Construction of an improved linkage map of diploid alfalfa (Medicago sativa)

An improved genetic map of diploid (2n=2x=16) alfalfa has been developed by analyzing the inheritance of more than 800 genetic markers on the F-2 population of 137 plant individuals. The F-2 segregating population derived from a self-pollinated F-1 hybrid individual of the cross Medicago sativa ssp. quasifalcata x Medicago sativa ssp, coerulea. This mapping population was the same one which had been used for the construction of our previous alfalfa genetic map. The genetic analyses were performed by using maximum-likelihood equations and related computer programs. The improved genetic map of alfalfa in its present form contains 868 markers (four morphological, 12 isozyme, 26 seed protein, 216 RFLP, 608 RAPD and two specific PCR markers) in eight linkage groups. Of the markers 80 are known genes, including 2 previously cytologically localized genes, the rDNA and the beta-tubulin loci. The genetic map covers 754 centimorgans (cM) with an average marker density of 0.8/cM. The correlation between the physical and genetic distances is about 1000-1300 kilobase pairs per centi-Morgan. In this map, the linkage relationships of some markers on linkage groups 6, 7, and 8 are different from the previously published one. The cause of this discrepancy was that the genetic linkage of markers displaying distorted segregation (characterized by an overwhelming number of heterozygous individuals) had artificially linked genetic regions that turned out to be unlinked. To overcome the disadvantageous influence of the excess number of heterozygous genotypes on the recombination fractions. we used recently described maximum-likelihood formulas and colormapping, which allowed us to exclude the misleading linkages and to estimate the genetic distances more precisely.