Genetic mapping and identification of QTL for
earliness in the globe artichoke/cultivated
cardoon complex
Portis et al.
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252 (23 May 2012)
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
RESEARCH ARTICLE
Open Access
Genetic mapping and identification of QTL for
earliness in the globe artichoke/cultivated
cardoon complex
Ezio Portis1, Davide Scaglione1, Alberto Acquadro1, Giovanni Mauromicale2, Rosario Mauro2, Steven J Knapp3,4
and Sergio Lanteri1*
Abstract
Background: The Asteraceae species Cynara cardunculus (2n = 2x = 34) includes the two fully cross-compatible
domesticated taxa globe artichoke (var. scolymus L.) and cultivated cardoon (var. altilis DC). As both are outpollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way
pseudo-test cross approach.
Results: A set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated
into the reference C. cardunculus genetic maps, based on segregation among the F1 progeny of a cross between a
globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups,
corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared
loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were
used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions
were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the
overall phenotypic variance.
Conclusion: The newly developed consensus as well as the parental genetic maps can accelerate the process of
tagging and eventually isolating the genes underlying earliness in both the domesticated C. cardunculus forms. The
largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the
phenotypic variance, thus representing a good candidate for marker assisted selection.
Keywords: Cynara cardunculus, Linkage map, Microsatellite, QTL, Earliness
Background
The Asteraceae (ex Compositae) species Cynara cardunculus L. comprises three taxa, namely the two domesticated form globe artichoke (var. scolymus) and cultivated
cardoon (var. altilis), along with their common ancestor
the wild cardoon (var. sylvestris). While the globe artichoke was selected for its large immature inflorescences,
the cardoon was selected for its fleshy leaves and stalks.
The three taxa remain fully cross-compatible with one another, and their F1 hybrids are fertile. The species complex
has a highly heterozygous diploid genome (2n = 2x = 34),
* Correspondence: sergio.lanteri@unito.it
1
Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci
44, I-10095, Grugliasco, Torino, Italy
Full list of author information is available at the end of the article
maintained by its cross-pollinating habit [1]. The domesticated forms produce a variety of nutraceuticals and
pharmaceutically active compounds like inulin, mono- and
di-caffeoylquinic acids [2–6] and sesquiterpene lactones, which are responsible for its characteristic bitterness [7–9]. Globe artichoke contributes significantly to
the Mediterranean agricultural economy in the form of an
annual production of ~750Mt worth over US$500 M annually. It is also cultivated in the Americas, North Africa and
China (http://faostat.fao.org).
Most of the Mediterranean globe artichoke germplasm
is vegetatively propagated, and a number of varietal
groups have been defined on the basis of the appearance
of the inflorescence and harvesting time of the head
(capitula) Flowering can be induced between autumn
and spring in early flowering types by watering dormant
© 2012 Portis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 2 of 15
underground shoots, whereas late flowering types flower
only during spring and early summer. A common breeding target for both vegetatively and seed-propagated varieties is the promotion of earliness since inflorescences
produced in the early part of the year command a higher
price than those produced in the summer. Unlike globe
artichoke, the cultivated cardoon is exclusively seedpropagated, and is generally handled as an annual crop.
Of late it has been promoted as a source of lignocellulosic
biomass [10–12] and the evidence suggests that it
should be possible to derive types able to flower
early, to produce stems with a high lignin content
and to generate biomass with a good level of energy
efficiency [13,14]. Earliness is therefore an important
trait in both domesticated forms.
The first generation of C. cardunculus marker-based
genetic maps [15–17] have resulted in a cultivated cardoon map composed of nearly 200 loci (17 major linkage
groups, LGs) spanning just over 10 M, and a globe artichoke one featuring 326 loci (20 major LGs) spanning
about 15 M. The two maps have since been integrated
on the basis of common loci with the inclusion of a
number of genes involved in the synthesis of caffeoylquinic acids [18,19]. More recently crosses between globe
artichoke and its ancestor wild cardoon have generated
highly segregating F1 populations exploitable as ornamentals [20] as well as for mapping studies [21].
The multi-allelism of many microsatellite (SSR) loci
makes them particularly well suited as bridging markers
to link independent maps. The design of SSR assays
requires DNA sequence, which in globe artichoke exists
at present largely in the form of expressed sequence tag
(EST) sequence (http://compgenomics.ucdavis.edu/).
Over 4,000 potential EST-SSR loci have been identified
from this sequence resource, and the experimental testing of a sample of 300 loci showed that more than one
half were informative between the parents of our two
mapping populations [22]. In the present report, we describe the integration into the globe artichoke and
cultivated cardoon maps of a large number of these
EST-SSR loci, and show that they can be used as bridging markers to merge the two maps. The resulting dense
maps was then used to identify a number of quantitative
trait loci (QTL) underlying early head production in C.
cardunculus.
Results and discussion
Genotyping
Six of the 178 informative Cynara Expressed Microsatellite (CyEM) markers, identified by Scaglione et al. [22],
were excluded from the analysis on the basis of excessive
missing values. Of the remaining 172, 54 segregated in
both parents (46 as 1:1:1:1, eight as 1:2:1) and 118 in just
one of the parents (85 in globe artichoke ‘Romanesco
C3’, 33 in cultivated cardoon ‘Altilis 41’). On the whole
228 microsatellite markers were available for map construction (Table 1). Eleven of these loci suffered from
mild segregation distortion (χ2α=0.05 < χ2 ≤ χ2α=0.01) but just
one (CyEM_58) from severe distortion (χ2 > χ2α=0.01).
