Table 2.
List of SNP Sequences Identified
| X CHROMOSOME | ||||||||||
| STS | Cytological location | Flanking sequence | Nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 Q1028 | P strain 2 | Release 1 v:cnbwsp | RFLP? |
| Dm3513 | 1F1–1F3 | TCACT−GGAAC | 78 | G(42) | C(42) | G(46) | G(51) | G | ||
| GGACA−CTCAA | 90 | G(42) | A(44) | G(35) | G(35) | G | Alul | |||
| ACCCA−ACACT | 144 | C(42) | A(44) | C(56) | C(56) | C | ||||
| ACAAA−ATGGG | 174 | A(47) | T(44) | A(40) | A(35) | A | ||||
| Dm1729 | 2B8–2B9 | GAGCT−CTCGA | 477 | T(56) | C(56) | T(40) | T(42) | T | Sacl | |
| Dm0127 | 2F1–2F6 | GTCGT−AGGGG | 1447 | C(37)AGT(40) | C(40)AGG(56) | C(30)AGT(42) | (A/C,22)AGG(33) | AAGG | ||
| CGCTC−CGCTC | 1450 | C(56) | T(43) | C(32) | C(35) | C | Acil BsrBl | |||
| Dm0106 | 3A6 | TCTGT−GAACG | 122, 125 | G(37)TGA(37) | A(56)TGG(42) | G(45)TGA(34) | A(35)TGG(34) | ATGG | ||
| Q1028 | 3D–E | Q1028 | Q1034 | |||||||
| Dm3247 | 4C7–4C8 | AGTTT−CTGCG | 1607 | T(42) | C(56) | C(24) | C/T(22) | C/T(11) | T | |
| CAGTC−GTGAA | 1628 | C(37) | G(37) | G(25) | G(28) | C/G(23) | C | |||
| GTGAA−ACGCC | 1634 | C(51) | T(44) | T(25) | C/T(19) | T/C(37) | C | |||
| GTTTT−CCGAA | 1766 | C(56) | T(56) | T(44) | T(42) | T(20) | C | |||
| Dm1954 | 4E1 | ACAAT−ATCGA | 149 | T(45) | A(56) | A(42) | T(56) | T(40) | T | Tsp5091 |
| Dm3001 | 5C1–5C2 | AATTC−GGATC | 695 | G(27) | G(35) | A(41) | G/A(22) | G(30) | G | |
| TCCAA–ACTTT | 704 | T(37) | T(41) | G(50) | T(30) | T(33) | T | |||
| ATTTT−ACAAT | 888 | T(30) | C(56) | T(42) | C(34) | C(42) | C | |||
| Q1034 | 6E | Q1034 | Q1030 | |||||||
| Dm2006 | 7A2–7A5 | CCCAG−ACATG | 582 | T(56) | C(45) | T(30) | T/C(26) | T/C(17) | T | Rsal |
| TACCT−CCCCC | 618 | DEL(56) | C(56) | DEL(98) | DEL(98) | DEL(98) | DEL | |||
| TCTTG−C | 624 | C(37) | C(46) | C(31) | A/C(26) | A/C(33) | C | |||
| C−CAATC | 626 | G(40) | A(45) | G(20) | G(42) | G(42) | G | |||
| ACTCG−CCAGC | 647 | A(40) | A(35) | A(42) | A/T(30) | A/T(29) | A | Taql BspGl | ||
| Dm1849 | 7D10–7D16 | GGTT−TCCCT | 180 | A(30) | A(51) | T(28) | T(28) | T(28) | A | |
| Dm0426 | 8C1–8C2 | CATAT−TA | 1223 | A(51) | A(51) | A(42) | G/A(24) | G/A(28) | A | |
| TA−GTACA | 1226–7 | T(51)G(42) | T(51)G(42) | T(44)G(42) | T/C(17), G/A(17) | T/C(18), G/A(18) | TA | |||
| ACATA−GTACT | 1234 | T(56) | T(56) | T(48) | C/T(17) | C/T(11) | T | Ndel Rsal SnaBl | ||
| TACTT−ATGTTG | 1241 | G(42) | A(51) | G(42) | A(40) | A(42) | A | Msel | ||
| ACAAC−TACAA | 1352 | T(40) | T(40) | T(42) | A/T(23) | A/T(14) | T | |||
| Dm3169 | 8D1–8D5 | GCCGC−CACGA | 1280 | T(45) | T(40) | T(44) | C/T(13) | C/T(19) | T | BsrBl |
| CCCGT−TGCTC | 1373 | G(37) | A(29) | G/A(37) | G/A(30) | G/A(39) | G | |||
| Dm1980 | 9B1–9B2 | GGTGA−TTCAC | 35 | A(48) | C(40) | C(40) | C(40) | C(40) | C | EcoRl Tsp5091 |
| ATCTA−CAAAA | 62 | A(51) | A(43) | T(40) | A(40) | A(45) | T | |||
| GCAAA−CATAA | 95, 98, 101 | A(51)TTA(51)AAG(56) | C(45)TTC(51)AAA(56) | C(35)TTC(40)AAA(40) | C(29)TTC(34)AAA(25) | C(29)TTC(27)AAA(27) | CTTCAAA | Msel Tsp5091 | ||
| Q1030 | 10E | Q1030 | Q1035 | |||||||
| Dm3746 | 10F7–10F8 | TACAC−TCTCT | 79–80 | G(51)C(51) | A(51)A(51) | G(40)C(40) | A(45)A(46) | A(35)A(35) | AA | |
| TCACA−CCGTA | 137 | G(42) | T(43) | G(35) | T(44) | T(37) | T | |||
| Dm2024 | 11B1–11B2 | GAAC(A)9−(A)5GAT | 172 | A(47) | C(44) | A | C(56) | C(42) | C | |
| Q1035 | 13E9 | Q1035 | ||||||||
| Dm0478 | 13A8–13A9 | TGGCA−TTGGC | 70 | A(40) | A(51) | G(35) | A(39) | A | Munl Tsp5091 | |
