Classification of deletion variants based on restriction enzyme digestion and Southern blot analysis

Recombinant classaNcoI fragments from Rp1-D parentFlanking
Rp1-D homozygotes1234 (Cin4)56789 Rp1-D
D*1, 2, 3, 8, 20, 22, 23, 27+++++----NAb
D*10, 11, 14, 16, 29+++++----NA
D*7, 12, 28+++++----NA
Rp1-A × Rp1-D
AD7, AD1, AD18-NDcNDND-----285-A, 3.04-D
AD22-NDNDND-----285-A, 3.04-D
AD19-NDNDND-----285-A, 3.04-D
AD20, AD4, AD10+NDNDND-----285-D, 3.04-A
AD5+NDNDND+++--285-D, 3.04-A
AD9+NDNDND++++-285-D, 3.04-A
AD2+NDNDND+----285-D, 3.04-A
AD15+NDNDND+----285-D, 3.04-A
AD8-NDNDND-----285-D, 3.04-A
DNCO1+NDNDND++++-285-D, 3.04-D
DNCO2+NDNDND+++++285-D, 3.04-D
DNCO3+NDNDND+++++285-D, 3.04-D
Rp1-B × Rp1-D
BD11++ND+-----285-D, 3.04-B
BD13++ND++++--285-D, 3.04-B
BD15++ND++----285-D, 3.04-B
BD1++ND++----285-D, 3.04-B
BD14++ND++----285-D, 3.04-B
BD3++ND++----285-D, 3.04-B
BD2++ND++----285-D, 3.04-B
BD4++ND++----285-D, 3.04-B
BD7++ND++++--285-D, 3.04-B
BD8++ND++++--285-D, 3.04-B
BD9++ND++----285-D, 3.04-B
BD12++ND++++++285-D, 3.04-B
BNCO1--ND------285-B, 3.04-B
DNCO4+NDND++++++285-D, 3.04-D
  • DNAs were purified from individuals that were homozygous for mutant or recombinant haplotypes that were selected from F1 crosses of Rp1-D homozygotes and test crosses of Rp1-A/Rp1-D and Rp1-B/Rp1-D heterozygotes. DNAs were digested with NcoI and probed with a NBS region probe. NcoI fragments are labeled according to their inferred position, from the centromere to telomere end of the array, and refer to the numbering of the HRp1-D haplotype fragments in Figure 3.

  • a Members of each class were indistinguishable based on gel blot analysis with Rp1 probes after digestion with NcoI and several other restriction enzymes.

  • b NA, flanking RFLP markers could not be analyzed in the Rp1-D homozygote derivatives due to the absence of marker segregation. The designations 285-B and 285-D indicate whether the recombinant had the Rp1-B or Rp1-D parent allele at the centromere-proximal RFLP marker npi285. The designations 3.04-A and 3.04-D indicate whether the recombinant had the Rp1-A or Rp1-D parent allele at the distal marker bnl3.04.

  • c ND indicates we could not determine the presence of the HRp1-D haplotype fragment because a fragment of similar size was present in the other Rp1 parent.