Since CyEM_58 was excluded from the mapping analysis, this left a total of 227 SSR loci. Co-dominant markers appear to be less affected by segregation distortion
than dominant ones [23,24], and this certainly was
the case for C. cardunculus, where ~13% of AFLP
and S-SAP loci [17], but only ~5% of SSRs and SNPs
are distorted. Segregation distortion has been associated
with statistical bias and/or with errors in genotyping, but
they can also stem from a number of biological phenomena affecting meiosis, fertilization and embryogenesis [25]
as well as the presence of null alleles. Null alleles at SSR
loci are not uncommon, as they can arise where either
one (or both) of the primers fail to anneal because of sequence mismatch or the deletion of the whole locus, and
cause an higher apparent number of homozygotes because
they can no longer be distinguished from the heterozygotes [26]. In this situation, the options are either to disregard the affected loci, to score segregation in the same
way as for a dominant marker [27], to attempt to redesign
Table 1 Polymorphism and segregation patterns for the SSR loci used for map construction
SR
Number
prefix of loci
Segregation type < Romanesco C3 x Altilis 41>
Marker type
References
<ab x aa><ab x cc> <aa x ab><aa x bc> <ab x ab> <ab x ac > <ab x cd>
CDAT
1
Genic
1
-
-
-
Acquadro et al. [63]
CLIB
3
Inter-genic
2
-
-
1
Acquadro et al. [63]
CMAL
5
Inter-genic
4
1
-
-
Acquadro et al. [64]
CMAFLP
2
Inter-genic
1
-
-
1
Acquadro et al. [65]
CsPal
1
Genic
1
-
-
-
Sonnante et al. [66]
CsLib
1
Inter-genic
1
-
-
-
Sonnante et al. [66]
CELMS
43
Genic and inter-genic1
19
4
1
19
Acquadro et al. [16]
CyEM
172
85
33
8
46
Scaglione et al. [22]
Total
228
114
38
9
67
1
Genic
27 out of the 61 CELMS microsatellites are reported to be genic SSR as they contain at least one ORF.
Portis et al. BMC Research Notes 2012, 5:252
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Page 3 of 15
p13/m47-240
e39/t80-330
e36/m59-164
e34/m50-404
15,1
CELMS-12
18,2
19,8
21,0
e35/t89-300
e35/t89-176
e35/t81-540
24,7
CyEM_136
23,9
e37/m50-290
28,6
e38/t82-176
27,8
29,5
29,9
e32/t80-178
rCyEM_188
CyEM_52
34,4
e38/t82-490
37,5
e33/t89-232
33,0
p13/m50-150
36,4
e39/t80-480
41,0
rCyEM_25
40,4
e32/t81-250
44,8
e39/m50-188
45,2
e32/t81-136
49,9
CyEM_32
53,7
rCyEM_279
rCyEM_9
e38/t82-212
74,2
e42/m50-204
78,0
rCyEM_66
0,0
11,4
19,4
21,5
21,7
27,5
C3_8
0,0
0,9
rCyEM_195
rCyEM_121
6,3
8,2
9,1
9,9
rCyEM_220
CyEM_236
CyEM_2
rCyEM_173
C3_5
rCyEM_63
e36/m48-164
rCyEM_13
CyEM_36
e35/m47-140
29,9
32,0
rCLIB-12
p45/m47-610
e36/m47-580
34,6
e35/m62-348
38,7
40,3
cyre5/t89-255
e38/t82-380
44,4
45,5
48,8
49,4
50,5
50,8
51,7
53,0
54,8
56,1
58,0
60,3
62,4
66,7
67,5
71,0
73,3
74,4
77,6
rCyEM_207
p13/m62-210
p45/m59-190
e33/t80-240
rCELMS-41
e33/t89-340
e35/t81-68
rCELMS-48
e35/t80-280
e38/t80-504
p13/m59-195
e37/m61-316
e35/m62-140
e35/m47-580
e35/t89-162
e38/m47-450
e35/m50-314**
p45/m61-192
CyEM_175
85,5
e38/m47-400
58,3
LOD 5
rCELMS-33
65,4
66,8
LOD 5
57,6
20,0
e42/m50 -298
22,9
25,4
CELMS -37
p12/m59 -180
28,6
30,8
CELMS -02
e36/m59 -306**
35,9
38,7
40,4
42,3
43,7
44,4
45,2
46,6
47,5
48,7
50,4
54,5
55,4
58,3
60,3
e32/t81 -340
66,7
67,7
e35/m48 -186
cyre5/t87 -320
72,8
p45/m47 -288
81,6
p13/m60 -100
rCELMS -21
p12/m47 -105
e33/t80 -132
e35/t81 -298
p12/m62 -100
e38/t82 -680
e35/t89 -142
e35/m48 -274
e34/m50 -340
e38/m47 -182
e36/m59 -500
e34/m50 -298
C3_1
0,0
3,8
4,9
6,7
8,6
13,3
14,3
15,8
17,2
18,6
19,3
19,9
21,6
25,5
28,9
31,3
33,8
38,6
40,2
41,3
43,3
46,7
48,5
50,3
52,3
55,3
58,2
61,3
63,8
64,9
65,3
70,3
72,0
73,7
74,7
76,8
82,7
83,4
84,1
85,7
88,6
89,9
91,9
93,8
94,9
96,5
97,2
98,0
99,1
99,7
100,1
101,2
102,7
102,9
103,1
103,3
104,0
105,1
106,1
107,2
107,8
109,5
110,4
111,9
113,8
114,6
116,6
119,5
121,6
124,3
128,5
130,5
140,9
rCyEM_91
e35/t81-190
e33/t89-620
CyEM_1
e39/t80-148
Acyltransf_4-snp
rCyEM_57
CELMS-05
CyEM_60
rCDAT-01
rCyEM_157
rCyEM_261
p12/m50-230
rCyEM_54
e32/t82-224
e32/t80-82
e32/t82-226
rC-PAL03
p13/m50-216
p12/m47-320
rCyEM_166
p13/m59-120
p45/m50-420
rCELMS-08
rCyEM_130
e39/m50-364
CyEM_259
p13/m60-142