| AGACT−TAGTT | 145 | A(45) | A(45) | C(35) | A(37) | A | Bfal | |||
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 Q1028 | P strain 2 | Release 1 v:cnbwsp | RFLP? |
| Dm3491 | 13D1–E4 | CATTG−CCGCC | 60 | T(46) | T(46) | C(46) | T(39) | T | Ecll | |
| CACTG−ACGAG | 170 | A(56) | G(40) | A(35) | A(35) | A | BspGl | |||
| Dm1911 | 14B3–14B4 | TGAAT−GAATG | 1134 | A(46)C(42) | A(40)C(37) | G(43)T(40) | G(21)T/C(21) | GT | ||
| Dm3790 | 15B1–15B2 | TGTGC−CTTAA | 106 | C(44) | A(45) | A(37) | C(50) | C | ApaLl CviRl | |
| ACTAT−CGCCT | 221 | C(40) | T(40) | T(40) | T(45) | T | Acil Ecil | |||
| Dm0509 | 16F5–16F8 | GAGGG−CCGCT | 58 | G(37) | T(45) | G(37) | T(40) | T | Haelll Siml | |
| Q1035 | 17C | |||||||||
| Dm1846 | 17A1–17A2 | ATTTC−ACTTG | 2150 | A(37) | C(45) | A(42) | A(46) | C | ||
| Dm2754 | 17B5–17C4 | AGTAG−GTATG | 402 | C(35) | C(38) | C(56) | T(34) | C | ||
| CATTT−CAGCG | 423 | C(33) | T(42) | C(40) | T(22) | C | ||||
| TGCGG−TTCTC | 444 | G(42) | T(38) | G(40) | T/G(34) | GT | ||||
| CAAAA−ACCGG | 465 | A(34) | A(34) | T(56) | T(26) | T | ||||
| CCGTT−GCTAA | 512 | T(27) | T(35) | T(40) | C(51) | C | ||||
| Dm0505 | 19E1–19E3 | GCTGC−TGGCT | 90 | A(42) | A(42) | A(30) | A(30) | A | CviRl NIallI | |
| CGGAG−ATATG | 170 | C(44) | T(56) | C(56) | C(37) | C | Ndel | |||
| ATATA−TATTG | 190 | A(56) | A(42) | A(42) | A(42) | A | ||||
| Dm0529 | 20B1–20B2 | GGCTC−GTGTC | 837 | G(45) | T(45) | T(42) | G(56) | G | ||
| 2nd Chromosome | ||||||||||
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 Q1037 | P strain 2 | Release 1 y:cnbwsp | RFLP? |
| Dm0447 | 21D1–21D2 | TCTCT−ACGGC | 449 | C(37) | C(40) | C(42) | T(17) | C | ||
| TCTCT−GACCT | 485, 487 | C(32)TT(32) | *(98)T*(98) | *(98)T*(98) | *(98)T*(98) | CTT | ||||
| Dm0375 | 21E3–21F3 | TACGG−AGTGT | 32 | A(29) | A(27) | G(30) | A(27) | A | BscGl | |
| GTCGC−CTGGT | 103 | C(32) | C(33) | A(21) | C(37) | C | ||||
| Q1037 | 22D1–D2 | Q1037 | Q1040 | |||||||
| Dm2641 | 23A1–23A3 | ACTTG−CCCAG | 32 | A(40) | A(51) | G(56) | A(47) | A(42) | G | Siml Haelll |
| TCCAT−AAGAA | 107 | G(56) | G(56) | A(48) | A(48) | A(46) | G | Nialll | ||
| GGCCA−CGGCT | 174 | G(35) | A(40) | G(37) | G(37) | G(35) | A | Acil | ||
| Dm0611 | 23E1–23E4 | ACAAA−CTTTA | 133, 135 | A(56)AC(42) | T(45)AG(40) | T(51)AG(45) | T(45)AG(45) | T(51)AG(51) | TAG | Alul |
| ATCTT−TATAG | 153 | C(48) | C(46) | T(56) | C(46) | C(46) | C | |||
| ACTCG−TGTGT | 169 | C(51) | C(51) | C(27) | G(56) | G(56) | C | |||
| GCCAC−CAGTT | 186 | T(45)G(45) | C(51)C(51) | T(34)G(34) | T(40)G(45) | T(51)G(51) | CC | CviRl Pstl | ||
| Dm2235 | 25A3 | TATTA−AAATC | 141 | ND | ND | G(48) | A(42) | A(37) | A | Msel |
| CATAT−GATAT | 156–163 | DEL(98) | DEL(98) | DEL(98) | TATAATAT(42) | TATAATAT(42) | TATAATAT | Ndel | ||
| GTAAT−ATTGT | 174 | A(40) | T(35) | T(56) | A(40) | A(42) | A | |||
| ATTGG−TTG | 233 | T(56) | T(56) | T(56) | C(44) | C(56) | T | |||
| TTG−AGTAA | 237–238 | G(56)A(56) | G(56)A(56) | G(56)A(56) | T(42)T(40) | T(42)T(40) | GA | |||
| Dm2207 | 26D1–26D2 | TCCGT−TCCAG | 28 | G(51) | G(51) | G(40) | A(45) | A(45) | G | BspGl |
| TCTTC−GT | 118 | G(56) | T(56) | T(42) | G(44) | G(43) | G | |||
| GT−TAGTT | 121 | G(51) | A(56) | A(37) | G(35) | G(40) | G | |||
| CGTCC−AGACG | 148 | T(51) | C(51) | C(40) | C(46) | C(46) | T | Bfal | ||
| AGGTA−TCGTT | 163 | G(40) | G(45) | G(40) | C(40) | C(45) | G | Rsal | ||
| Dm3015 | 29A2 | AACTG−CTTTT | 23 | T(40) | C(56) | T(34) | T(35) | C(42) | C | |
| TGTTT−AAAGT | 114 | A(56) | G(56) | A(44) | A(56) | G(56) | G | Dral Msel | ||
