Rationale:
The aim of the methods in this section was to develop reliable and easy-to-use DNA markers for the genomic region in A. magna K 30097 that confers rust resistance. Although A. magna K 30097 was of primary interest for this study, A. batizocoi K9484 also is being used in our research and for introgression in breeding programs (Leal-Bertioli et al. 2014b). Therefore, we aimed to develop markers that would function for both these species (Leal-Bertioli et al. 2014a,b).
Because introgression will be in allotetraploid cultivated peanut, the markers must function in this genetic context, but for SNP discovery, we used a strategy of SNP calling in the diploid context. This strategy relies on the very close relationship of A. ipaënsis and the B genome of A. hypogaea (Moretzsohn et al. 2013). Because of this close relationship, a polymorphism identified between A. magna and A. ipaënsis is very likely to be conserved between A. magna and the B genome of A. hypogaea. After marker design, this conservation was confirmed by marker assays.