Dynamic rearrangements determine genome organization and useful traits in soybean

Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the changes in genome structure produced by the relatively recent polyploidy event, but little is known about the ancient polyploidy due to the high frequency of gene loss after duplication. Our previous study, regarding a region responsible for bacterial leaf pustule, reported two homeologous Rxp regions produced by the recent whole-genome duplication event. In this study, we identified the full set of four homeologous Rxp regions (ranging from 1.96 to 4.60 Mb) derived from both the recent and ancient polyploidy events, and this supports the quadruplicated structure of the soybean genome. Among the predicted genes on chromosome 17 (linkage group D2), 71% of them were conserved in a recently duplicated region, while 21% and 24% of duplicated genes were retained in two homeologous regions formed by the ancient polyploidy. Furthermore, comparative analysis showed a 2:1 relationship between soybean and Medicago truncatula, since M. truncatula did not undergo the recent polyploidy event that soybean did. Unlike soybean, M. truncatula homeologous regions were highly fractionated and their synteny did not exist, revealing different rates of diploidization process between the two species. Our data show that extensive synteny remained in the four homeologous regions in soybean, even though the soybean genome experienced dynamic genome rearrangements following paleopolyploidy events. Moreover, multiple Rxp quantitative trait loci on different soybean chromosomes actually comprise homeologous regions produced by two rounds of polyploidy events.