| AACAC−CGGTT | 147 | T(39) | A(56) | T(35) | T(39) | A(38) | A | |||
| CAACC−GGTGC | 171 | T(31) | A(32) | A/T(14) | A(56) | A(42) | A | |||
| Dm0274 | 29A5–29B4 | GGTAC−CGGTA | 741 | G(29) | G(35) | G(38) | T(42) | G(37) | Acil Thal | |
| TTAAT−CAATT | 805 | G(40) | G(42) | G(51) | A(44) | G(42) | CviRl | |||
| GCCGA−AGGTG | 832 | C(40) | C(40) | C(42) | T(46) | C(56) | T | |||
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 | P strain 2 | Release 1 y:cnbwsp | RFLP? |
| Q1040 | 29C1–C2 | Q1040 | Q1042 | |||||||
| Dm0434 | 30A3–30A6 | TTTTT−AACAT | 73–75 | A(35)A(35)A(35) | T(35)A(35)A(34) | A(21)A(27)A(27) | T(21)T(27)T(29) | T(4)T(4)T(4) | TAA | |
| TAGGC−AAAAA | 113–114 | A(56)A(56) | A(47)C(47) | A(13)A(13) | DEL(98) | DEL(98) | AC | |||
| Dm0652 | 31F3–32A1 | AGCAA−CGAAA | 742–743 | C(9)A(9) | C(37)A(37) | C(24)A(24) | T(46)T(33) | C(24)A(25) | CA | Bsbl |
| AGTTT−AACGA | 821 | A(51) | A(51) | A(42) | G(42) | A(26) | A | Dral Msel Pmel | ||
| TTATG−AATGC | 900 | G(51) | G(56) | G(44) | C(37) | G(42) | G | CviRl | ||
| TACAA−TTGTC | 929 | C(51) | T(56) | T(48) | T(13) | T(44) | T | Tsp5091 | ||
| Dm4048 | 32A1–32A2 | CATAC−TTAGA | 113 | T(56) | A(56) | A(42) | A(35) | T(42) | A | |
| GGTTG−CGATA | 168 | C(46) | G(42) | G(37) | G(35) | C(35) | G | |||
| Dm3374 | 33A1–33A2 | GATAT−GCAGT | 733 | T(51) | G(40) | G(44) | G(42) | T(44) | G | CviRl |
| TCCCA−CGGAT | 758–759 | A(29)A(42) | G(34)T(42) | G(42)T(42) | G(26)T(35) | A(24)A(46) | GT | |||
| TAAAA−GAAAT | 769 | T(47) | C(51) | C(56) | C(42) | T(44) | C | |||
| GCATT−ACACA | 802 | G(40) | A(51) | A(56) | A(33) | G(33) | A | Msel | ||
| CACAG−GAA | 809 | C(37) | T(56) | T(44) | T(42) | C(33) | T | |||
| GAA−GTACG | 813 | T(42) | A(56) | A(42) | A(51) | T(42) | A | |||
| Dm2112 | 33A1–33A2 | TAAAA−TTATG | 67 | T(35) | G(42) | T(56) | T(56) | G(45) | T | Tsp5091 |
| AACAT−AATCG | 104 | A(42) | T(45) | A(56) | A(56) | A(42) | A | |||
| GAGAA−AGCGG | 125 | A(56) | G(51) | A(42) | A(46) | G(42) | A | BsrBl | ||
| Dm0240 | 33A3–33A8 | ATGTG−GTGCA | 514 | C(24) | C(24) | T(56) | C(37) | C(47) | T | |
| CATAT−TTTGG | 546 | DEL(27) | DEL(52) | DEL(48) | GTAT(44) | DEL(33) | DEL | Ndel | ||
| Dm2479 | 33D4 | ATAGT−GGCAA | 75 | A(17) | A(40) | A(40) | A(45) | T(40) | ||
| TTTTC−CATTG | 110 | G(37) | G(56) | G(44) | G(56) | T(44) | G | |||
| Dm3635 | 34C1–34C2 | CCGCA−AATGC | 1494 | C(27) | C(27) | T(40) | C(44) | C(42) | T | |
| GCTTG−ATAAA | 1552 | A(27) | G(14) | A(42) | A(56) | G(42) | A | |||
| AAAAT−TAAGA | 1560 | G(33) | T(13) | G(56) | G(44) | T(29) | G | Msel Tsp5091 | ||
| Dm0393 | 34D1–34D6 | TAACA−TAATT | 50 | A(42) | A(42) | T(37) | A(33) | A(37) | A | Msel Vspl |
| ACTGC−GTGAG | 191–192 | T(46)C(33) | A(42)A(42) | A(48)A(56) | A(29)A(29) | T(38)C(38) | TC | BssSl CvlRl | ||
| Dm0012 | 35A1–35A2 | AATTT−TAAAG | 74 | T(42) | G(23) | T(42) | G(51) | T(44) | T | Dral Msel |
| Q1042 | 35E1–E2 | Q1042 | Q1805 | |||||||
| Dm0043 | 35F1–35F2 | GATGG−CAGTC | 60 | A(30) | A | A(35) | A(40) | T(37) | A | |
| Dm2451 | 36B3–36C1 | TCCTT−AGACA | 108 | G(40) | A(45) | G(44) | A(56) | A(32) | G | Aflll Msel |
| AGAAT−AA | 125 | T(51) | C(45) | T(40) | C(56) | C(56) | T | |||
| AA−AGT | 128, 130 | A(40)AT(40) | T(45)AA(51) | A(45)AT(56) | T(56)AA(51) | T(56)AA(40) | AAT | |||
| AGT−AAT | 134 | T(40) | C(56) | T(45) | C(51) | C(38) | T | |||
| AAT−CCCAA | 138–139, 141, 143, 145 | *(98)G(56)T*(98)T* (98)TC(40) | A(45)T(45)TA(45) TA(51)TT(56) | *(98)G(56)T*(98)T* (98)TC(56) | A(45)T(45)TA(51) TA(40)TT(40) | A(56)T(56)TA(46) TA(38)TT(40) | *GT*T*TC | |||
