Comparative genome study within the papilionoideae subfamily using gene-specific cross-species markers

The core genetic map of Medicago truncatula, the model legume system, was constructed. The map consists of 289 PCR-based genetic markers (141 EST-based gene-specific markers, 79 BAC end sequence-tagged markers, 66 resistance gene analog markers and 3 morphological markers) and covers 513 cM with an average distance between two markers of 1.8 cM. The sequence analysis of markers containing both introns and exons revealed that intron nucleotide sequences were approximately 3.6 times more highly diverged than exons.; Cross-genome comparative markers were developed by designing oligonucleotide primers from the best conserved regions of unique or low copy number genes selected from ∼2700 Medicago truncatula EST sequences. 111 individual genes were converted into comparative markers for genetic mapping among 6 legume species (M. truncatula, P. sativum, L. japonicus, V radiata, P. vulgaris, and G. max). A composite comparative genetic map between five legume species (Mt, Ms, Ps, Vr, Gm) was constructed based on a combination of gene-specific comparative markers and BAC end sequence-tagged markers. The comparative analysis between M. truncatula and M. sativa (Ms) revealed extensive colinearity throughout the entirety of both genomes. Synteny was also evident between M. truncatula and G. max, although the analysis was confounded by high level of duplication and low polymorphism of the soybean genome. Comparison of M. truncatula and P. sativum also revealed extensive colinearity between these two genomes: MtLGI-PsLGII; MtLG2-PsLGVI; MtLG3-PsLGIII; MtLG4-PsLGVII; MtLG5-PsLGI; MtLG6-PsLGVI, PsLGVII; MtLG7-PsLGV; MtLG8-PsLGIV. The comparative analysis between M. truncatula and V. radiata revealed 9 syntenic blocks out of 11 linkage groups.; 24 phylogenetic markers were developed producing high quality data for 6 legume species selected from 4 tribes (Trifoleae, Viceae, Loteae, and Phaseoleae). In most cases, our results are in good agreement with the established phylogenetic relationships. In the case of L. japonicus, however, the consensus tree derived from the 24 gene analysis produced an ambiguous affinity between the “galegoid” and “phaseoloid” clades. The results suggest a need to reconsider the phylogenetic relationship of the temperate legumes in relation to the Loteae tribe, as questioned previously (Lavin and Doyle, 1990; Corby, 1981; Tucker, 1987).