CyEM_150
e35/t81-104
CyEM_296
p45/m59-232
p45/m59-460
e35/t80-364
p12/m50-350*
e37/m49-104
e32/t82-166
CyEM_234
CyEM_254
e38/m50-340*
rCyEM_147
p12/m62-268
CELMS-16
e32/t81-610
e35/m62-440
CyEM_124
rCyEM_176
e32/t81-98
e38/t82-230
e38/t80-630
rCyEM_104
p13/m50-176
CELMS-58
e35/t81-348
CELMS-26
rCyEM_84
e33/t89-430
rCELMS-40
rCyEM_223
e38/t80-190
CELMS-52
e32/t82-272
e35/t89-296
e32/t82-86
e35/m50-354*
CELMS-09
e34/m50-216
e36/m47-260
e33/t89-174
e38/t80-550
cyre5/e33-350
e39/t80-178
e36/m59-112
C3_3
0,0
e38/t82-214
5,3
rCyEM_289
25,8
27,4
CyEM_260
e38/t82-600
30,8
31,8
p12/m62-340
e37/m61-136
41,6
43,9
45,6
e38/m50-234
e39/t80-560
e35/m50-282
49,4
e36/m59-130
53,9
56,3
57,6
58,0
58,8
60,2
63,0
e38/t80-252
rCELMS-45
CELMS-01
e33/t89-280
rCyEM_266
rCyEM_29
e32/t80-474
67,5
69,3
71,0
72,9
75,4
e35/t81-220
CyEM_199
rCyEM_209
e38/m47-280
e33/t80-252
81,5
e36/m48-600
86,0
87,1
88,4
p13/m60-86
p13/m60-420
rCyEM_210
93,9
101,5
103,3
105,6
114,3
rHCTsnp97
p12/m61-290
p12/m60-235
CELMS-10
p13/m61-272
99,8
rCyEM_202
104,0
rCyEM_7
107,5
CyEM_183
131,0
rCyEM_120
134,4
p13/m47-175
e38/m50-206
p13/m59-320
e38/m47-350
e38/t80-212
rCyEM_294
e35/m50-280
e33/t89-338**
CyEM_128
rCyEM_56
e32/t80-190
Acyltransf_2-snp
p45/m60-690
CyEM_77
p12/m60-395**
e38/m50-230
e35/m50-220
e32/t81-460
rCELMS-15
CyEM_190
C4H-snp
e32/t82-140
CELMS-42
p12/m62-106
CLIB-02
rCyEM_231
e38/t80-450
p12/m47-196
e33/t80-224
CyEM_250
p13/m60-110
CyEM_282
e38/t80-390
e32/t82-92
rCELMS-03
rCyEM_221
rCyEM_86
p45/m59-116
e42/m50-590
e42/m50-176
e32/t81-380
p12/m60-116*
e38/m50-108
e34/m49-322
CELMS-13
e36/m48-82
rCyEM_94
94,9
120,0
e38/m47-530
8,4
9,6
12,9
16,7
19,2
24,5
25,3
26,2
27,9
29,2
29,7
30,0
31,2
32,5
34,8
35,8
37,4
e36/m47-112
p12/m62-120
e42/m50-144*
e38/t82-288
p45/m50-390
e38/t80-430
e32/t82-182
p45/m60-76*
e32/t80-170
p13/m50-98
CyEM_15
e32/t80-260
CyEM_155
e32/t81-372
e33/t89-530
e35/t80-128*
CyEM_189
7,4
e36/m59-334**
43,8
44,8
e38/m59-186
e38/m59-178
48,7
49,5
rCyEM_280
CyEM_135
54,2
57,7
58,6
59,2
e33/t89-144
rCMAL-21
CyEM_106
rCyEM_53
67,9
68,8
rCYEM_226
rCyEM_181
77,0
78,5
CyEM_243
rCyEM_169
rCyEM_145
rCyEM_288
CyEM_73**
rCyEM_8
rCyEM_291
p45/m60-200
CyEM_43
80,7
82,2
84,4
85,5
87,6
89,5
95,1
CyEM_178
97,8
e32/t81-400
100,7
e32/t80-410
110,1
e32/t82-258
13,6
CyEM_80
19,2
e35/m62-220
C3_6
0,0
13,9
e32/t80-282
20,1
p45/m60-64
e35/m62-432
26,1
e39/m50-270
33,2
e32/t82-206
43,5
49,0
p12/m50-160
55,2
e35/t89-312
61,3
63,2
p12/m60-125
rCyEM_214
73,0
rCMAFLP-11
76,2
rCyEM_47*
81,4
CyEM_112
86,5
p12/m47-670
92,2
CyEM_55
29,7
e35/m50-420
34,2
e38/t80-242
41,9
e38/m50-214
9,8
e35/t89-284
15,7
e36/m59-322
5,5
C3H-snp
CyEM_144
CyEM_248
29,2
CELMS-39
34,5
p45/m47-162
e32/t82-160
62,1
92,4
p12/m62-166
rCyEM_45
e35/m47-228
10,9
CyEM_225
13,8
p45/m60-428*
14,0
rCyEM_19**
19,0
e33/t89-234
23,3
rCyEM_97
25,8
p13/m47-542
28,9
31,4
p13/m47-550
35,3
rCyEM_244
38,7
40,4
CyEM_293
rCyEM_300
47,7
49,5
e38/m59-450**
e33/t80-232
C3_4b
0,0
e33/t89-154
6,4
e38/m59-214
rCyEM_163
rCyEM_72
rCs-LIB-14
11,3
29,6
p13/m47-188
33,2
rCELMS-36
37,5
39,3
42,1
43,8
46,1
48,7
50,8
52,3
53,9
54,5
55,5
56,8
59,3
61,5
64,4
66,8
68,9
70,4
e32/t80-162
e33/t80-504*
rCMAL-24**
e42/m50-242**
rCyEM_107
e35/t89-310
rCyEM_138
e32/t81-570
e35/t89-292
CELMS-17
rCELMS-24
rCyEM_146
HQT-snp359
e36/m48-620
e38/t80-496
p13/m61-340
rCyEM_271
rCELMS-44
77,9
CyEM_35
80,6
rCyEM_20
83,9
rCyEM_232
p12/m50-220
e38/m47-114
p13/m59-164
e33/t80-280
4,5
10,5
8,3
76,2
C3_17
0,0
22,4
e35/m48-222
27,6
e37/m50-172
104,2
e35/m48-158
0,0
2,5
p13/m62-148
C3_12
0,0
e32/t82-420
5,2
7,1
rCELMS-31
p12/m62-245
13,5
15,9
18,2
e39/t80-190
20,9
22,8
24,8
26,7
28,9
30,2
32,8
35,0
rCELMS-23
e34/m49-178
e35/t89-64
e35/t81-272
e38/t82-696
e35/t81-560
e38/t82-662
e35/m49-320
37,9
38,9
41,2
43,8
CyEM_218
e35/t89-224
e39/m50-690
e42/m50-162
47,2
e35/m50-302
e32/t82-254
e34/m49-128
cyre5/e35-70
rCyEM_141
13,4
CyEM_277
18,3
e32/t82-294
23,0
e35/m50-230
31,1
p13/m47-560
p13/m47-330
23,5
24,2
25,1
rCyEM_158
C3_4a
0,0
C3_9
p12/m61 -140
0,0
e35/m49-192
C3_15
0,0
p13/m50-520
0,0
39,3
e35/m49-324
46,7
e35/m49-164
0,0
e37/m50-340
6,6
6,7