| TCAAA−GTGAA | 157 | C(42) | T(56) | C(51) | T(56) | T(56) | C | Tall | ||
| GTGAA−GTACT | 163–164 | A(42)T(42) | *(38)*(38) | A(56)T(56) | *(98)*(98) | *(98)*(98) | AT | Scal | ||
| Dm0353 | 39A3–39A7 | CTGCT−CAGCT | 26 | G(40) | A(51) | G(40) | A(42) | A(42) | G | CvlRl Patl |
| TTCCG−GTATC | 41 | A(51) | C(40) | C(42) | C(42) | C(37) | C | Acil Thal | ||
| CTCGA−ACAGC | 60 | C(47) | T(45) | C(40) | C(42) | C/T(21) | C | |||
| CTGTG−TTTTC | 85 | G(51) | A(42) | A(51) | A(51) | A(56) | A | |||
| TGGGA−AAATC | 212 | A(56) | A(56) | A(56) | T(42) | A(47) | A | |||
| Dm0627 | 40A6–40B2 | GCAAT−TCTGA | 304 | A(33) | T(56) | T(25) | T(51) | T(40) | T | Tsp5091 |
| Dm0975 | 41C1–41C6 | GCGTG−CGTGC | 140–143 | *** *(40) | *** *(40) | CGTG(51) | *** *(51) | *** *(40) | *** * | |
| Dm3495 | 42A1–42A2 | CGGGG–CTTGT | 83 | G(56) | T(37) | G(35) | G(51) | G/T(17) | T | Siml |
| CGAGA−GTCAG | 132 | T(45) | C(46) | T(20) | C(16) | C(19) | C | Aatll Tall | ||
| Dm2609 | 42A8–42A16 | TTTTT−AAATT | 77–78 | *(43)A(40) | T(47)A(40) | T(56)A(56) | T(56)T(56) | T(56)A(23) | *A | |
| Dm2106 | 42B4–42C2 | ACCGA−GCTAC | 114 | A(56) | G(45) | G(39) | G(25) | A(22) | A | Alul |
| AGTTT−TAAGC | 140 | C(51) | C(51) | T(56) | C(56) | C(56) | C | Msel | ||
| AGCAG−AGTCC | 148 | G(56) | G(56) | A(34) | G(34) | G(32) | G | |||
| TGCGA−GGAGA | 160 | C(46) | C(46) | T(35) | C(34) | C(35) | C | Bccl | ||
| GCTTT−ACAGG | 176 | C(42) | C(51) | T(39) | C(40) | C(40) | C |
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 | P strain 2 | Release 1 v:cnbwsp | RFLP? |
| Q1805 | 43E9 | Q1805 | Q1049 | |||||||
| Dm0735 | 43E12–43F2 | CCAAG−TGCGC | 74 | C(51) | T(40) | C(40) | T(34) | T(34) | T | Alul |
| ATCTA−GACAT | 97 | C(42) | T(46) | C(40) | C(45) | C(36) | T | Pfl1108l | ||
| Dm0746 | 44B1 | GTATC−GTTCT | 140–145 | GCACGG(51) | *** **T(56) | GCACGG(33) | GCACGG(40) | GCACGG(51) | GCACGG | BscGl |
| Dm2209 | 44D1–44D2 | CAATA−AAGTA | 128 | A(45) | G(51) | A(26) | G/A(10) | G(29) | G | |
| TATCA−AACAT | 155 | A(46) | G(40) | A(35) | G/A(16) | G(32) | G | |||
| Dm0722 | 44D5–44E2 | CACCG−TTACT | 101, 104 | G(56)TTT(51) | *(41)TTC(45) | G(32)TTC(14) | G/*(11)TTC/T(11) | *(39)TTC(40) | *TTC | Mspl PinAl |
| Dm3845 | 46B1–46B2 | TTTTT−AATAC | 159 | A(39) | C(51) | A(51) | C(35) | C | Dral Msel | |
| Dm0340 | 47D6–47E2 | GCGAA−TTTTA | 205 | T(28) | A(32) | T(37) | T(40) | T(40) | T | |
| Dm0084 | 48C5–48D2 | CTCAT−CAGCT | 762 | T(56) | T(51) | T(56) | C(35) | T(49) | T | |
| TTATT−GAGAG | 772 | C(51) | C(56) | A(44) | C(42) | C(47) | C | Taql | ||
| TAAGT−ATTTC | 808 | A(51) | G(51) | G(40) | G(40) | G(40) | A | Tsp509l | ||
| TGAGA−GCCGA | 866 | C(51) | C(51) | C(40) | C(42) | T(40) | C | |||
| Q1049 | 49D1–D3 | Q1049 | Q1047 | |||||||
| Dm2480 | 50A3–50A4 | CCTAA−GACGT | 1032 | A(51) | DEL(51) | DEL(53) | A(35) | A(33) | A | |
| TATCC−ACAAC | 1060 | C(37) | T(37) | T(51) | C(44) | C(42) | C | |||
| Dm0064 | 50C23–50D1 | TTTAC−TTTCT | 119 | A(37) | T(31) | A(40) | A(31) | A(37) | A | |
| GCTAA−TTACT | 140 | G(33) | A(29) | G(40) | A(40) | A(40) | G | Tsp509l | ||
| TATTA−TACAT | 154 | T(40) | A(30) | T(43) | A(35) | A(42) | T | Msel Vspl | ||
| TTTTT−AAAAA | 164 | G(9)T(13) | A(36)A(36) | G(35)T(50) | G(27)A(44) | G(42)A(44) | GT | Dral Msel | ||
| Dm3709 | 51E10–51E11 | AGAAT−GAATC | 83, 85, 87–90 | C(35)AG(35)AATAA(42) | *(98)A*(98)A*** *(98) | *A*A*** * | C(31)AG(29)AATAA(35) | C(35)AG(35)AATAA(37) | CAGAATAA | |
