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E. Ritter et al.UHD linkage map of Pinus pinaster
Original article
Towards construction of an ultra high density linkage map
for Pinus pinaster
Enrique Ritter
a*
, Ana Aragonés
a
, Torsten Markussen
b
, Virginie Acheré
c
, Santiago Espinel
a
,
Matthias Fladung
b
, Sandra Wrobel
b
, Patricia Faivre-Rampant
c
, Sylvain Jeandroz
c
and Jean-Michel Favre
c
a
NEIKER, Apartado 46, Vitoria, Alava, 01080, Spain
b
BFH, Institute for Forest Genetics, Sieker Landstrasse 2, Grosshansdorf, 22927, Germany
c
UMR UHP-INRA Plant-Microbes Interactions, Faculté des Sciences, BP 239, 54506 Vandœuvre-lès-Nancy, France

(Received 16 August 2001; accepted 22 February 2002)
Abstract – Two parental linkage maps have been constructed from the P. pinaster reference population (0024 × C803) based on AFLP, SSR and
EST markers. Although segregating polymorphism was low due to a high degree of homozygosity in the parents, 12 linkage groups with 26 to
46 markers each were obtained for each parent. The availibility of 70 anchor points based onfragmentscommontoboth parents and based on co-
dominant SSR and EST markers allowed to determine homologous chromosomes for both maps and to construct one integrated map. Total ge-
nome length of the integrated map is around 2000 cM including 1182 markers. Since some of the EST and SSR markers are also mapped in
different pine species, association of linkage groups of our reference population with those of other published maps was possible.
AFLP, SSR, EST markers / genetic mapping
Résumé – Vers la construction d’une carte génétique ultra-haute densité chez Pinus pinaster. Deux cartes génétiques ont été construites à
partir d’un croisement intra-spécifique de P. Pinaster (0024 Landes × C803 Corse) avec des marqueurs AFLP, SSR et EST. Malgré un faible po
-
lymorphisme dû à la forte homozygotie des parents, 12 groupes de liaison comprenant 26 à 46 marqueurs ont été obtenus pour chacune des car
-
tes. La présence de 70 points d’ancrage déterminés à partir des fragments communs aux deux parents a permis d’identifier les chromosomes
homologues des deux cartes et de construire une carte consensus d’une longueur totale d’environ 2000 cM et comprenant 1182 marqueurs. La
présence de quelques marqueurs EST et microsatellites déjà cartographiés chez différentes espèces de pins a permis d’aligner un certain nombre
de groupes de liaison avec cette carte de pin maritime.
marqueurs AFLP, SSR, EST / cartographie génétique
1. INTRODUCTION
Several linkage maps have been produced in a variety of
forest species including Pinus. They are based on different
marker types such as RFLPs in Pinus taeda [6, 19] and
RAPDs in Pinus pinaster [4] and Pinus radiata [7]. Also
AFLP maps are available for Pinus pinaster [4] , P. radiata
[2] and Pinus edulis [22]. Recently a high-density map of P.
pinaster has been constructed [5]. Other marker types such as
proeins and isozymes are integrated in these maps [4, 6, 15]
as well as EST [3] and SSR markers [8] which may be useful
for aligning different maps.
In order to apply DNA marker technology in breeding of

coniferous species a project has been initiated with the aim of
constructing an ultra-high-density linkage map (UHD map)
of Pinus pinaster based on several thousands AFLP markers
and numerous published microsatellites (SSR). The reference
map will be used for comparative genome and QTL analyses
in different genetic backgrounds. It is the aim to align other
Ann. For. Sci. 59 (2002) 637–643 637
© INRA, EDP Sciences, 2002
DOI: 10.1051/forest:2002049
* Correspondence and reprints
Tel.: 34 945 121 381; fax: 34 945 281 422; e-mail:
published linkage maps in forest species with this reference
map. Based on a reduced number of markers, comparative ge
-
nome and QTL analyses will be performed in different pine
species and related gymnosperms.
In this paper we present the first project results, which
consist of an integrated linkage map derived from two P.
pinaster genotypes and some associations of linkage groups
of our map with those of different pine species.
2. MATERIALS AND METHODS
2.1. Plant material
The F1 reference population of P. pinaster descended from the
cross 0024 Landes × C803 Corsica. The parental trees had been se
-
lected in cooperation by INRA-Pierroton and AFOCEL SW re
-
search stations. The cross was performed in 1987 and the
129 resulting progeny trees were established in the field by
AFOCEL in 1990. A total of 80 out of the 129 progeny genotypes,

