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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.