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Table 3 Chloroplast polymorphisms within olive (Olea europaea subsp. europaea var. europaea) cultivars.

From: Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison

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   
  1. The position of the polymorphic regions refers to the cv. Frantoio sequence.
  2. The new markers identified on olive cultivars are given in bold.