| Dm0788 | 51E5–51E8 | AAAAA−CAACA | 1012 | C(40) | T(51) | T(33) | C(26) | C(42) | C | |
| Dm2663 | 51E5–51E8 | TCATT−TTTTT | 156 | A(42) | G(22) | G(36) | A(42) | A(42) | A | |
| Dm0754 | 52B1–52B2 | AATCA−ATATA | 916 | C(33) | T(51) | T(37) | T(44) | T(46) | C | |
| Dm2192 | 54A2–54B1 | AAATG−TGGTT | 608 | T(56) | G(56) | T(42) | G(37) | G(51) | T | |
| ATTTC−GGAAT | 639 | G(51) | C(42) | G(32) | G(48) | G(51) | G | BspEl Mspl | ||
| Dm2427 | 54C3–54C11 | TCGCT−CCTAC | 185 | T(42) | A(53) | T(36) | T(45) | T(40) | T | |
| Dm3490 | 54E8–54F2 | AGTGT−TTTTT | 169 | T(44) | *(56) | T(56) | T(56) | T(46) | A | |
| Dm0851 | 55A2–55B1 | GAGTT−CGAGT | 737 | G(56) | A(42) | A(35) | A(40) | A(17) | A | |
| Dm1720 | 55A2–55B1 | ACTGG−GAAAA | 251 | G(56) | A(48) | G(35) | G(27) | G(14) | G | |
| TAAGT−TGCCA | 271 | C(40) | C(45) | C(21) | G(35) | G(38) | C | |||
| Dm2631 | 55A2–55B1 | TTTTA−TTGCG | 161 | T(46) | T(51) | T(20) | G(56) | G/T(11) | T | |
| TGCCA−CATCG | 179 | T(40) | C(37) | T(34) | T(34) | T/C(28) | T | |||
| Q1047 | 57A3 | Q1047 | ||||||||
| Dm0602 | 56B1–56B2 | ATCCC−CCGGT | 80 | T(44) | G(40) | T(23) | T(44) | T | Acil | |
| GGATT−CTC | 95 | A(37) | G(56) | A(35) | A(33) | A | ||||
| CTC−TTCT | 99 | T(33) | C(56) | T(42) | T(33) | T | ||||
| TTCT−GGCAG | 104 | T(56) | G(56) | T(42) | T(35) | T | ||||
| GGTGT−TTCCG | 152 | A(56) | G(56) | A(50) | A(40) | A | ||||
| CTGGG−CACCT | 178 | C(40) | A(56) | C(42) | C(40) | C | Haeill | |||
| AGTTC−GTTTG | 221 | T(56) | C(56) | T(37) | T(17) | T | ||||
| Dm0800 | 56B1–56B2 | AAAA−TAAAA | 1298 | T(42) | T(40) | A(51) | T(45) | A | ||
| TTTAT−AAGTG | 1319 | T(31) | A(42) | T(45) | T(33) | T | Msel | |||
| CTAGG−AATAT | 1336, 1339 | A(29)TAC(25) | A(43)TAC(17) | T(40)TAA(51) | A(12)TAC(24) | TTAA | Msel | |||
| AATAT−ATATA | 1345 | G(32) | C(35) | G(51) | G(29) | G | ||||
| ATAGT−GCAAC | 1364 | A(10) | A(29) | G(45) | A(15) | G | ||||
| Dm0824 | 57A4–57A6 | GAGCT−GGCGC | 64 | G(42) | T(42) | G(44) | T(42) | T | ||
| TATAT−CAGCT | 198, 200 | A(51)TT(42) | *(51)T*(51) | A(51)TT(51) | *(98)T*(98) | *T* | ||||
| Dm0063 | 57E2–57E8 | TTAGC−TAAAC | G(35) | G(45) | G(34) | G |
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 | P strain 2 | Release 1 y:cnbwsp | RFLP? |
| Q1047 | 57A3 | Q1047 | ||||||||
| Dm2274 | 58A4 | CCCCC−TTTTC | 129–138 | TATTTTCCCG(42) | GA*** *** **(56) | AATTTTCTCG(56) | GA*** *** **(30) | T | BscGl | |
| Dm1544 | 58B10–58C4 | GGTGA−GGTAT | 99 | C(19) | C(51) | C(42) | C/T(13) | C | Bccl | |
| GTGGT−AACGA | 144 | A(33) | A(56) | G(56) | G/A(17) | A | ||||
| Dm1639 | 58F2–58F7 | TTCCA−CGGAT | 87, 90 | A(40)ATC(39) | G(35)ATT(56) | A(35)ATC(37) | A(40)ATC(40) | AATC | BspEl Mspl | |
| ATGAT−GGTTT | 175 | C(40) | G(56) | C(56) | C(30) | C | Dpnl Sau3Al Bccl | |||
| Dm2101 | 59A1–59A3 | AGTAA−TAGAA | 690 | T(11) | T(45) | G(42) | A(37) | T | Tsp509l | |
| ACTTC−TTACT | 811 | A(40) | G(51) | T(42) | G(42) | |||||
| CAGCC−CTGGA | 858 | G(22) | T(37) | G(40) | T(32) | G | Acll | |||
| Dm2487 | 59F2 | TATCT−ATACT | 49 | A(40) | G(45) | A(40) | A(33) | A | ||
| ATTCC−AACAA | 71 | A(46) | A(45) | G(51) | A(30) | G | ||||
| AGGCA−GCGAT | 107 | T(51) | C(39) | T(42) | T(42) | T | Niaill Sphl Thal | |||
| CAGAC−CCGCA | 173 | A(40) | G(35) | G(40) | G(35) | G | ||||
| CAGCA−ACGGA | 182 | G(33) | C(43) | C(56) | C(42) | C | ||||
| Dm0327 | 60B2–60B10 | TATGTGTG−TGTGTGCT | 100–101 | T(39)A(39) | DEL(98) | DEL(98) | DEL(98) | TA | ||
