Hi, We have one population consisted of 192 F3 lines resulting from a cross between two plant genomes (GBS). I ran MSTmap which lead to more than 100 linkage groups. Unfortufuntaly, after filtering out linkage groups with less than 15 markers, I remained only with one linkage group. The input file for MSTmap has been generated by Genotype-Corrector (https://www.nature.com/articles/s41598-018-28294-0).

What did I miss?

Thank you in advance,