Estimating genome conservation between crop and model legume species

Abstract

Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion͞deletion of individual genes or groups of genes and lineage-specific expansion͞contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.

Bridging Model and Crop Legumes through Comparative Genomics

“…M. truncatula and alfalfa share highly conserved nucleotide sequences and exhibit nearly perfect synteny between the two genomes (Choi et al, 2004a). Although the pea genome is approximately 10 times larger than that of M. truncatula and has one less chromosome, the colinearity of genes is also remarkably conserved between the two genomes, with major evident differences being inferred interchromosomal rearrangements (Choi et al, 2004b). It was suggested that chromosomal rearrangements involving Medicago (alfalfa and M. truncatula) chromosome 6 might be responsible for the difference in chromosome number between Medicago and pea (Choi et al, 2004b;Kalo et al, 2004).…”

“…Although the pea genome is approximately 10 times larger than that of M. truncatula and has one less chromosome, the colinearity of genes is also remarkably conserved between the two genomes, with major evident differences being inferred interchromosomal rearrangements (Choi et al, 2004b). It was suggested that chromosomal rearrangements involving Medicago (alfalfa and M. truncatula) chromosome 6 might be responsible for the difference in chromosome number between Medicago and pea (Choi et al, 2004b;Kalo et al, 2004). Interestingly, the same chromosome seems to have also been associated with the interchromosomal rearrangements between M. truncatula and chickpea (H. Zhu and D. Cook, unpublished data).…”

“…A more recent study, however, using Arabidopsis (Arabidopsis thaliana) as a bridging species revealed that homoeologous segments of soybean chromosomes showed a higher degree of synteny with chromosomes of common bean and mungbean than previously thought (Lee et al, 2001). The most in-depth analysis of legume macrosynteny recently was reported by Choi et al (2004aChoi et al ( , 2004b using M. truncatula as a central point of comparison. This research took advantage of abundant EST sequence information from the model legume M. truncatula to develop cross-species genetic markers where locus orthology was tested through phylogenetic analysis.…”

“…Gene-specific PCR primers were designed to anneal to highly conserved exon sequences that span predicted introns, which allowed for efficient PCR amplification across species and for developing single nucleotide polymorphism markers for linkage mapping in multiple taxa. These putatively orthologous markers were mapped in M. truncatula, alfalfa, pea, mungbean (Choi et al, 2004a(Choi et al, , 2004b, and chickpea (H. Zhu and D. Cook, unpublished data). In addition, 60 markers developed based on homology to mapped genetic markers of soybean were mapped in M. truncatula.…”

New genetic sources of resistance in the genus Phaseolus to individual and combined aluminium toxicity and progressive soil drying stresses

“…They allow evaluation of a large number of genotypes quickly and have been used to identify parental stock for soybean breeding (Bianchi-Hall et al 1998;Campbell and Carter 1990;Carter and Rufty 1993;Spehar 1994;Bianchi-Hall et al 2000;Silva et al 2001). Common bean and soybean both pertain to the tribe Phaseoleae, much more closely related to each other than they are to Lotus, Medicago, or other grain legumes such as lentils or chickpeas (Choi et al 2004). This opens the possibility of common genes and/or mechanisms between the species, and suggests that the application of methods used in soybean might serve to discriminate genetic differences in common bean as well.…”