rCyEM_233
rCyEM_113
10,8
rCyEM_37
13,4
p45/m47-335
17,3
rCyEM_193
21,0
CELMS-04
25,8
rCyEM_75
30,9
rCyEM_126
34,5
CyEM_156
37,3
rCLIB-04
40,7
rCELMS-20
52,5
e39/t80-90
e36/m48-150
C3_16
C3_11
rCELMS -19
p12/m47-498
C3_7
p45/m59-172
e37/m61-510
C3_19
Minor group
C3_13+18
0,0
0,0
C3_20
90,9
C3_2
0,0
2,8
8,6
9,1
11,3
15,2
16,6
21,0
21,5
22,5
24,7
25,8
27,7
28,6
30,8
32,3
34,2
34,7
36,0
36,2
38,3
39,7
40,2
40,3
40,9
42,1
42,6
43,0
43,1
43,6
44,1
44,7
45,6
46,3
47,3
47,8
48,2
51,7
54,9
58,0
58,5
59,2
63,5
65,3
67,5
82,9
p13/m61-192
130,0
The globe artichoke ‘Romanesco C3’ map (LOD 6.0)
consisted of 473 loci falling into 20 LGs, each containing
at least eight loci (Figure 1). The number of mapped
SSRs has now risen from 46 to 185. The largest LG contained 73 loci, and the range in genetic length of the individual LGs was 34.5-140.9 cM. CyEM loci (139
markers) were mapped to all the major LGs, and their
inclusion allowed the integration of six AFLP loci which
previously had remained unlinked [17]. Two LGs (C3_13
and C3_18) which were previously separated have now
been merged, while LG C3_4 has been split into C3_4a
and C3_4b as a consequence of more stringent LOD applied (Figure 1). LG C3_17 has increased in genetic
0,0
2,3
rCyEM_172
cyre5/t87-230
7,8
e33/t89-166
11,1
14,1
10,0
CyEM_48
13,4
rCyEM_152
rCELMS-32
18,9
CyEM_286
e35/t80-660
21,5
23,7
rCyEM_185
e36/m47-248
32,2
32,9
34,7
37,0
rCyEM_24
CyEM_211
p13/m50-140
CyEM_237
18,3
rCyEM_111
21,2
23,2
24,9
26,4
29,4
30,7
rCyEM_246
e32/t81-188
e35/t80-98
e35/t81-154
e38/m59-130
p13/m60-148
34,1
36,4
p45/m61-102
p45/m61-248
38,9
e35/t81-278
42,0
43,9
e35/m50-254
CyEM_93
42,5
44,1
45,4
47,0
50,3
51,8
CyEM_240
rCMAL-110
CyEM_117
p45/m59-164
rCyEM_42
rCyEM_127
48,0
50,2
p45/m50-220
e35/t89-198
58,1
p12/m62-280
55,2
e37/m61-262
63,2
e33/t80-322
14,1
e39/t80-406
19,0
21,2
21,9
e38/t80-250
CyEM_34
rCyEM_123
29,8
CyEM_10
CyEM_64
32,3
36,1
p13/m50-430
42,2
rCyEM_229
49,3
50,4
51,6
CyEM_108
e33/t80-174
CELMS-60
61,0
e32/t81-122
67,6
69,5
p13/m62-164
rCyEM_54b
72,3
74,0
CyEM_200
e38/t80-340
79,4
81,4
rCyEM_70*
CyEM_231*
rCyEM_174
e37/m49-278
50,3
52,1
e39/t80-206
cyre5/m49-352
55,3
57,7
58,1
e35/t81-680
e36/m48-640
p12/m61-530
LOD 5
11,0
18,1
19,5
C3_14
0,0
Globe artichoke map
LOD 5
e42/m50-520
LOD 5
C3_10
0,0
before [17] and is thought to be a consequence of the
sustained vegetative propagation used in globe artichoke, in contrast to the seed propagation applied to
the cultivated cardoon, which led to a certain degree
of purifying selection aimed at stabilizing production.
LOD 5
the primers [28,29], or to adjust allele frequencies on the
basis of a global estimate of the frequency of null alleles.
As recently described by Lanteri et al. [20] the null alleles
segregating in a Mendelian fashion were identified, thus
limiting the segregation distortion in our populations. As
noted previously [15,17], although the inclusion of loci
distorted at the 1% level and above increases the frequency of type I errors, it does help to maintain marker
density throughout the map.
The updated ‘Romanesco C3’ map was built from 574
loci (359 AFLPs, 19 S-SAPs, 189 SSRs and seven SNPs),
and the ‘Altilis 41’ one from 373 loci (246 AFLPs,
8 S-SAPs, 114 SSRs and five SNPs); of these, 78 (76
SSRs and two SNPs) were in common between the
two parental genotypes. The CyEM SSRs were less informative in the cultivated cardoon than in the globe
artichoke. Of the 228 assayed SSR loci 189 (83%) segregated in ‘Romanesco C3’, but only 114 (50%) in
‘Altilis 41’ (Table 1). The difference in level of heterozygosity between these parents has been remarked on
76,1
p12/m47-283
82,3
p12/m47-305
Figure 1 Genetic map of globe artichoke ‘Romanesco C3’. Marker names are shown to the right of each LG, with map distances (in cM) to
the left. One LG containing <4 loci is labelled as ‘minor group’. Loci showing significant levels of segregation distortion are identified by asterisks
(0.1 > *P ≥ 0.05; 0.05 > **P ≥ 0.01). Segments shaded in red indicate where a pair of LGs has merged as a result of reducing the stringency to
LOD 5.
