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Table 3 Musa RGA contig characteristics and polymorphic RFLP-RGA marker identification

From: Analysis of non-TIR NBS-LRR resistance gene analogs in Musa acuminata Colla: Isolation, RFLP marker development, and physical mapping

RGA contiga Primer pairs Size (bp) Additional contig sequence information Cladeb Polymorphisms observed on M. acuminataparentalsc
      DraI HindIII EcoRV
MaRGA01 1F-P3B 273 short, low homology ni nt nt nt
MaRGA02 1F-P3B 493 contiguous ORF 4 nt nt nt
MaRGA03 1F-P3B 481 contiguous ORF 14 Monomorphic monomorphic polymorphic (multiple loci)
MaRGA04* 1F-P3B 493 contiguous ORF 4 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA05 1F-P3B 316 contiguous ORF ni nt nt nt
MaRGA06 1F-P3B 647 contiguous ORF 3 nt nt nt
MaRGA07* 3F2-13R1 563 contiguous ORF ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA08* 3F2-13R1 630 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA09 3F2-13R1 630 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA10 3F2-13R1 629 frameshift ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA11 3F2-13R1 583 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA12* 3F2-13R1 531 frameshift, stop codon ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA13* 3F2-13R1 587 contiguous ORF ni monomorphic polymorphic (multiple loci) monomorphic
MaRGA14* 3F2-13R1 501 contiguous ORF ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA15 3F2-13R1 634 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA16* 3F2-13R1 454 contiguous ORF ni polymorphic (single locus) monomorphic monomorphic
MaRGA17 3F2-13R1 631 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA18 3F2-13R1 525 contiguous ORF ni monomorphic polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA19 3F2-13R1 655 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA20 3F2-13R1 585 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA21 3F2-13R1 629 contiguous ORF 6 n/t n/t n/t
MaRGA22* 3F2-13R1 597 contiguous ORF 3 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA23 3F2-13R1 583 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA24 3F2-13R1 525 contiguous ORF ni monomorphic polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA25 3F2-13R1 524 contiguous ORF ni monomorphic polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA26 3F2-13R1 610 contiguous ORF 11 nt nt nt
MaRGA27 3F2-13R1 467 frameshifts, stop codons ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA28 3F2-13R1 526 frameshift ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA29 3F2-13R1 551 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA30 P1B-RNBS-D 675 translation unclear ni nt nt nt
MaRGA31 P1B-RNBS-D 1314 frameshift ni nt nt nt
MaRGA32 P1B-RNBS-D 633 contiguous ORF 4 nt nt nt
MaRGA33 P1B-RNBS-D 673 contiguous ORF 5 nt nt nt
MaRGA34 P1B-RNBS-D 792 contiguous ORF 4 nt nt nt
MaRGA35 P1B-RNBS-D 624 contiguous ORF 5 nt nt nt
MaRGA36 P1B-RNBS-D 675 contiguous ORF ni nt nt nt
MaRGA37* P1B-P3D 472 contiguous ORF 11 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA38 P1A-P3A 472 contiguous ORF 11 monomorphic monomorphic monomorphic
MaRGA39 P1A-P3A 480 frameshift ni monomorphic monomorphic monomorphic
MaRGA40 P1A-P3A 860 contiguous ORF 3 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA41* P1B-P3A 1365 contiguous ORF 3 polymorphic (multiple loci) monomorphic monomorphic
MaRGA42 3F2-13R1 619 contiguous ORF 3 No hybridization No hybridization No hybridization
MaRGA43* 1F-P3B 359 low homology ni polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA44 3F2-13R1 631 contiguous ORF 6 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA45 3F2-13R1 625 contiguous ORF 3 polymorphic (multiple loci) polymorphic (multiple loci) polymorphic (multiple loci)
MaRGA46* 3F2-13R1 604 contiguous ORF 3 monomorphic polymorphic (multiple loci) monomorphic
MaRGA47 P1B-RNBS-D 636 contiguous ORF 4 nt nt nt
MaRGA48 P1B-RNBS-D 704 contiguous ORF 22 nt nt nt
MaRGA49 P1B-RNBS-D 1674 contiguous ORF 4 nt nt nt
MaRGA50 P1B-RNBS-D 633 frameshift ni nt nt nt
MaRGA51 P1A-RNBS-D 668 contiguous ORF 9 nt nt nt
MaRGA52 P1B-RNBS-D 669 contiguous ORF 3 nt nt nt
  1. a Contigs marked with asterisks were selected as polymorphic markers for inclusion on a M. acuminata genetic map
  2. b ni = not included in phylogenetic analysis
  3. c nt = not tested as genetic markers