Synteny mapping between common bean and soybean reveals extensive blocks of shared loci

Abstract

BackgroundUnderstanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species.ResultsGenetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points.ConclusionThe collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.

A reference genome for common bean and genome-wide analysis of dual domestications

“…Typically, two chromosomal blocks in G. max mapped to a single region of P. vulgaris owing to the most recent WGD in G. max (Fig. 1) 14,24,25 . Most of the P. vulgaris genes (91%; 24,861) were in identifiable synteny blocks in G. max, and 57% were in synteny blocks in P. vulgaris itself-a result of the ancient WGD event 55 million npg years ago.…”

Evolutionary Patterns and Coevolutionary Consequences of MIRNA Genes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean

“…These genomes were estimated to have diverged from each other for 0.7 to 1.1 million years and are quite representative of the natural G. soja population . Interspecific comparison was performed with orthologous sequences between soybean and common bean (Schmutz et al, 2014), reflecting levels of nucleotide divergence obtained up to the past 19 million years (Lavin et al, 2005;McClean et al, 2010;Schmutz et al, 2014), although the birth and loss of a particular MIRNA may have occurred more recently. In the intraspecific comparison, the pattern of nucleotide divergence (K) of MIRNAs was different among the three categories in comparison with synonymous substitution (Ks) and nonsynonymous substitution (Ka) of PEG genes (Supplemental Figure 4).…”

“…It is proposed that the Glycine lineage has undergone at least two rounds of WGD after its divergence from the lineage that gave rise to Arabidopsis thaliana. One WGD occurred ;59 million years ago (MYA) and a second ;13 MYA (Schmutz et al, 2010), after the split of the Glycine lineage from its close relative, common bean (Phaseolus vulgaris), ;19 MYA (Lavin et al, 2005;McClean et al, 2010;Schmutz et al, 2014). With the availability of the reference genome sequences from both soybean and common bean (Schmutz et al, 2010(Schmutz et al, , 2014, and two clearly defined duplication events before and after their split, these two leguminous crops have become an important model system suitable for investigation of the nature, timing, and evolutionary dynamics and consequences of recurrent WGD events.…”

Identification of new QTLs for seed mineral, cysteine, and methionine concentrations in soybean [Glycine max (L.) Merr.]

“…is one of the most widely grown legume crops in the world. Soybean has a fully sequenced genome (Schmutz et al 2010) and results from soybean studies may be translated to other legumes due to extensive synteny (Bordat et al 2011;Lucas et al 2011;McClean et al 2010;Severin et al 2011). Soybean seed has approximately 40% protein in commercial cultivars (Kim et al 2012).…”