Identifying regions of conserved synteny between pea (pisum spp.), lentil (lens spp.), and bean (phaseolus spp.)

Abstract

The identification of conserved synteny in legumes can facilitate many different types of gene discovery. Techniques like marker assisted selection and the candidate gene approach can benefit greatly by identifying conserved synteny and genes located within those regions. Both Pisum and Phaseolus have detailed linkage maps, but a limited number of markers have been located in both species. In the present study I mapped 21 genes in Phaseolus vulgaris, 16 of which had already been located on the Lens and Pisum sativum linkage maps, the markers were used to look for conserved synteny between Pisum, Lens and Phaseolus. In particular, I was able to target marker/gene-rich regions of pea linkage groups V and VII, as well as pea linkage group III, with Pisum STS markers and universally designed gene-specific markers already located on the pea linkage map.About 50% of the tested genes amplified an appropriate sized fragment in Phaseolus, but less than 40 % of the gene-specific markers showed polymorphism by cleaved amplified polymorphic sequence (CAPS) analysis in bean. The data reveals little evidence for extensive gene order conservation, and even some closely linked (<5cM) loci in Pisum are not linked in Phaseolus vulgaris. The only example of conserved synteny was approximately 15cM on pea and lentil linkage group V and bean linkage group 1. Paal, Enolase, and TufM were first identified in the syntenic area and allowed identification of fin/det, one of several TFL genes already mapped in bean, as another orthologous loci between pea and bean. Finding conservation of synteny with Paal, identified Paal3 and TFL1 genes as linked loci in Arabidopsis thaliana on linkage group 5. The pea locus Paal1,2 is then speculated to be a tandem duplication of a Paal3 homolog in a ancient common ancestor and probably occurring after the speciation of Pisum.