Targeted BSA mapping of Scmv1 and Scmv2 conferring resistance to SCMV using PstI/MseI compared with EcoRI/MseI AFLP markers

In a previous study, two chromosome regions (Scmv1 and Scmv2), conferring sugarcane mosaic virus (SCMV) resistance in maize, were enriched with EcoRI/MseI AFLP (Eco-AFLP) markers (methylation insensitive) by targeted bulked segregant analysis (tBSA). The objective of the present study was to further saturate these two regions with PstI/MseI AFLP (Pst-AFLP) markers (methylation sensitive) using the same tBSA approach, and to compare the genomic distribution of both Pst-AFLP and Eco-AFLP markers. Out of 470 PstI/MseI primer combinations screened, four Pst-AFLP markers were identified in the Scmv1 region (chromosome 6), and none in the Scmv2 region (chromosome 3). These Pst-AFLP markers were more closely linked to the Scmv1a gene than any of the Eco-AFLP markers, and could be useful for marker-assisted selection and even map-based cloning. In addition, Pst-AFLP and Eco-AFLP markers were dissimilarly distributed in both target regions. Pst-AFLP markers were equally distributed across both regions, while Eco-AFLPs were clustered in the Scmv2 region.