established in the AFOCEL experimental stands of Troussas and
Arsague (Landes; SW, France), were used for linkage mapping.
2.2. Molecular methods
Genomic DNA was extracted from needles using the DNeasy
Plant Kit from Qiagen with slight modifications of the supplier’s
protocol.
AFLP analysis was performed according to [23] using
EcoRI/MseI adapters. Preamplification was performed with one se-
lective nucleotide and specific amplification with 3 selective nu-
cleotides (+1/+3 amplification). Also +2/+4 amplifications were
performed. Amplification products were separated on 6 or 8% dena-
turing polyacrylamide gels. Different techniques were used for de-
tecting amplification products. AFLP fragments were detected on a
LI-COR 4200-S1 DNA sequencer using primers labelled with the
fluorescent infrared dye IRD800 (LI-COR, Lincoln, Nebraska,
USA) or on a ALFexpressII (Amersham Pharmacia Biotech, Ger
-
many) with Cy5-Amidite labelled primers (MWG-Biotech, Ger
-
many). Analysis was performed according to the manufacturer
instructions in each case.
SSR primers developed in different species were analyzed
for polymorphism and segregation. SSR developed in Pinus
pinaster and P. halepensis [13] in P. strobus ([9, 10];
in P. radiata
and P. sylvestris ([11, 20, 21]; />Data/hardssr.html) were used for this purpose. Furthermore, several
other as yet unpublished SSR primers from Pinus radiata were ob
-
tained from Gavin Moran (CSIRO, Australia) and from Craig Echt
(Forest Research Inc., New Zealand) and from Picea abies from

Giovanni Vendramin (IMGPF, Italy). SSR analysis was performed
as described by [13] or based on the information given in the men
-
tioned WEB pages. EST primers were obtained from the informa
-
tion provided on />primers.htm. EST analysis was performed according to [12].
2.3. Data analysis and linkage mapping
Polymorphic DNA fragments were scored for presence or ab
-
sence in parents and F1 progenies. Linkage analysis between marker
fragments, estimation of recombination frequencies, and determina
-
tion of linear order between linked loci including multipoint linkage
analysis and the EM algorithm for handling missing data were per
-
formed as described in [16, 17]. The MAPRF program [17] was ap
-
plied for the computational methods. Firstly, linkage groups were
constructed based on fragments specific to either parent. Linked
fragments were arranged into linkage groups using a minimum,
commonly accepted LOD threshold of 3.0 between consecutive
markers. Subsequently, fragments common to both parents were in
-
tegrated into linkage groups as anchor points as described in [16].
Only common markers linked with recombination frequencies of
zero to at least one parent (LOD > 6) and linked with a minimum
LOD threshold of 3.0 to the other parent were considered for this
purpose.
3. RESULTS
3.1. Generation of polymorphic DNA markers

Nearly 300 different primer combinations (PCs) were ana
-
lyzed for the generation of AFLP-fragments. More than 100
fragments were often produced with specific primer combi
-
nations, with from one to 25 segregating fragments in the
mapping population. However, some primer combinations
produced no segregating fragments. This was generally the
case for primer combinations with high AT contents. In gen-
eral, better quality of gels were obtained with the +2/+4 am-
plification system.
A total of 239 AFLP primer combinations were used for
the molecular analyses and generated 1740 segregating frag-
ments. Thus on average, 7.3 polymorphic bands per primer
combination were obtained. Approximately 39% of the seg-
regating fragments were specific for either one parent of the
cross, while 22% of the fragments were present in both par
-
ents. Around 16% of the fragments showed significant devia
-
tions (α > 5%) from the expected segregation ratios.
Furthermore, a total of 120 SSR and 30 EST primer pairs
were used in this study. Amplification products were ob
-
tained in most cases after adapting the particular PCR condi
-
tions in each case. However, as with AFLP markers, a low
degree of polymorphism between parental alleles together
with a large degree of homozygosity (i.e. non segregating
polymorphic fragments) was observed. Only 21 SSR and

10 EST markers showed one or more segregating bands.
3.2. Construction of linkage maps
Initially, individual linkage maps of 12 linkage groups
each were obtained for the two parents of the mapping popu
-
lation. Their characteristics are summarised in table I. Details
of the maps, parental AFLP profiles as well as the obtained
polymorphisms are displayed on the project WEB page
( Linkage groups of the P1
map (parent 0024) contained 26 to 46 individual and common
markers each and were between 107.8 and 180.1 cM in
length. The total P1 map length (female parent 0024) was
638
E. Ritter et al.
1736 cM. The P2 map (male parent C803) was 1942 cM in
length and made up of linkage groups with 23 to 41 markers
each. The size of the linkage groups varied between 115.1
and 190.5 cM.
Further 217 fragments were linked with recombination
frequencies of zero to other fragments in these linkage maps
and have not been not considered in these counts.
Linkage to mapped markers on linkage groups was appar
-
ent for 206 additional markers. However, these were highly
distorted or consisted of common fragments linked to other
fragments with reduced LOD values and could not be placed
in a single interval with high certainty. Since the standard er
-
rors of the estimates of the recombination frequencies were
high, these 206 markers are included in this map as so called

