Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa

Cultivated alfalfa (Medicago sativa) is an autotetraploid. However, all thr ee existing alfalfa genetic maps resulted from crosses of diploid alfalfa. The current study was undertaken to evaluate the use of Simple Sequence Rep eat (SSR) DNA markers for mapping in diploid and tetraploid alfalfa. Ten SS R markers were incorporated into an existing F-2 diploid alfalfa RFLP map a nd also mapped in an F-2 tetraploid population. The tetraploid population h ad two to four alleles in each of the loci examined. The segregation of the se alleles in the tetraploid mapping population generally was clear and eas y to interpret. Because of the complexity of tetrasomic linkage analysis an d a lack of computer software to accommodate it, linkage relationships at t he tetraploid level were determined using a single-dose allele (SDA) analys is, where the presence or absence of each allele was scored independently o f the other alleles at the same locus. The SDA diploid map was also constru cted to compare mapping using SDA to the standard co-dominant method. Linka ge groups were generally conserved among the tetraploid and the two diploid linkage maps, except for segments where severe segregation distortion was present. Segregation distortion, which was present in both tetraploid and d iploid populations, probably resulted from inbreeding depression. The ease of analysis together with the abundance of SSR loci in the alfalfa genome i ndicated that SSR markers should be a useful tool for mapping tetraploid al falfa.