Defining the locations of cM regions from the Oat-Consensus-2018 (2018 Mrg) map on the OT3098 v2 sequence

This genome browser track accompanies the article “One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa L.)”, by Wight, et al. (2023) (under review).

The ‘Avgbs’ SNP marker set (Bekele, et al. (2018) DOI: 10.1111/pbi.12888) was used to define the chromosomal regions covered by the markers at each cM distance along the 2018 Mrg map linkage groups. There are large numbers of Avgbs markers on the 2018 Mrg map, and a JBrowse track showing the locations of Avgbs markers with perfect 64 base matches to OT3098 v2 was already available (here; N. Tinker, unpublished). Not every marker with a perfect match to OT3098 v2 was on the 2018 Mrg map, and vice versa. For those that were, the physical distances covered by the Avgbs markers at each cM location along the 2018 Mrg map linkage groups were determined. On the JBrowse track presented here, cM regions assigned to each chromosome are designated as ‘Mrg##_###’, with the final digits being the cM distances. Some markers had more than one perfect match, and these were assigned to two or more locations. Whether the location assigned is primary or secondary (i.e., expected or unexpected, based on the linkage group as a whole) is included in the description of each region. Also included is whether or not the region is defined by more than one marker.