| Dm2247 | 60D10–60D11 | TTCGG−GGGCG | 158 | C(42) | T(56) | T(44) | T(42) | C | Acll | |
| 3rd Chromosome | ||||||||||
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1Q1050 | P strain 2 | Release 1 y:cnbwsp | RFLP? |
| Dm2467 | 61C1–61C2 | ATCTT−ACTGG | 219 | T(45) | T(46) | T(29) | A(22) | A | Msel | |
| CTGTC−TTTTT | 235 | *(56) | T(48) | T(27) | T(30) | |||||
| Dm0688 | 61D1–61D2 | AATTT−GGAGA | 203 | A(51) | C(56) | A | C | A | ||
| AGAAT−TGGAA | 252 | G(51) | C(51) | G | C | G | ||||
| Q1050 | 62B4–62B5 | Q1050 | Q1052 | |||||||
| Dm3835 | 62F1–62F2 | CAACA−GCTAA | 202 | G(40) | G(42) | G(42) | A(44) | A(42) | G | |
| Dm2200 | 6303 | GCCGC−TTCCC | 151 | C(45) | T(45) | C(29) | T(30) | T(42) | C | |
| TTCCC−CCCTC | 157 | A(45) | G(51) | A(44) | G(42) | G(37) | G | Acll | ||
| Dm2086 | 65A6–65A10 | TACGA−AAGCT | 35 | T(33) | C(37) | C(47) | T(38) | T | T | |
| TATTT−AAA | 85–86 | C(35)A(12) | *(98)A(51) | *(98)C(56) | C(15)A/C(11) | CA | CA | |||
| AAA−TTTAA | 90–94 | TTT(51)AA(45) | ***(98)A*(98) | ***(98)A*(98) | TTT(24)AA(28) | TTTAA | TTTAA | |||
| TTAAT−TTATA | 101–110 | ATATATTTAA(48) | *T*TA***A*(98) | *T*TA***A*(98) | ATATATTTAA(33) | ATATATTTAA | ATATATTTAA | |||
| TTATA−GTATT | 116–128 | TATATAATATATA(56) | *(98) | *(98) | TATATAATATATA(28) | TATATAATATATA | TATATAATATATA | |||
| ATTAA−GTATA | 136 | T(42) | C(40) | C(42) | T(42) | T | T | Vspl Tall | ||
| Dm0929 | 67A1–67A2 | TAATG−GTTT | 508 | T(56) | C(56) | C(42) | C(18) | C(42) | C | |
| GTTT−GTGGT | 513 | A(40) | T(42) | A(40) | T(24) | T(44) | T | |||
| Dm2202 | 67C10–67D1 | CATTT−CCGAA | 880 | G(42) | A(40) | G(40) | A(37) | A(35) | G | |
| Q1052 | 68A1–68A2 | Q1052 | Q1060 | |||||||
| Dm2215 | 68B1–68B2 | ATTCA−CTAAT | 593, 596 | G(40)TTC(38) | G(42)TTC(38) | T(56)TTT(40) | G(35)TTC(28) | G(42)TTC(40) | GTTC | |
| TTCCC−TATCC | 607 | T(42) | T(37) | A(42) | T(42) | T(46) | T | |||
| TTCAC−AATA | 619 | A(45) | A(37) | G(30) | A(42) | A(42) | A | |||
| ATAA−AAC | 624 | G(47) | G(42) | A(44) | G(42) | G(44) | G | |||
| AAC−TTCAC | 628 | A(47) | A(44) | T(47) | A(42) | A(42) | A | |||
| TCAAC−ATTTT | 641 | T(45) | T(40) | C(42) | T(38) | T(40) | T | |||
| GTTTT−GTGGG | 753 | T(45) | T(40) | C(42) | T(42) | T(42) | T | |||
| Dm2544 | 69D1 | TACTT−CGCTG | 642 | G(27) | G(40) | G(40) | A(51) | A(40) | G | Hhal |
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 | P strain 2 | Release 1 v:cnbwsp | RFLP? |
| Dm3239 | 71F1–71F2 | AGAGC−GAACT | 73 | C(40) | C(37) | T(35) | T(35) | C(40) | T | Alul |
| GTGTG−GAGAT | 88 | G(46) | G(51) | A(30) | A(42) | G(40) | G | |||
| AATTC−TCCTA | 114–132 | **T*** *A**G *** *** *G*(56) | **T*** *A**G *** ***G*(44) | AATTTTTAATGT TTCTAGG(33) | AATTTTTAATGT TTCTAGG(37) | **T*** *A**G *** ***G*(35) | AATTTTTAATGT TTCTAGG | Bfal Msel Tsp509l | ||
| Dm1809 | 72C1–72D6 | AGGCG−AGGAT | 714 | C(40) | C(39) | A(19) | A | C | C | Hhal |
| Q1060 | 73A1–A4 | Q1060 | Q1056 | |||||||
| Dm3626 | 74F4–75A2 | AGTGG–AAAGC | 1267 | A(30) | A(56) | G(56) | A(33) | A(56) | A | |
| ATGGG−GGTGG | 1301 | A(22) | T(51) | T(56) | A(42) | T(47) | T | |||
| Dm2220 | 76B6–76B10 | GCAAT−CCGAT | 124 | T(16) | T(29) | G(33) | T(22) | T(42) | G | Tsp509l |
| Dm3089 | 76C3 | CGATG−TTTAT | 51 | *(98) | *(98) | T(51) | *(98) | *(98) | T | |
| AATAT−TA | 156, 158 | A(51)TG(51) | A(45)TG(45) | G(44)TA(44) | A(40)TG(45) | A(56)TG(56) | GTA | |||
| TA−TATAT | 161–167 | TATGTAG(45) | TATGTAG(45) | CTACGTA(56) | TATGTAG(42) | TATGTAG(37) | CTACGTA | |||
| Q1056 | 83A7–A8 | Q1056 | Q1058 | |||||||