“associated markers”, anchored to the marker with the high
-
est probability.
Based on the integration of 70 markers common to both
parents and codominant markers like SSRs and ESTs into
linkage groups for both parents, it was possible to assign all
12 homologous chromosomes for P1 and P2, and to obtain in
this way an integrated consensus map with a total of
759 markers (table I, figure 1). Linkage groups of the inte
-
grated map varied between 123.2 and 191 cM in length and
contained between 45 and 74 markers each. Considering the
217 markers linked without recombination to other displayed
markers and the 206 associated markers, an integrated map of
1182 markers was achieved with an average of 99 markers
per linkage group.
3.3. Associations of linkage groups between
the reference map and other published maps
The SSR and EST markers amplified one or two loci each
with variable number of alleles. A total of 14 SSR (19 loci)
and 7 EST markers (7 loci) could be placed on the reference
map (figure 1). Since some of them were also mapped in other
pine species, an association of several linkage groups from
our reference population with those of other published maps
was possible. The summarized results are shown in table II.
4. DISCUSSION
4.1. The generation of segregating polymorphic DNA
markers
The pine genome is known to be relatively large and con
-

tains large amounts of repetitive elements [24]. Thus a highly
increased number of AFLP amplification products can be ex
-
pected. It is also well known that increased AT contents in the
selective nucleotides leads to a higher number of amplifica
-
tion products. However, the resolution of the gel is limited so
that different amplification products may comigrate, hiding
in this way possible segregating polymorphisms. Therefore
using PCs with lower AT content and/or increasing the num
-
ber of selective nucleotides in the primers to 4, potentially re
-
sults in less amplification products, but in higher segregating
polymorphisms of variable number of bands with good qual
-
ity.
UHD linkage map of Pinus pinaster 639
Table I. Characteristics of the P. pinaster maps from the cross 0024 × C803.
P1 – MAP (0024) P2 – MAP (C803) Integrated Map
LG Length IM CM TM Length IM CM TM Length IM CM TM AP
1 160.4 35 9 44 173.3 27 10 37 175.6 62 12 74 7
2 153.2 28 12 40 171.1 28 10 38 168.9 56 13 69 9
3 131.8 26 9 35 174 25 6 31 176.5 51 9 60 6
4 151.2 27 10 37 190.5 23 7 30 175 50 11 61 6
5 146.3 27 8 35 187.3 30 7 37 179.3 57 11 68 4
6 107.8 20 6 26 153.7 19 4 23 151.5 39 6 45 4
7 121.5 24 7 31 116.7 23 6 29 123.2 47 8 55 5
8 135.3 22 7 29 130.5 22 5 27 142.5 44 8 52 4
9 180.1 38 8 46 181.5 27 8 35 191 65 10 75 6

10 148.7 33 7 40 115.1 24 7 31 156.5 57 9 66 5
11 149.2 27 8 35 175.1 24 12 36 182.8 51 13 64 7
12 150.3 28 7 35 172.7 32 9 41 171.4 60 10 70 6
Total: 1735.8 335 98 433 1941.5 304 91 395 1994.2 639 120 759 70
Mean: 144.7 27.9 8.2 36.1 161.8 25.3 7.6 32.9 166.2 53.3 10 63.3 5.8
+ 217 markers linked with recombination frequencies of zero to other markers
+ 206 associated fragments: Total Markers: 1182
Legend:
LG = linkage group; IM = individual markers (parent specific); CM = markers common to both parents; TM = total number of markers for linkage group; AP = number of anchor points.
640 E. Ritter et al.
8/2
77/11
8.4
148/8
18.7
222/10
19.9
39/6
221/5
240/3
22.5
96/1
27.5
268/7
30.0
229/4
33.4
NZPR386a
35.1
RSO1D5

56/10
152/4
35.2
152/18
38.3
239/3
39.2
NZPR823
43.8
140/5
44.5
157/4
158/7
57/9 189/6
49.1
58/8
53.1
111/4
54.6
156/3
62.5
138/2
64.6
76/5
75.0
149/14
75.9
157/2
80.9
228/2

84.3
159/2 239/1
86.1
244/4
89.7
62/5
94.0
92/9
96.1
215/7
96.9
216/7
101.0
78/7
101.9
152/14
198/2
104.0
14/7
105.7
149/3
107.8
212/10
110.6
66/11
111.4
31/1
152/15
116.7
213/2

122.9
59/1
64/1
147/5
126.0
63/8
131.6
ASO1F3
136.1
225/2
138.2
NZPR0413
140.1
182/2
140.5
237/3
142.8
263/4
152.5
190/9
153.5
23/8
35/14
153.6
143/5
154.5
183/2
155.6
185/3
157.7

149/8
158.3
255/5
159.8
156/2
160.2
150/2
163.0
54/18
164.1
143/9
165.8
92/8
165.9
4/2
168.7
77/4
175.6
8/23
0.0
257/5
7.3
62/6
15.4
69/5
18.1
221/7
21.9
148/1
24.6