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
length by 36 cM (86%), while that of LG C3_3 and C3_8
has increased by ~30% and ~20%, respectively. The map
spanned 1543.8 cM, with a mean inter-marker distance
of 3.40 cM, corresponding to a 3.8% increase in length
over the earlier map [17], but in a ~28% decrease in the
mean inter-marker distance. The proportion of intervals
shorter than 7 cM is now 88% (previously 77%), and
only six gaps of >15 cM remain. The SSRs appeared to
be rather quite uniformly dispersed, although some clustering is present in the distal regions of C3_8, C3_2 and
C3_17, and around the putative centromeric region, of
C3_3, C3_15 and C3_20. These chromosomal regions
are typically enriched for SSRs [30–35]. The relatively
low marker saturation present in the distal regions of
C3_3 and C3_14 presumably reflects a localized reduced
level of polymorphism between the mapping parents.
Some segregation distortion was present at five of the
CyEM loci (CyEM_19, _47, _70, _73 and _231; three at
α = 0.05 and two at α = 0.01, Figure 1) which affected a
cluster of loci on both C3_17 and C3_9. In both cases
the distortion was due to an excess of the band detected in
the female parent, thus it is likely to have a biological basis,
rather than being due to either scoring error or chance
[36]. Biological mechanisms causing segregation distortions
have been extensively studied in Drosophila [37], and are
known to occur in many plant species [38–42]. On the
other hand, the other 18 distorted loci were scattered across
the genome, a common feature in the genetic maps of both
plant and animal species [43].
By lowering the LOD threshold from 6.0 to 5.0, three
pairs of LGs were merged: C3_10 with C3_5, C3_14 with
C3_8 and C3_4a with C3_4b, resulting in the formation
of 17 LGs (corresponding to the haploid chromosome
number, Figure 1). It also allowed the inclusion of two
unlinked pairs of loci (one into C3_2 and the other into
C3_12) and the singlet AFLP locus e35/m46-156 (into
C3_7). This generated an increase in the genetic length
of the map of ~60 cM; one doublet still remains
unlinked (Figure 1).
Both the goodness-of-fit of marker placement (mean
χ2 contribution) and nearest neighbour fit (cM) were
evaluated. Compared to the earlier ‘Romanesco C3’ map
[17], the average mean χ2 contribution of markers across
the LGs has been significantly reduced from 5.38 to 4.42
(t test at α = 0.005), highlighting the improvement in robustness. The variation in this parameter for each LG is
illustrated in Figure 2, which confirms that LGs C3_1,
C3_2, C3_5, C3_8, C3_10, C3_17 and C3_20 have all
shown an improved goodness-of-fit. C3_12 remained
largely composed of AFLP loci (only two CyEM loci
were integrated) and thus its robustness was hardly
improved. The mean nearest neighbour fit of the CyEM
loci (24.3 ± 3.7 cM) was markedly lower (t test at
α = 0.005) than that of the AFLP loci (51.0 ± 4.6 cM),
Page 4 of 15
confirming the desirability of including co-dominant
markers to obtain reliable marker placement.
Cultivated cardoon map
The genetic map of the cultivated cardoon ‘Altilis 41’
parent (LOD 6.0) was constructed from 373 segregating
loci (82 CyEM loci), of which 273 were ordered into 21
major LGs, whose length ranged from 27.1 to 125.2 cM,
with the largest LG consisting of 29 loci. The result of
integrating the CyEM loci was an increase in the number of major LGs from 17 to 21. This involved the recognition of four new LGs (Alt_18 to _21), the splitting
of Alt_1 into two (Alt_1a and Alt_1b) and the merging
of Alt_16 and Alt_1b (Figure 3). The updated ‘Altilis 41’
map included 107 SSR loci distributed across all but one
(Alt_13) of the major LGs, with a total genetic length of
1485.7 cM and a mean inter-marker distance of
5.44 cM. This represents a marked increase in both
length (+42%) and number of loci (+50%), together with
a minor decrease in the mean inter-marker distance
(−5%). The proportion of intervals smaller than 10 cM
(about 80%) was not significantly reduced. Some of the
LGs recorded large increases in their genetic length –
for example, that of Alt_17 by 64.7 cM, Alt_14 by
58.9 cM and Alt_18 by 57.8 cM. The only LG which
recorded a reduction in length was Alt_5. There was
some clustering of CyEM loci in the distal region of
Alt_2 and around the putative centromeric region of
Alt_1b and Alt_15. Three CyEM loci (CyEM_73, _3 and
_231; Figure 3) showed a degree of segregation distortion (two at α = 0.05 and one at α = 0.01), but none of
these were linked to other distorted loci, similar to the
other nine markers showing segregation distortion. The
addition of the new SSR markers decreased the mean inter-marker distance on Alt_11 by ~60%, and some gaps
in the previous map have been filled; but ten gaps of
>15 cM remained, perhaps reflecting regions of genetic
fixation which have arisen during cultivated cardoon
domestication.
Lowering the LOD threshold to 5.0 led to the merging
of four pairs of LG: Alt_1a with Alt_1b, Alt_11 with
Alt_2, Alt_7 with Alt_10, and Alt_19 with Alt_13. At
this level of stringency the number of LGs corresponded
to the haploid chromosome (Figure 3). The lowered
stringency also allowed the incorporation of two groups
of three linked loci into LGs Alt_20, and Alt_5, and of
one doublet into LG Alt_6. As a result, the overall length
of the map was increased by 133.5 cM; one triplet and
four doublets still remain unlinked (Figure 3).
