Molecular and Chromosomal Evidence for Allopolyploidy in Soybean  

Abstract

Recent studies have documented that the soybean (Glycine max) genome has undergone two rounds of large-scale genome and/or segmental duplication. To shed light on the timing and nature of these duplication events, we characterized and analyzed two subfamilies of high-copy centromeric satellite repeats, CentGm-1 and CentGm-2, using a combination of computational and molecular cytogenetic approaches. These two subfamilies of satellite repeats mark distinct subsets of soybean centromeres and, in at least one case, a pair of homologs, suggesting their origins from an allopolyploid event. The satellite monomers of each subfamily are arranged in large tandem arrays, and intermingled monomers of the two subfamilies were not detected by fluorescence in situ hybridization on extended DNA fibers nor at the sequence level. This indicates that there has been little recombination and homogenization of satellite DNA between these two sets of centromeres. These satellite repeats are also present in Glycine soja, the proposed wild progenitor of soybean, but could not be detected in any other relatives of soybean examined in this study, suggesting the rapid divergence of the centromeric satellite DNA within the Glycine genus. Together, these observations provide direct evidence, at molecular and chromosomal levels, in support of the hypothesis that the soybean genome has experienced a recent allopolyploidization event.

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

“…The ancestor of genus Glycine was coincident with a polyploidization event 5 to 10 MYA (Doyle and Egan, 2010). Furthermore, observations at molecular and chromosomal levels support the hypothesis that the recent tetraploid event was allopolyploidy and the putative ancestral diploid genomes of soybean are extinct (Gill et al, 2009). Soybean differs from some paleopolyploid genomes in that it has been diploidized (disomic pairing), but the level of genetic collinearity between duplicated segments is much higher than seen in maize, which had a roughly contemporaneous duplication event Innes et al, 2008;Van et al, 2008).…”

“…Previous studies have shown that a recent genome duplication in soybean occurring ;13 MYA was correlated with the distribution of Ks ranging from 0.03 to ;0.39 (Schlueter et al, 2004;Shoemaker et al, 2006;Schmutz et al, 2010). Because the distribution of Ks between Gm8 and Gm15 in this study located within the range of the distribution of Ks from the recent genome duplication in soybean, we concluded that the divergence time for Gm8 and Gm15, 13 million years, precedes the polyploidization event ;5 to 10 MYA (Doyle and Egan, 2010;Gill et al, 2009). …”

“…The putative evolution of soybean includes the divergence of ancestral soybean genomes ;13 MYA and an allopolyploidization event ;5 to 10 MYA (Gill et al, 2009;Doyle and Egan, 2010;Schmutz et al, 2010). Therefore, the structural variation between Gm8 and Gm15 (inversions and deletions) could be derived either from the divergence event (;13 MYA), the polyploidization (5 to 10 MYA), or ensuing diploidization/fractionation.…”

“…For instance, variation at the grain hardness locus (Ha) from the A, B, or D genome of hexaploid wheat was compared with their diploid and tetraploid progenitors (Chantret et al, 2005). However, all modern diploid Glycines (both annuals and perennials) are at 2n = 40 (Doyle and Egan, 2010), and the ancestral diploid genomes of soybean are hypothesized to be extinct (Gill et al, 2009;Doyle and Egan, 2010). As a result, it is impossible to trace the differences between Gm8 and Gm15 that were derived from the divergence of the ancestral genome versus those from the polyploidization/ diploidization event.…”

“…Given that the most recent polyploid event in soybean may have been an allopolyploid event (Gill et al, 2009), we hypothesized that the ancestral structures of Gm8 and Gm15 were the same following the divergence of the soybean diploid ancestors. After divergence, two deletions occurred on Gm15 corresponding to the two physical gaps on Gm8.…”