68/1
25.8
58/13
150/1
179/8
42.8
61/4 264/9
44.0
73/1
49.2
151/14
52.2
253/6
52.4
229/3
55.0
171/7
57.5
183/4
61.4
159/15
61.9
191/1
63.4
35/17
63.8
138/3 146/3
66.2
105/5
67.5

157/3
72.1
45/7
146/9
72.4
155/5 NZPR1702a
73.5
54/15
66/2
73.6
212/6
75.8
254/8
82.2
164/2
89.2
137/5
250/3
89.3
35/18
91.8
164/3
95.8
159/13
97.0
78/1
103.3
77/13
106.7
54/2

81/1
108.3
8/5
92/11
57/7
110.4
107/6
112.2
139/1
113.7
148/5
120.0
14/5
182/6
120.1
267/2
126.6
53/2
130.6
77/1
135.8
29/3
158.6
52/2
162.5
33/10
163.8
ITPH4516a
166.3
40/12

172.7
188/7
176.5
109/9
0.0
Lg:1
10/2
2.8
39/3
228/4
224/2
5.7
216/2
9.4
241/5
22.3
238/4
25.2
152/12
158/12
25.3
NZPR006
27.5
56/11
36.5
212/7
43.1
54/10
234/4
56/12

58/11
52.1
23/4
23/7
150/9
54.0
RTPEST11
220/2
55.9
54/7
56.7
11/1
60.1
40/9 236/8
64.5
92/6
65.6
257/10
74.6
216/6
78.9
151/16
80.5
222/8
82.0
8/6
84.1
216/3
88.4
181/3

254/4
89.4
145/6
93.8
235/1
96.5
52/5
96.7
241/2
101.2
59/4
102.7
33/8
104.2
28/1
104.8
139/2
139/4
105.9
146/5
108.6
-E28072
109.5
54/6
23/6
113.2
54/1
116.1
230/11
117.6

244/9
122.1
63/11
159/9
241/8
123.4
71/5
124.7
156/4
129.6
31/3
130.6
231/8
132.1
56/8
232/6
136.1
244/11
136.3
188/4
142.4
61/7
143.8
-E87909
144.1
242/6
152.2
99/4
156.9
22/2

168.9
31/2
0.0
Lg:2
Lg:3
245/1
0.0
179/13
1.6
56/9
10.8
20/5
222/3
228/6
14.7
ITPH4516b
27.5
152/2
145/3
27.6
60/3
29.6
237/1
30.6
142/6
153/3
30.7
76/20
37.8
100/8

40.5
97/1
41.3
140/3
42.6
245/5
50.1
175/5
58.8
245/8
59.5
34/2
60.4
56/3
151/4
61.5
NZPR386b
70.1
231/7
75.2
76/21
81.9
215/13
83.1
148/4
84.0
58/10 191/3
84.5
190/11
85.3

147/16
85.8
195/11
89.0
112/8
91.9
159/14
100.7
7/8 59/6
79/1
255/7
108.7
189/3
112.8
232/2
118.6
98/2
132.0
111/13
133.8
222/2
138.5
143/10
142.3
57/4
144.5
34/4
145.8
92/2
147.1

142/8
154/3
147.4
8/1
148.7
58/5
151.3
75/6
154.1
23/1
111/2
157.1
106/8
161.9
35/22
167.3
109/3
167.6
145/5
175.0
Lg:4
FRPP94a
0.0
221/3
5.1
267/12
11.7
167/1
18.1
145/4

19.7
92/4
149/1
31/4
21.1
58/1
23.0
PR092a
25.0
236/4
27.0
241/3
28.0
53/6
29.9
FRPP94b
31.9
238/1
40.0
41/8
58/2
75/3 150/4
43.8
111/14
49.6
255/6
53.9
189/2
54.6
241/4

58.8
66/7
112/3
62.9
187/5
78.1
169/3
81.7
231/4
82.3
56/7
231/3
86.2
256/1
90.7
152/7
93.0
PPA8
241/9
96.2
8/3 198/5
96.3
159/8
97.7
157/5
99.2
162/4
99.8
181/2
103.5

236/6
105.2
60/2
115.1
63/2
230/12
115.7
158/14
126.0
253/5
127.2
53/4
129.6
35/6
59/9
129.7
105/2
130.8
171/8
131.3
240/10
135.7
189/5
137.2
148/2
144.6
151/6
229/2
144.7
8/22

148.5
182/3
150.4
152/1
150.5
104/11
230/5
151.8
249/2
156.1
30/8 254/3
163.3
142/4
148/6
165.7
97/3
179.3
Lg:5
145/2
0.0
222/6
1.2
69/6
11.0
271/2
14.9
52/8
26.2
222/9
27.5