The C. Cardunculus consensus map
The number of informative shared co-dominant markers
was raised from 19 to 66 (64 SSRs, two SNPs), representing from one to 15 bridging markers per LG. As a
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 5 of 15
Figure 2 Variation in the mean goodness-of-fit of markers for each ‘Romanesco C3’ LG. Variation detected by comparing the current
‘Romanesco C3’ map with that published by Portis et al. [17]. LGs C3_13 and C3_18 have been merged.
result, 19 of the ‘Romanesco C3’ LGs were alignable with
20 of the ‘Altilis 41’ ones (Table 2). There was a one to
one correspondence between 18 LG pairs, but C3_1
e34/m49-380*
Al t_11
0,0
p13/m62-138
4,1
CyEM_1
Al t_7
e32/t80-76
0,0
Alt_3
0,0
e32/t81-200
Alt_19
e35/m62-280
0,0
Alt_20
p45/m60-420
0,0
Al t_5
aCyEM_197
0,0
e35/m62-238
18,2
24,2
26,5
e32/t80-220
CyEM_136
33,4
p13/m47-335
22,8
aCyEM_264
32,7
e34/m50-196
aCMAFLP-07
9,2
14,1
p45/m50-280
17,7
p45/m47-88
20,8
e35/t81-554
23,9
CELMS-12
33,5
CyEM_52
36,1
p13/m50-690
aCyEM_76
CyEM_32
e33/t80-302
39,1
e34/m50-198
43,7
p45/m61-66
p12/m62-136
68,8
e39/m50-186
LOD 5
65,0
0,0
7,7
12,0
LOD 5
e38/t80-230
Alt1b+16
e37/m61-204**
cyre5/t90-145
p12/m47-315
49,8
e35/m62-252
Alt_2
0,0
e35/t80-358
aCyEM_133
aCyEM_14
aCyEM_30
11,9
CyEM_259
16,8
19,2
20,5
CyEM_150
CyEM_296
aCyEM_12
29,3
p12/m62-150
p12/m62-164
0,0
e32/t82 -308
CyEM_236
CyEM_2
e35/m62 -248
e32/t81-168
p45/m60-258
e35/m48-650*
45,2
47,0
e37/m61-228
e37/m61-240
52,3
e39/t80-124
24,3
e32/t81-82
35,2
CyEM_93
e38/t82-306
60,5
CELMS-01
aCyEM_90
42,0
CyEM_293
55,7
e36/m48-326
16,3
p13/m50-90
20,6
aCELMS-14
23,5
e35/t80-200
34,9
e33/t89-510
43,7
45,2
e39/m50-410*
e39/t80-78
e39/t80-224
CyEM_112
47,8
49,9
54,1
56,7
39,4
e38/t82-78
60,5
72,2
e32/t81-328
75,3
CyEM_199
25,5
CELMS -37
32,0
32,2
32,9
CELMS -02
p45/m47 -250
e38/m59 -102
89,9
0,0
Alt_13
e36/m47-290
75,1
80,2
16,1
16,0
p12/m62-114
24,9
26,7
27,6
e38/t82-406
CyEM_15
CyEM_155
35,0
CyEM_189
38,2
e35/t81-86
41,7
CyEM_135
51,8
CyEM_106
25,8
26,7
28,1
aCyEM_38
aCELMS-59
aCyEM_99
39,2
41,7
42,6
45,3
CyEM_234
CyEM_254
CELMS-16
e34/m49-212
38,3
40,8
42,6
p45/m60 -122
p45/m60 -68
e32/t80 -226
35,2
37,5
e33/t80-200
p12/m50-295
49,9
CyEM_124
46,4
e35/t80 -148
e32/t82-64
49,6
p13/m50 -278
40,9
57,7
CELMS-26
61,5
CELMS-58
56,0
57,2
e35/t89 -322
e35/t89 -212
62,7
p45/m47 -134
e38/t82-540
54,8
e38/m50-600
100,6
83,3
p13/m60-108
89,4
p12/m62-256
36,1
e39/m50-240
48,6
CELMS-17
60,9
p13/m60-230
e37/m49-164
58,0
e35/m48-500
63,7
65,1
e35/t80-540
e32/t82-228
70,9
CyEM_243
77,5
CyEM_73**
87,7
CyEM_43
p12/m50-160a
e38/m47-354
77,3
e35/m62-390
81,1
CyEM_35
0,0
e37/m50-232
11,0
aCyEM_153
e35/m47-590**
e33/t80-272
21,8
24,1
CyEM_286
e34/m49-272
33,5
CyEM_211
38,1
CyEM_237
43,0
44,7
e32/t82-510
CyEM_240
51,0
CyEM_117
3,0
e35/m50-198
Alt_21
0,0
0,0
aCELMS-18
e36/m47-272
0,0
e32/t81-268
3,0
e35/t89-164
0,0
p45/m61-154
3,0
p45/m61-328**
0,0
CELMS-04
5,2
e39/t80-86
p13/m59-105
14,1
e37/m49-196
3,0
Alt_15
Alt_12
Minor groups
e37/m61-194
e38/m59-190
63,9
66,3
p13/m50-365
aCyEM_284
70,8
aCELMS-25
80,2
e32/t82-124
84,7
p13/m62-410
96,1
CyEM_183
9,3
e34/m49-108
9,2
CyEM_34
CyEM_277
17,6
aCELMS-11
21,0
aCyEM_3*
27,1
Myb12-snp
CyEM_156
0,0
p13/m50-124
CyEM_144
CyEM_248
CELMS-39
21,0
p12/m50-95
24,5
p13/m62-230
24,9
27,9
e35/t80-340
39,5
e39/m50-360
40,2
aCyEM_148
27,7
CyEM_10
30,8
CyEM_64
CyEM_218
cyre5/m47-160
8,0
e36/m59-270
14,8
16,8
20,5
22,0
24,3
26,7
27,9
29,3
30,0
30,7
