) Walp are used as out-groups.

Figure 4

Phylogenetic tree and phylogeography of G. canescens. A) The phylogenetic tree is based upon 367 gene sets in the 11 accessions. The letter next to the PI numbers indicates the subgroup designation assigned by Brown et al. (1990). G. canescens accessions followed by “ND” were not included in the Brown et al. (1990) study and thus, their subgroup was not determined. Nodes are based on 100 bootstrap replicates. Phaseolus vulgaris L. and Vigna unguiculata (L.) Walp are used as out-groups. B) The geographicorigin of each accession of the phylogeny is indicated as a dot on the map and the accessions defined as the same genome group by Brown et al. (1990) are assigned the same color. The PI number and the genome group of each accession is indicated next to the dot and the three subclades are indicated.

Figure 5

Distribution of genes with different number of trans-specific polymorphisms.