50/1
31.2
147/1
31.6
233/1
34.2
152/10
35.5
166/1
36.9
61/8
40.0
69/2
60/6
43.2
157/1
44.2
39/1
239/5
46.0
170/2
257/6
17/5 37/1
48.1
92/10
50.2
3/1
52.4
152/6
54.5

267/9
59.4
62/4
62.1
188/1
66.6
240/2
74.5
8/9
80.8
252/4
82.3
215/1
86.0
63/9
88.2
NZPR1078
143/8
149/13
94.6
181/4
95.9
32/4 63/3
97.3
105/8
100.0
67/2
106.6
255/2
109.6

224/5
111.8
107/9
120.5
13/4
139.9
76/4
151.5
Lg:6
UHD linkage map of Pinus pinaster 641
241/11
0.0
77/8
2.7
54/4
13.7
76/14
14.3
188/3
21.1
170/5
22.7
171/1
24.0
52/4
171/2
29.6
169/1
32.2
175/4

34.9
145/7
36.3
182/1 230/7
232/1
39.1
40/3
40.4
198/4
41.7
152/8
43.2
58/7
46.6
76/9
47.3
148/10
49.8
218/2
51.5
4/1 12/6
55.9
252/2
62.5
158/1
68.8
154/2
73.8
76/12
79.8

114/10
82.7
55/2
76/6
83.9
39/7
108/9
ISSR9
138/4
239/6
87.0
188/2 245/7
88.8
58/3
66/1
93.6
253/2
98.3
242/4
100.6
143/13
221/2
234/1
103.0
189/1
104.3
149/6 149/7
105.6
63/6
106.9

151/8
109.3
241/10
110.6
68/4
111.1
30/5
112.6
104/5
117.3
214/6
123.2
Lg:7
257/9
0.0
80/1 153/4
9.7
147/2
220/5
15.2
77/12
17.1
57/10
19.2
73/3
25.5
56/4
59/5
143/3
39/2

28.3
255/4
30.6
76/11
37.8
76/8
39.7
35/20
146/2
41.7
55/4
44.3
34/5
46.9
145/8
50.3
144/2
52.9
75/1
54.8
102/1
56.7
102/4
57.4
106/2
59.7
8/4
39/2
198/12
65.7

90/3
68.4
253/4
68.6
158/10
71.5
212/15
73.8
190/13
74.2
112/7
85.7
7/2
98.5
101/14
99.4
142/12
230/16
101.2
230/17
102.3
155/4
103.0
8/10
104.4
180/4
106.8
190/10
109.0
69/1

117.3
181/6
120.4
147/11
127.0
147/17
130.5
33/1
158/3
146/7
132.2
35/1
140.0
17/4
142.5
Lg:8
198/9
0.0
66/3
4.9
143/17
149/9
6.3
232/4
10.4
147/12
16.4
30/6 173/4
23.0
155/7

25.6
104/1
26.5
147/20
31.8
92/7 147/6
32.9
249/3
33.1
150/8
229/7
35.1
231/6
37.1
146/12
45.7
35/12
47.4
PR092b
52.6
78/2
57.4
190/5
58.0
147/18
63.0
164/1
63.2
33/11
234/5

65.0
154/6
71.9
14/6
72.9
57/6
257/7
79.6
254/5
83.3
4CL
85.5
142/7
158/9
87.3
225/3
91.1
139/3
94.9
143/2
98.9
142/3
236/7
99.3
54/12
104.0
155/1
105.0
159/6
109.3

55/3
110.1
190/4
111.1
61/5
112.9
76/19
115.5
57/3
120.0
185/2
122.8
178/4
124.8
241/6
126.8
254/6
127.7
190/6
131.5
262/1
135.1
53/3
136.9
80/6
140.6
139/6
143/7
146.6
142/1

148.4
10/1 111/5
149.4
143/6
150.1
159/12
228/8
153.4
35/4
160.0
63/4
160.1
33/2
54/16
161.3
253/7
164.2
234/8
166.4
183/3
171.0
141/1
171.9
59/12
173.2
6/4
179.2
90/2
183.4
65/1

191.0
Lg:9
57/11
0.0
154/5
3.7
222/4
10.0
158/6
11.3
92/3
13.8
152/9
18.9
90/1
171/3
25.6
244/5
36.7
159/1
39.1
172/4
44.1
80/8
236/5
48.3
144/1
49.8
59/8
50.5

165/1
54.2
152/16
152/17
216/1
218/3
220/1
57.0
158/11
63.3
156/6
63.7
80/9
69.8
147/14
75.6
8/25
77.3
8/14
194/6
79.0
141/3
80.9
7/4
81.4
105/3
81.9
108/2
82.9
162/3

86.1
4/6 167/5
86.2
41/4
93.6
59/11
225/5
95.2
181/7
97.4
143/4
99.6
169/6
100.6
151/9
111.3
173/6
111.5
182/5
114.6
146/1
117.9
102/3
142/10
122.4
49/2
123.8
228/3
125.8
172/6

