Resistance to Diploidization in Soybean (Glycine max L.)

Nearly all plants show a whole-genome duplication (WGD) or polyploidy event somewhere in their evolutionary history. While many plants remain polyploid today, still many have become diploids over time due to the process of fractionation or diploidization. In this process, duplicated genes are deleted, paralogs gain new functions or lose certain functions, and duplicate segments are reorganized to form a condensed diploid genome. Soybean (Glycine max L.) is a prime example of this process at work, as although its genome is diploid, it has at least two major WGD events in its lineage: one shared with other papilionoid (Faboideae) legumes, which occurred approximately 55Mya, and one specific to Glycine from about 15Mya. Despite being a diploid plant, soybean still retains many genes in duplicate, with most genes being present in 2 or 4 copies. An analysis of synteny in Glycine max shows large contiguous blocks of synteny present in the genome covering about 91% of all genes therein, with most blocks belonging to the more recent Glycine duplication. Comparing the characteristics of these syntenic blocks in soybean to those in its fellow papilionoid Phaseolus vulgaris (common bean) shows that soybean blocks are longer, contain more genes, have slightly higher transposon insertion levels, and show less expression differentiation than those in P. vulgaris. Furthermore, these patterns of lower fractionation in G. max hold even when only considering syntenic blocks arising from the shared papilionoid duplication between the two species. As such, higher levels of transposon insertion and lower levels of expression differentiation within syntenic blocks in G. max are putative drivers of resistance to diploidization and fractionation in soybean.