Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean    

Abstract

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.

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

“…This comparison reveals that 29.2% 6 1.7% of the genes were retained in duplicate (see Supplemental Data Set 1E online). These average values of gene retention for the homoeologous segments are similar to gene retention values of 71 and 24% determined on four different homoeologous regions in soybean described by Kim et al (2009). Schmutz et al (2010) reported a genome-wide estimate for gene retention after the Glycine and legume WGD events of 43.4 and 25.9%.…”

Whole-genome sequencing and intensive analysis of the undomesticated soybean ( Glycine soja Sieb. and Zucc.) genome

“…S2). Only 21.46% (42,145) of the indels were positioned within genic boundaries ( Table 1). The 2,398 indels in coding sequences caused frameshifts in 2,235 genes, which is a reasonable number of frameshift variants for the soybean genome in comparison with a previous study in Arabidopsis (20).…”

“…An allopolyploid event shared with the Medicago lineage, originating from the hybridization of two different ancestral legumes (2n = 20) at 59 Mya, was followed by another independent whole-genome duplication at 14 Mya (30). Tetrad homeologous regions are expected to exist in soybean genomes (41,42), but divergence among these homeologous regions accumulated over time, resulting in triplet or paired homeologous regions. In particular, most duplicated genes generated by duplication events have high sequence homologies.…”

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

“…After speciation, soybean underwent another lineage-specific WGD event approximately 10 MYA (Schmutz et al, 2010), resulting in a distinctive chromosome number for the genus Glycine (mostly 2n = 40) as compared with other members of the tribe Phaseoleae (mostly 2n = 22; Hadley and Hymowitz, 1973;Lackey, 1980). Due to a relatively recent WGD and lack of immediate diploidization (Kim et al, 2009), the soybean genome remains duplicated, with nearly 75% of the genes present in multiple copies (Schmutz et al, 2010), more than most diploid plant genomes (De Smet et al, 2013). Thus, the soybean genome provides a model to study the evolutionary aspects of epigenetic marks on retained duplicate and single-copy genes in comparison with related species, such as common bean, that lack the recent WGD event.…”