127.5
195/9
128.1
261/2
129.5
152/11
130.7
259/3
130.9
58/9
132.0
235/3
133.2
191/2
134.0
65/4
134.5
262/3
135.8
63/1
138.2
147/10
140.1
34/3
141.4
101/12
143.4
60/7 252/1
149.4
30/1

156.5
Lg:10
23/5
0.0
60/5
10.0
150/6
65/2
16.4
103/8
17.9
171/4
19.8
151/10
27.2
32/1
32/2
29.8
222/7
30.0
148/9
32.3
100/1
34.7
66/6
141/2
153/1
35.9
136/1
45.4

266/1
46.4
40/10
146/15
48.5
56/1
52.7
236/3
59.7
100/2
63.3
80/10
65.2
153/2
194/1
83/4 230/8
69.8
188/6
70.8
82/1
120/6
73.1
14/8
105/7
78.4
8/17
79.7
160/3
94.0
59/10

95.9
68/2
100/5
107/2
148/7
97.8
236/2
99.3
242/3
109.3
101/8
110.7
225/1
112.7
66/9
113.8
222/1
168/3
234/6
118.9
208/1
120.2
FRPP91
127.3
68/3
221/6
4/5
71/4
143.9
227/1

144.6
7/5
146.8
63/7
69/8
NZPR472
155/2
150.6
54/17
151.9
171/5
157.1
80/7
166.0
158/2
167.4
180/6
182.8
Lg:11
104/9
0.0
103/2
11.4
7/12
17.0
244/13
18.5
149/10
19.9
35/19

21.2
150/7
23.7
140/2
24.9
7/10
139/8
241/7
26.3
97/4
27.5
17/7
28.2
187/3
31.0
35/21
32.0
83/3
38.2
76/1
39.8
236/1
41.2
140/1
238/3
41.9
66/10
RPS-160
159/3
46.0

53/7
57/8
47.9
138/5
50.9
149/12
143/11
147/19
58.0
234/2
59.1
147/15
66.8
212/8
71.2
253/3
76.5
249/1
82.8
254/1
84.1
239/4
86.5
176/3
86.8
240/8
87.6
145/9
89.9
105/6

91.9
31/6
146/10
92.3
184/4
93.4
240/6
99.2
187/6
105.8
212/4
110.5
NZPR1702b
112.9
AF028073
116.6
241/1
118.1
151/12
118.7
150/5
122.1
188/5
122.7
143/16
125.5
63/5
125.9
59/3
128.9

224/1
134.8
146/13
137.1
158/13
158/16
144.9
89/1
151.6
230/1
151.7
33/12
58/6
152.9
238/2
154.2
250/1
260/1
156.7
190/7
159.4
216/4
163.6
101/13
168.2
209/6
171.4
Lg:12
Figure 1. Integrated map of Pinus pinaster Cross: 0024 × C803. Positions in cM [Kosambi units] are given on the left of the linkage group bars. Marker names and fragment numbers
on the right of the bar. Markers common to both parents are underligned. Most of them represent anchor points. EST and SSR markers are indicated in bold. For details on marker

names and fragment numbers including parental AFLP profiles see />Independently of these findings, the unexpected low de
-
gree of polymorphism of AFLP, SSR and EST markers ob
-
served in our progeny is surprising considering the well
marked differentiation between the original provenances of
the parents [14] and the similar level of genetic diversity en
-
countered in P. pinaster and other Pinus species [9, 20].
Many polymorphic fragments exist between the parents of
our mapping population, which represent different ecotypes
from Landes and Corsica, respectively. However, a large de
-
gree of homozygosity exists, since parent specific fragments
do not segregate. This increased homozygosity is probably
due to a low degree of biodiversity, which exist at the specific
sites (i.e., trees are quite different between sites but very sim
-
ilar within a site).
4.2. Arrangement of DNA markers into linkage maps
The analysis of segregating DNA markers established
twelve independent linkage groups for the P. pinaster geno
-
types 0024 and C803, respectively (i.e., lateral markers were
not statistically linked to any other lateral marker of any other
linkage group). These 12 linkage groups may correspond to the
12 chromosomes of the haploid pine genome (2n = 2x = 24).
Moreover, the presence of common markers made it possible
to identify all homologous chromosomes in each parent. With
several common markers present in the same order on chro

