I think this the common phenomena because there are homologous and homoeologous in different chromosomes

Genes and markers can be duplicated in the genome. This can explain your observation that the markers have multiple localizations on different chromosomes. 

I hope this helps!

thank you Reniout for your reply... I do not have duplication. For instance. Two SNP markers were mapped in the same linkage group and those are located in different chromosome in Medicago one on chromosome one and another in chromosome 5. This is a simple example. In antoher linkage group (LG05), marker in this linkage groups were found in three different chromosome. I know that there is a different between a position in linkage group and postilion on chromosome. What I expected is to find the same markers in one linkage group and one one chromosome regardless the order of markers and actual distance . 

Gregor, have you used the same segregating populations/plants for genetic mapping and for chromosome marker localization?

No.. my population consisted of 260 lines. I genotyoped them with 12000 markers (GBS) and position of these marker were determined in Medicgao (legume model) chromosomes. So, I got 15 Linkgae groups. I expected that e.g. that SNPs of LG01 are positioned in Ch1 or 2 or 3...6. but what I found is that these SNPs which are in the same LG were assigned to different chromosome say 1 and 2.  

Have you used a single plant to locate SNPs on chromosomes?

Actually, I do not know. The data was sent to us

Hi Gregor

Are you actually working with Medicago or another Legume? Chromosomal mutations (i.e, translocations) occur during evolution.

On the other hand, be aware genome duplications occurred flowering plants evolution. I do not think SNPs will detect such homoeology (at least if primers have 50bp length); but amplification of homoeologous genes was rather common in re-sequencing studies. You can see an example in our paper Bodénès et al., 2012, BMC Plant Biology.

Hope this helps

Pablo