31,1
32,1
33,6
36,2
38,6
40,4
e34/m50-130
e34/m49-90
e36/m47-148
e35/t80-144
e38/m50-274
aCELMS-57
e35/m50-272
e33/t80-154
e32/t82-178
e39/t80-500
e35/t80-440
aCyEM_16
e33/t89-492
p12/m59-228
e35/m62-198
aCyEM_204
23,6
aCyEM_196
39,3
41,0
e38/m47-440
aCyEM_11
46,1
e38/m50-350
57,7
p45/m61-150
e35/m48-108
13,1
20,3
20,9
19,3
0,0
1,5
p45/m62-370
CyEM_48
75,9
77,7
e35/m62-394
0,0
0,0
e35/m49-206
18,8
3,0
Alt_17
Alt_8
e33/t89-180
e38/m47-158*
CELMS-52
p12/m50-105
6,0
e37/m49-336
Alt_18
CELMS-09
e34/m50-212**
CELMS-13
60,0
CyEM_178
e35/m47-686
64,3
66,6
68,1
0,0
100,4
Acyltransf_3-snp
72,2
e35/t89-144
e34/m50-282
CyEM_190
CELMS-42
e35/t81-340
CLIB-02
e38/t80-90
CyEM_250
e32/t82-90
e33/t89-490
CyEM_282
e32/t82-260
e35/t80-238
e38/t82-638
e33/t89-402
aCyEM_122
Alt_6
125,2
0,0
e36/m47-158**
e38/t82-182
e35/m47-332
p13/m59-170
23,9
26,0
28,0
30,7
32,3
33,5
34,1
35,4
36,0
37,0
37,6
39,4
41,2
46,2
49,1
p12/m62-390**
110,3
113,5
44,0
90,4
CyEM_77
17,2
19,0
p13/m62-190
p13/m59-450
29,2
e32/t81-590
Acyltransf_2-snp
55,6
CyEM_175
aCyEM_118
e32/t81-248
28,1
96,6
100,7
CyEM_128
p12/m62-455
93,1
49,3
8,1
aCyEM_227
Alt_4
0,0
5,2
6,9
e36/m59-140
p45/m60-102
e32/t81-352
CELMS-10
CyEM_225
11,8
e32/t81-160
65,1
Alt_9
0,0
p12/m60-118
13,5
e32/t82-164
20,2
e35/m62-144
CyEM_36
e32/t81-258
99,8
26,3
33,4
35,3
79,7
81,0
10,8
11,9
14,9
19,1
76,0
CyEM_260
Alt_10
32,1
67,6
69,0
19,6
9,0
e32/t82-158
10,2
e34/m50-470
12,6
e37/m49-146
58,9
4,1
6,0
8,6
aCyEM_110
44,5
aCyEM_247
p45/m59-402
aCyEM_59
e38/m50-162
55,3
61,9
e32/t82-148
39,2
LOD 5
40,5
44,9
47,0
47,8
8,4
9,8
12,1
LOD 5
CELMS-05
CyEM_60
LOD 5
Acyltransf_4-snp
9,9
12,7
14,7
LOD 5
e32/t82-112
e38/m47-248
CyEM_80
6,1
9,1
Al t_14
0,0
p12/m47-162
44,0
p13/m47-430
54,7
e33/t80-178
56,6
CyEM_108
58,8
e33/t89-190
60,5
CELMS-60
p12/m50-310**
67,4
CyEM_200
67,9
72,4
p13/m62-174
76,8
p13/m62-170
82,1
CyEM_231*
81,0
e38/m50-170
65,2
65,4
aCyEM_69
aCyEM_256
70,7
4CL-snp
87,9
e36/m48-410
54,3
e35/t89-336
58,1
59,2
aCyEM_219
e32/t80-152
63,5
aCELMS-49
LOD 5
Alt_1a
0,0
shared markers with both Alt_11 and Alt_2 (Table 2).
C3_4b remained non-aligned, but did harbour a number
of SSR loci which were informative for the second step
80,2
e39/m50-120
91,7
e39/m50-490
Figure 3 Genetic map of cultivated cardoon ‘Altilis 41’. Marker names are shown to the right of each LG, with map distances (in cM) to the
left. LGs containing <4 loci are labelled as ‘minor groups’. Loci showing significant levels of segregation distortion are identified by asterisks
(0.1 > *P ≥ 0.05; 0.05 > **P ≥ 0.01). Segments shaded in red indicate where a pair of LGs has merged as a result of reducing the stringency to
LOD 5.
Portis et al. BMC Research Notes 2012, 5:252
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Page 6 of 15
Table 2 Characteristics and alignment of the consensus C. cardunculus linkage map
Linkage group name
Altilis
41
Shared
markers
Size
(cM)
Total
markers
Marker
density
Alignment with globe artichoke x wild cardoon map 1
Consensus
LG
Romanesco
C3
Aligned LGs
Shared markers
LG_I
C3_1
Alt_2 + _11
15
143.6
92
1.6
LG_I
21
LG_II
C3_2
Alt_4
10
144.5
72
2.0
LG_II
10
LG_III
C3_3
Alt_3
4
140
50
2.9
LG_III
7
LG_IV
C3_4a + _4b
Alt_20
1
107.8
27
4.1
LG_VI
4
LG_V
C3_5 + _10
Alt_1a + _1b
4
132.5
81
1.7
LG_V and LG_X
14
LG_VI
C3_6
Alt_18
1
105
19
5.8
Mola-18
3
LG_VII
C3_7
Alt_5
2
106.1
28
3.9
LG_VII + LG_XVII
5
LG_VIII
C3_8 + _14
Alt_10 + _7
6
117.8
68
1.8
LG_VIII + LG_XV + tripl.