-
mosomes of both parents, it is possible to combine the infor
-
mation of markers from different individuals as described in
[17]. In this way the number of markers available per chro
-
mosome can be increased.
The total length of linkage maps did not differ between the
parents of the mapping population and is in agreement with
other linkage maps obtained in this species. Our P. pinaster
reference map represents one of the maps with the highest
number of markers in forest species.
4.3. Alignment with other Pinus maps
Alignment between different linkage maps can be
achieved, if identical markers have been used in these maps
642
E. Ritter et al.
Table II. Locations of mapped SSR and EST markers in our P. pinaster reference map and in other published Pinus maps.
No Name Type Origin Location in reference map Location in other published maps
1 4CL EST P. taeda Lg 9 P. abies Lg6 (1)
2 AFO28073 EST P. taeda Lg 12 P. pinaster Lg8 (2)
3 ASO1F3 EST P. pinaster Lg 1 P. pinaster Lg4 (2)
P. abies Lg4 (1)
4 E28072 EST P. taeda Lg 2 P. pinaster Lg5 (2)
5 E87909 EST P. taeda Lg 2 P. pinaster Lg8 (2)
6 PPA8 EST P. pinaster Lg 5 P. pinaster Lg10 (2)
7 RSO1D5 EST P. pinaster Lg 1 P. pinaster Lg7 (2)
8 FRPP91 SSR P.pinaster Lg 11 P. pinaster Lg9 (3)
9 FRPP94a/b SSR P.pinaster Lg 5/Lg 5 P. pinaster Lg5 (3)
10 ISSR9 ISSR Lg 7 –

11 ITPH4516a/b SSR P.halepensis Lg 3/Lg 4 P. pinaster Lg3 (3)
12 NZPR0413 SSR P. radiata Lg 1 P. pinaster Lg4 (2)
P. radiata Lg4 (4)
13 NZPR1702a/b SSR P. radiata Lg 12/Lg 3 P. pinaster
Lg8/Lg11(2)
P. radiata Lg10 (4)
14 NZPR1078 SSR P. radiata Lg 6 P. pinaster Lg2 (2)
P. radiata Lg2 (4)
15 NZPR386a/b SSR P. radiata Lg 1/Lg 4 P. radiata Lg2 (4)
16 NZPR472 SSR P. radiata Lg 11 P. pinaster Lg1 (2)
P. radiata Lg1 (4)
17 NZPR006 SSR P. radiata Lg 2 P. radiata Lg5 (4)
18 NZPR823 SSR P. radiata Lg 1 P. pinaster Lg5 (2)
P. radiata Lg5 (4)
19 PR092a/b SSR P. radiata Lg 5/ Lg 9 P. radiata Lg3 (5)
20 RPS-160 SSR P.strobus Lg 12 –
21 RTPEST11 SSR P. taeda Lg 2 P. pinaster Lg5(2)
(1) />(2) and Chaumeil P., Développement de marqueurs hypervariables (microsatellites) chez le pin maritime (Pinus pinaster Ait.) et ap-
plications en génétique, 2001, DEA Biologie Forestière, Université de Nancy (several markers are only cited in the DEA but will be published on this web site).
(3) Mariette et al., 2001.
(4) P. radiata map aligned with P. taeda reference population [1]; Phil Wilcox and Craig Echt, personal communication.
(5) Devey et al., 1999.
and if comigrating bands map to identical positions. SSR and
EST markers are mainly codominant, highly polymorphic
and represent powerful tools for different genetic analyses.
Since they seem to be conserved among species and to a cer
-
tain degree also within families, they have been used for map
-
ping and alignment of linkage maps in several forest species

[1, 3, 8, 13]. We have evaluated numerous SSR and EST
markers in our study and several could be used to associate
linkage groups in different parents (table II). However, the
low level of polymorphism of EST and SSR markers ob
-
served in our reference population has led to association of
linkage groups between maps. Since this goal is crucial for
the usefulness of our map, additional SSR/EST primers will
be evaluated in order to achieve a complete alignment.
Alignments between maps were achieved also with
comigrating AFLP markers in potato, involving different
Solanum species [18]. However, it will be necessary to prove
if this is also possible for pine species by comparing parental
profiles and map locations of comigrating fragments from
AFLP primer combinations which have been used in differ
-
ent mapping populations.
Acknowledgements: This study was supported by EC DGXII
under the contract QLK5-CT1999-01159 of the 5th Framework
Programme.
REFERENCES
[1] Brown G.R., Kadel E.E. III, Bassoni D.L., Kiehne K.L., Temesgen B.,
van Buijtenen J.P., Sewell M.M., Marshall K.A., Neale D.B., Anchored refe-
rence loci in loblolly pine (Pinus taeda L.) for integrating pine genomics, Ge-
netics 159 (2001) 799–809.
[2] Cato S.A., Corbett G.E., Richardson T.E., Evaluation of AFLP for ge
-
netic mapping in Pinus radiata D. Don., Mol. Breed. 5 (1999) 275–281.
[3] Cato S.A., Gardner R.C., Kent J., Richardson T.E., A rapid PCR-based
method for genetically mapping ESTs, Theor. Appl. Genet. 102 (2001)

