Integrated genetic linkage map based on UGMS and gSSR markers in Brassica rapa

• We mapped 309 SSRs, 226 UGMS, and 5 other markers in one or more of 3 individual mapping populations derived from different subspecies of Brassica rapa.
• These markers were aligned to construct a high-density integrated genetic map.
• The map was 1086.6 cM with an average distance of 1.98 cM between adjacent markers.
• The copy numbers of the markers were analyzed by aligning the primer sequences of the markers in the map to the genome sequence of B. rapa.

Simple sequence repeats (SSRs) such as gSSRs and expressed sequence tag (EST)-SSRs, especially for UniGene-derived microsatellite (UGMS), are widely used in the construction of genetic maps of Brassica species, because they are highly polymorphic, co-dominant, and efficient for plant genome analysis. In this study, 309 gSSRs, 226 UGMS, and five additional markers were mapped in one or more of the three individual mapping populations derived from different subspecies of Brassica rapa and aligned in order to construct a integrated genetic map. A total of 540 markers, including 548 loci, were mapped in 10 linkage groups. The total length of the integrated linkage map was 1086.6 cM with an average distance of 1.98 cM between adjacent markers. In addition, the copy numbers of the markers were analyzed by aligning the primer sequences of the markers in the map against the genome sequence of B. rapa. Single-copy markers were identified for future applications in marker-assisted selection of important economic traits.