| Dm1568 | 86A5 | TTGCA−CAAGA | 155 | A(51) | A(38) | C(27) | A(33) | A(30) | A | |
| AACTC−TCCAC | 165 | C(56) | A(46) | C(31) | A(35) | C(42) | A | |||
| Dm3326 | 87F13−88A1 | GCTGG−AAATA | 71–91 | ACATGAACTTAT TCAGCA ACG(35) | *** *** *** * *** *** *** *(98) | ACATGAACTTAT TCAGCAACG(31) | *** *** *** *** ***(98) | *** *** *** *** **(98) | ACATGAACTTAT TCAGCAACG(31) | BspGl |
| Dm3478 | 88A1 | TCCGT−CAGCA | 90 | G(37) | G(35) | A(37) | G(37) | G(40) | A | CviRl Rsal |
| Dm0337 | 89C2–89C5 | TCCTG−TATAT | 856 | C(51) | G(56) | G(31) | C(40) | C(42) | G | |
| Dm2709 | 89D2–89D4 | CAGGG−GATGA | 668 | A(15) | G(56) | A(42) | A(48) | A(44) | A | |
| GAGCT−TCCAT | 677, 680, 683 | C(27)CTG (46)TAT(39) | G(30)CTC(33) TAC(42) | A(42)CTG(38) TAT(38) | C(56)CTG(42) TAT(56) | C(42)CTG(46) TAT(42) | ACTGTAT | Sacl | ||
| ATGAT−CCGCG | 692 | A(37) | T(56) | A(34) | A(42) | A(35) | A | |||
| CCGCG−CCCAT | 698 | A(37) | G(35) | A(30) | A(37) | A(31) | A | Haelll Sacll Siml | ||
| GCCGA−GAATG | 710–711 | G(42)C(42) | A(41)A(41) | G(38)C(38) | G(46)G(46) | G(42)C(42) | GC | |||
| GAATG–AGCGA | 717, 720–722 | A(41)GAA(56) A(56)G(56) | C(27)GAC(38) T(38)C(38) | A(42)GAA(46) A(42)G(44) | A(42)GAA(56) A(56)G(51) | A(42)GAA(56) A(56)G(46) | A | |||
| AGCGA−CAGAG | 731, 734, 737, 740 | G(32)GAG(44) CAC(45) GTG(45) TGT(45) | A(48)GAA(37) CAG(45) GTT(51)TGC(45) | G(46)GAG(37) CAC(42) GTG(44)TGT(42) | G(51)GAG(46) CAC(44) GTG(40)TGT(51) | G(56)GAG(48) CAC(37) GTG(45)TGT(56) | GGAGCACGTGTGT | Pmll Tall | ||
| Dm2494 | 89F4–90A2 | GGATG−CATCC | 503 | C(38) | C(20) | C(56) | T(44) | C(42) | C | Bccl |
| TCGGG−TACTA | 623 | C(37) | A(51) | C(39) | A(40) | C(35) | C | |||
| GATTT−CAACT | 659 | G(45) | G(45) | G(42) | C(29) | G(35) | G | CvlRl | ||
| ATGCT−AGCTA | 678 | T(45) | A(51) | T(38) | A(30) | T(42) | T | |||
| Dm3952 | 90D1–90E2 | AATTC−TTTTT | 717 | T(27) | T(30) | T(44) | *(98) | *(98) | * | |
| Q1059 | 91A1–A2 | Q1058 | Q1059 | |||||||
| Dm3293 | 92D1–91D2 | TTGTG−GACCC | 94 | T(51) | C(40) | C(35) | C(42) | T(42) | C | |
| CTGAG−ACTGA | 112 | G(56) | C(42) | C(38) | C(42) | G(35) | C | |||
| GGAAT−AGAAT | 183 | T(40) | C(45) | C(35) | C(35) | T(33) | C | Tsp509l | ||
| Dm1705 | 92D1–92D2 | GATAT−CCAAT | 473 | C(51) | C(42) | T(42) | T(42) | C(28) | C | EcoRV |
| TCATA−AAG | 518 | C(33) | C(28) | A(42) | A(33) | C(28) | C | |||
| AAG−CGGAT | 522 | C(42) | C(56) | A(37) | A(44) | C(42) | C | |||
| TGCGG−AGATC | 617 | T(45) | G(51) | G(26) | G(17) | G(32) | G | |||
| Dm2772 | 94C1–94C5 | CATTT−GGCGG | 409 | C(45) | C(40) | T(40) | T(42) | C(42) | C |
| STS | Cytological location | Flanking sequence | Relative nucleotide position | Oregon R | Canton S | w:iso2:iso3 | P strain 1 | P strain 2 | Release 1 v:cnbwsp | RFLP? |
| Dm1690 | 94E6–94E12 | AGTTT−GGATT | 802 | G(56) | G(56) | T(56) | G(33) | G(9) | G | |
| TAAAT−TGGAA | 872 | T(44) | T(45) | T(42) | G(36) | G(9) | T | Tsp509l | ||
| AACAT–TCTGA | 902–903 | A(44)T(48) | A(51)T(51) | A(40)T(45) | T(42)A(42) | T(9)A(9) | TA | |||
| TCTTT−GCCTG | 916 | T(56) | C(40) | C(40) | C(44) | C/T(9) | T | |||
| GCCTG−TTATT | 922 | T(56) | A(56) | A(45) | A(40) | T(9) | T | |||
| TTATT−AAGTG | 940–950 | *** *** *A***(98) | *** *** *A***(98) | *** *** *A***(98) | TGTTCTTATTG(37) | TGTTCTTATTG(11) | *** ***A*** | Msel | ||
| AGTGA−ATTGT | 957 | C(51) | T(56) | T(44) | T(27) | T(11) | C | |||
| GTATT−TTCAA | 966 | C(56) | C(56) | C(56) | T(42) | T(20) | C | |||
| AATAA−TTAGT | 996 | T(45) | T(43) | T(40) | A(17) | A(16) | T | |||