396–306.
[4] Costa P., Pot D., Dubos C., Frigerio J M., Pionneau C., Bodénès C.,
Bertocchi E., Cervera M., Remington D.L., Plomion C., A genetic map of ma
-
ritime pine based on AFLP, RAPD and protein markers, Theor. Appl. Genet.
100 (2000) 39–48.
[5] Chagné D., Lalanne C., Madur D., Kumar S., Frigério J M., Krier C.,
Decroocq S., Savouré A., Bou-Dagher-Kharrat M., Bertocchi E., Brach J.,
Plomion C., A high-density genetic map of maritime pine based on AFLPs,
Ann. For. Sci. 59 (2002) 627–636.
[6] Devey M.E., Fiddler T.A., Liu B H., Knapp S.J., Neale B.D., An
RFLP linkage map for loblolly pine based on a three-generation outbred pe
-
digree, Theor. Appl. Genet. 88 (1994) 273–278.
[7] Devey M.E., Bell J.C., Smith D.N., Neale D.B., Moran G.F., A genetic
map for Pinus radiata based on RFLP, RAPD and microsatellite markers,
Theor. Appl. Genet. 92 (1996) 673–679.
[8] Devey M.E., Sewell M.M., Uren T.L., Neale D.B., Comparative map
-
ping in loblolly and radiata pine using RFLP and microsatellite markers,
Theor. Appl. Genet. 99 (1999) 656–662.
[9] Echt C.S., May-Marquardt P., Hseih M., Zahorchak R., Characteriza
-
tion of microsatellite markers in eastern white pine, Genome 39 (1996)
1102–1108.
[10] Echt C.S., Vendramin G.G., Nelson C.D., Marquardt P., Microsatel
-
lite DNA as shared genetic markers among conifer species, Can J. For. Res. 29
(1999) 365–371.
[11] Fisher P.J., Richardson T.E., Gardner R.C., Characteristics of single–

and multi-copy microsatellites from Pinus radiata, Theor. Appl. Genet. 96
(1998) 969–979.
[12] Harry D.E., Temesgen B., Neale D.B., Codominant PCR-based mar
-
kers for Pinus taeda developed from mapped cDNA clones, Theor. Appl. Ge
-
net. 97 (1998) 327–336.
[13] Mariette S., Chagné D., Decroocq S., Vendramin G.G., Lalanne C.,
Madur D., Plomion C., Microsatellite markers for Pinus pinaster Ait., Ann.
For. Sci. 58 (2001) 203–206.
[14] Mariette S., Chagné D., Lezier C., Pastuszka P., Raffin A., Plomion
C., Kremer A., Genetic diversity within and among Pinus pinaster popula
-
tions: comparison between AFLP and microsatellite markers, Heredity (2002)
in press.
[15] Plomion C., Costa P., Bahrman N., Genetic analysis of needle pro
-
teins in Maritime pine 1. Mapping dominant and codominant protein markers
assayed on diploid tissue, in a haploid-based genetic map, Silvae Genet. 46
(1997) 161–165.
[16] Ritter E., Gebhardt C., Salamini F., Estimation of recombination fre-
quencies and construction of RFLP linkage maps in plants from crosses bet-
ween heterozygous parents, Genetics 224 (1990) 645–654.
[17] Ritter E., Salamini F., The calculation of recombination frequencies
in crosses of allogamous plant species with application to linkage mapping,
Genet. Res. 67 (1996) 55–65.
[18] Rouppe van der Voort J.N.A.M., van Zandvoort P., van Eck H.J., Fol-
kertsma R.T., Hutten R.C.B., Draaistra J., Gommers F.J., Jacobsen E., Helder
J., Bakker J., Use of allele specificity of comigrating AFLP markers to align
genetic maps from different potato genotypes, Mol. Gen. Genet. 255 (1997)

438–447.
[19] Sewell M.M., Sherman B.K., Neale D.B., A consensus map for lo
-
blolly pine (Pinus taeda L.), Genetics 152 (1999) 321–330.
[20] Smith D.N., Devey M.E., Occurrence and inheritance of microsatelli
-
tes in Pinus radiata, Genome 37 (1994) 977–983.
[21] Soranzo N., Provan J., Powell W., Characterization of microsatellite
loci in Pinus sylvestris L, Mol. Ecol. 7 (1998) 1260–1261.
[22] Travis S.E., Ritland K., Whitman T.G., Keim P., A genetic linkage
map of Pinyon pine (Pinus edulis) based on amplified fragment length poly
-
morphisms, Theor. Appl. Genet. 97 (1998) 871–880.
[23] Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Hornes M.,
Frijters A., Pot J., Peleman J., Kuiper M., Zabeau M., AFLP: a new technique
for DNA fingerprinting, Nucleic Acids Res. 23 (1995) 4407–4414.
[24] Wakamiya I., Newton R.J., Johnston J.S., Price H.J., Genome size and
environmental factors in the genus Pinus, Am. J. Bot. 80 (1993) 1235–1241.
UHD linkage map of Pinus pinaster 643