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