The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

Abstract

Background: The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism.

Results: An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM) and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16). Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa), implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7.

Conclusions: These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant.

Figure 1

Phenotypic patterns which distinguish Jemalong 6 and DZA315.16 lines. Bars = 5 mm. (A) Typical leaf pigmentation found on adaxial leaf surface of Jemalong 6 (left) and DZA315.16 (right). (B) Pod shape of Jemalong 6 (above) and DZA315.16 (below). (C) Anticlockwise pod coiling of Jemalong 6 (above). Clockwise pod coiling of DZA315.16 (below).

Figure 2

Global F2 genetic map of Medicago truncatula. The number above the linkage groups refers to the homologous linkage group in M. sativa [29]. The code to the right of the linkage groups refers to the marker name. The numbers to the left of the linkage groups refers to the genetic distances (Kosambi cM) from the top and have been rounded up for clarity. The sign + indicates that two RAPD markers have been transformed into a codominant marker. In the case of codominant AFLP markers, the codes of the two bands are given together. Stars refer to known genes used for synteny studies. Circles refer to known genes not used for synteny studies.

Figure 3

Distribution of the 281 intervals between adjacent markers on the F2 genetic map of M. truncatula. X-axis: genetic distance in Kosambi cM. Y-axis: frequency of intervals (%). The average distance between two markers is 4.4 cM with a standard deviation of 4.3 cM. 90% of the markers are closer than 10 cM.

Figure 4

Segregation distortion of the female and male markers along linkage group 3 of the overall F2 genetic map of M. truncatula. Circles and triangles refer to female and male alleles respectively. X-axis: genetic distance from the top of the linkage group in Kosambi cM. Y-axis: frequency (%) of segregation of female and male alleles in the mapping population. A dominant marker is considered to be a male marker if the recessive allelic form is male (and the same for the female markers). If no distortion occurs, the segregation value should be close to 25% for both male and female markers (dashed line).