Table 3.
Chloroplast polymorphisms within olive (Olea europaea subsp. europaea var. europaea) cultivars.
| Polymorphic sites | Marker | Polymorphism type | Motif | Position (bp)(1) | Region | Polymorphisms already known (Authors) |
|---|---|---|---|---|---|---|
| P1 | Oe-rpl2-trnH | SNP | A/G | 2 | rpl2-trnH | |
| P2 | Oe-trnH-psbA-1 | SNP | A/T | 221 | ||
| P3 | Oe-trnH-psbA-2 | SNP | C/T | 470 | trnH-GUC - psbA2 | |
| P4 | Oe-trnH-psbA-3 | SSR | T10-12 | 505 | ||
| P5 | Oe-trnK-rps16-1 | SSR | T11-12 | 4,690 | trnK-UUU - rps16 | |
| P6 | Oe-trnK-rps16-2 | SSR | T11-12 | 4,883 | ||
| P7 | Oe-trnK-rps16-3 | SNP | A/C | 5,011 | ||
| P8 | Oe-psbK-psbI | SSR | T10-11 | 9,072 | psbK - psbI | Besnard et al., 2003 |
| P9 | Oe-trnS-trnG-1 | SNP | C/T | 9,463 | trnS-GCU - trnG-UCC | |
| P10 | Oe-trnS-trnG-2 | SNP/indel | A/T/- | 9,535 | ||
| P11 | Oe-trnS-trnG-3 | Indel | TTAGATA/- | 9,536 | Besnard et al., 2003 | |
| P12 | Oe-trnS-trnG-4 | Indel | A4(G)A5/- | 9,574 | Besnard et al., 2003 | |
| P13 | Oe-trnS-trnG-5 | SSR | A11-14 | 9,579 | Besnard et al., 2003 | |
| P14 | Oe-trnS-trnG-6 | SNP | G/T | 9,960 | ||
| P15 | Oe-atpA-atpF | SSR | A15-16 | 12,790 | atpA - atpF | |
| P16 | Oe-rps2 - rpoC2-1 | SSR | C10-11 | 17,433 | rps2 - rpoC2 | Besnard et al., 2007 (ccmp5) |
| P17 | Oe-rps2 - rpoC2-2 | SSR | T10-11 | 17,443 | Besnard et al., 2007 (ccmp5) | |
| P18 | Oe-rps2 - rpoC2-3 | SSR | A12-13 | 17,455 | Besnard et al., 2007 (ccmp5) | |
| P19 | Oe-rpoC1 | SNP | C/T | 23,981 | rpoC1 intron | |
| P20 | Oe-trnE-trnT-1 | SSR | A12-13 | 32,682 | trnE-UUC - trnT-GGU | Intrieri et al., 2007; Besnard, 2008 |
| P21 | Oe-trnE-trnT-2 | SNP | C/T | 32,813 | Intrieri et al., 2007 | |
| P22 | Oe-psbZ-trnG-1 | SSR | A10-11 | 38,011 | psbZ - trnG-GCC | |
| P23 | Oe-psbZ-trnG-2 | SNP | C/T | 38,129 | ||
| P24 | Oe-psaA-ycf3-1 | SNP | A/G | 43,868 | psaA - ycf3 | |
| P25 | Oe-psaA-ycf3-2 | SSR | A11-12 | 44,077 | ||
| P26 | Oe-psaA-ycf3-3 | SNP | C/T | 44,302 | ||
| P27 | Oe-atpB-rbcL-1 | SNP | A/G | 56,929 | atpB - rbcL | |
| P28 | Oe-atpB-rbcL-2 | SSR | A6-7 | 57,116 | Besnard et al., 2007 (ccmp7) | |
| P29 | Oe-petA-psbJ-1 | SNP | C/T | 65,656 | petA - psbJ | |
| P30 | Oe-petA-psbJ-2 | SNP | G/T | 66,340 | ||
| P31 | Oe-rps8-rpl14-1 | SSR | T11-18 | 83,112 | rps8 - rpl14 | |
| P32 | Oe-rps8-rpl14-2 | Indel | TTAATCTAGTTC/- | 83,195 | ||
| P33 | Oe-rpl14 | SNP | G/T | 83,307 | rpl14 exon | |
| P34 | Oe-rps12-trnV-1 | SNP | A/T | 101,265 | rps12 - trnV-GAC | |
| P35 | Oe-ndhF | SNP | A/G | 114,454 | ndhF exon | |
| P36 | Oe-ndhF-rpl32 | SSR | T9-10 | 114,885 | ndhF - rpl32 | |
| P37 | Oe-rpl32-trnL-1 | SSR | A14/A7(T)A5 | 115,359 | rpl32 - trnL-UAG | |
| P38 | Oe-rpl32-trnL-2 | SNP | A/C | 115,598 | ||
| P39 | Oe-ycf1-1 | SNP | A/C | 127,793 | ycf1 exon | |
| P40 | Oe-ycf1-2 | SNP | G/T | 128,292 |
The position of the polymorphic regions refers to the cv. Frantoio sequence.
The new markers identified on olive cultivars are given in bold.