| TTAGT−TATAT | 1002 | A(51) | A(51) | A(40) | T(42) | T(33) | A | |||
| TATAT−TAAAC | 1008 | A(51) | A(51) | C(40) | C(17) | C(20) | C | |||
| Dm1592 | 95D1–95D6 | AGACA−TTCAC | 911 | C(56) | T(44) | T(31) | C(56) | C(56) | C | |
| Dm0667 | 98E11–98F3 | TTTAA−ATTTC | 1032 | C(29) | G(35) | G(56) | G(42) | C(30) | G | |
| CTAGC−TTGAA | 1042 | C(51) | T(56) | T(46) | T(37) | C(35) | G | Alul | ||
| GTCCG−CGA | 1081 | A(29) | A/G(21) | A(26) | G(33) | A(14) | G | |||
| CGA−TTTAG | 1085–1100 | **T*T***A***G(36) A**(45) | GGTATGGCAT TCTATG(37) | GGTATGGCAT TCTATG(48) | GGTATGGCAT TCTATG(42) | **T*T***A*** G(42)A**(98) | GGTATGGCAT TCTATG(48) | |||
| AAACT−TTTTT | 1138, 1142 | T(56)ATTG(37) | G(56)ATTA(51) | G(44)ATTA(45) | G(37)ATTA(37) | T(22)ATTG(15) | GATTA | |||
| CAGAA−ATTGA | 1156 | A(56) | T(51) | T(30) | T(29) | A(40) | T | Tsp509l Sspl | ||
| TTGGC−AAAAT | 1170 | C(42) | A(51) | A(44) | A(44) | C(26) | A | Haelil Mscl | ||
| AAAAT−TATTT | 1176, 1178 | A(38)CG(40) | G(56)CA(56) | G(50)CA(37) | G(30)CA(35) | A(32)CA(21) | GCA | SnaBl Tall CvlRl Nsil | ||
| Q1058 | 96F10–F11 | Q1058 | Q1059 | |||||||
| Dm1657 | 97C1–97C3 | CATGG−CGCAT | 968 | C(37) | C(40) | A(30) | C(38) | C(24) | C | Acil Haelil |
| AGTTT−TGTTT | 1024 | G(56) | T(56) | G(56) | G(37) | G(37) | T | |||
| GCCCC−CCATC | 1049 | G(40) | A(40) | A(40) | A(37) | G(40) | A | Acll | ||
| Dm2473 | 99D1–99D2 | GTCGC−GAATC | 1029 | *(19) | T(40) | T(30) | T(40) | C(40) | C | Nrul Thal |
| ATTGG−CCGGA | 1049–1049, 1052 | C*(11)T(11)CAG(22) | T(40)T(40)CAA(40) | T(23)T(25)CAA(23) | T(38)T(37)CAA(33) | T(35)C(35)CAG(33) | CTTCAA | Drdll | ||
| Dm2288 | 100C1–100C4 | CTGCT−CATTT | 1040 | C(42) | T(44) | T(47) | C(21) | C(29) | C | |
| TTGGC−GTTCC | 1110–1113, 1116 | *** *GG*(98) | GTTT(40)GGT(40) | GTTT(42)GGT(38) | *** *GG*(98) | *** *GG*(98) | ATTTGGT | Acil | ||
| CAAAG−TGCGT | 1139 | T(51) | C(37) | C(42) | T(42) | T(56) | C | Alul |
-
List of SNP sequences identified among CS, OreR, w;iso2;iso3, y;cnbwsp, and pairwise combinations of 17 single P-element insertion strains. Identified SNPs are listed according to the STS from which they were derived. For each SNP entry, the approximate cytological location and ∼10 bp of sequence flanking the polymorphic site are indicated. Cytological locations are derived from the P1-based genome physical map (Kimmerly et al. 1996) and confirmed by comparison of the STS sequence to a database of Release 1 genome sequences with associated cytological locations (Adams et al. 2000). “Nucleotide Position” refers to nucleotide positions within sequence assemblies and is included to provide relative, rather than absolute, positions for each polymorphism. The identity of the dimorphic base for each SNP is listed for each strain, and the corresponding Phredquality score of that base in the sequence trace is listed parenthetically. Sequences from the y;cn bw sp strain were derived from the Release 1 sequence, where available. Restriction endonucleases listed under “RFLP?” are those for which the recognition site is present in one allele and absent in the other. The location of P-element insertions (designated as Q1040, etc.) is indicated; SNP sequences are listed between each pairwise set of P-element strains that can be used for eye-color-based selection of recombinants in that interval. All polymorphisms between the w;iso2;iso3 and P-element strains were initially detected by Denaturing HPLC. For additional data, see http://www.fruitfly.org/SNP/index.html.