11
LG_IX
C3_9
Alt_17
7
83.5
27
3.2
LG_IX
5
LG_X
C3_11
Alt_12
2
61.3
19
3.4
LG_XI
6
LG_XI
C3_12
Alt_6
1
97.6
49
2.0
LG_XII
4
LG_XII
C3_(13 + 18)
Alt_14
9
123.2
54
2.3
LG_IV
13
LG_XIII
C3_15
Alt_8
6
66.5
26
2.7
LG_XIV
6
LG_XIV
C3_16
Alt_19
1
54.6
23
2.5
LG_XIII
2
LG_XV
C3_17
Alt_9
3
92.4
36
2.6
LG_XVI
9
LG_XVI
C3_19
Alt_21
1
66.7
12
6.1
LG_XIV
2
LG_XVII
C3_20
Alt_15
3
44.5
11
4.5
LG_XI
3
Total
76
1687.6
694
Average
4.05
99.3
40.8
1
125
2.5
7.4
Alignment with the map published by Sonnante et al. [21] and based on a cross between a globe artichoke (“Mola”) with a wild cardoon (“Tolfa”) genotypes.
of the analysis; this was not the case for Alt_13 (Table 2).
The alignment was followed by the construction of a
consensus map based on a LOD threshold of above 5.0
(Figure 4), which succeeded in capturing 694 loci, 227
(217 SSRs, ten SNPs) of which involved co-dominant
markers. The map generated 17 LGs with a total genetic
length of 1687.6 cM and a mean inter-marker spacing of
2.5 cM; consensus LG numbers (from LG I to LG XVII)
have been assigned (Table 2, Figure 4). The length of
each individual LG varied from 44.5 to 144.5 cM (mean
99.3 cM), with the largest containing 92 loci. Only three
of the CyEM loci (the intercross locus CyEM_134 and
the two ‘Altilis 41’ testcross loci CyEM_167 and _79)
remained unlinked.
The consensus map, obtained from the domesticated
C. cardunculus forms, was compared with the Sonnante
et al. [21] map constructed from a cross between the
var. scolymus cultivar ‘Mola’ and the var. sylvestris (wild
cardoon) accession ‘Tolfa’, by considering 125 (117 SSRs,
eight SNPs) common markers. The common markers
identified each of the 17 LGs on the consensus map,
with between two and 21 present on each LG (Table 2).
Ten of the LGs aligned readily; LGs V and VII aligned
with two ‘Mola’/‘Tolfa’ LGs, and LG VIII with two major
groups and a triplet of markers. LGs X/XVII, and XIII/
XVI each aligned with only a single ‘Mola’/‘Tolfa’ LG. In
general, marker order and genetic separation were
comparable, with some exceptions. It has been established that wild cardoon is more divergent from the two
cultivated forms (globe artichoke and cultivated cardoon) than are the two cultivated forms with respect to
one another [44,45]. Somewhat surprisingly, therefore,
over 100 SSR loci featured in the consensus map but apparently were either non-informative or remained as
singlet loci in the ‘Mola’/‘Tolfa’ population.
EST-SSRs as functional markers
Putative functions can be deduced for markers derived
from ESTs using homology searches with public protein
databases. Annotation of mapped loci was performed via
BlastX search as well as InterPro scan and GO categorisation made it possible to tag some biological functions.
A set of 17 CyEM markers were annotated with GO
terms involved in the ‘response to stimulus’ (Table 3),
five of which were derived from transcripts related to
‘response to cold stress’ and eight to ‘response to salt
stress’ terms. In particular, the marker CyEM-42, developed from the contig CL4773Contig1 (1281 bp, 267
aminoacids) [22] and mapped on LG_12 of “Romanesco
C3” map, showed high amino acid similarity (81%) with
the Arabidopsis protein kinase PBS1 (NP_196820.1, unigene At.23518). To consider reliable orthology, a reciprocal tblastx analysis against the whole EST collection,
currently available for C. cardunculus, was performed
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
I
C3-1 / Alt-2+11
0,0
2,0
5,5
6,9
7,2
10,2
13,4
14,7
16,3
16,8
17,5
18,0
18,6
19,7
22,6
23,2
a-p13/m62-138
r-CyEM-91
r-e35/t81-190
CyEM-1
a-p45/m61-66
r-CyEM-54a
CELMS-05
CyEM-60
r-CDAT-01
Acyltransf-4-snp
r-CyEM-157
a-e38/m50-162
r-CyEM-261
r-CyEM-57
r-p12/m50-230
r-e33/t89-620
27,3
28,7
30,1
32,4
33,2
34,9
37,4
40,3
41,1
42,2
44,4
47,8
49,5
50,3
51,4
52,6
53,5
55,2
56,7
58,3
61,1
61,8
65,3
66,3
67,7
68,9
70,3
74,6
75,4
76,2
77,3
81,0
82,0
86,0
87,7
88,3
90,8
91,7
93,3
93,9
95,1
95,8
97,1
98,4
99,0
99,6
101,0
101,9
102,6
103,4
103,6
104,8
105,7
106,4
106,7
107,5
107,9
108,3
109,8
110,3
111,3
112,8
113,0
114,0
115,5
117,4
118,3
119,8
120,1
123,0
124,6
126,9
130,1
133,6
138,4
143,6
a-e34/m50-196
r-e39/t80-148
r-e32/t82-224
r-e32/t80-82
a-e34/m50-198
r-e32/t82-226
a-CyEM-264
r-p12/m47-320
r-p13/m50-216
r-Cs-PAL03
r-CyEM-166
r-p13/m59-120
r-p45/m50-420
a-CyEM-133
r-CELMS-08
a-CyEM-14
r-CyEM-130
a-CyEM-30
r-e39/m50-364
a-e35/t80-358
CyEM-259
r-p13/m60-142
CyEM-150
r-e35/t81-104
CyEM-296
a-CyEM-12
r-p45/m59-232
r-p12/m50-350*
r-p45/m59-460
r-e38/t80-630
a-p12/m62-150
r-cyre5/e33-350
a-e34/m49-212
r-e32/t82-166
CyEM-234
CyEM-254
r-e38/m50-340*
r-p12/m62-268
r-CyEM-147
a-e35/t89-144
CELMS-09
a-p12/m62-164
CELMS-16
r-e35/m62-440
r-CyEM-176
CyEM-124
r-e32/t81-610
r-CyEM-104
r-e38/t82-230
r-e32/t81-98
CELMS-26
r-p13/m50-176
r-CyEM-84
r-e33/t89-430
r-e35/t81-348
CELMS-58
a-e38/m47-158*
r-CELMS-40
r-CyEM-223
CELMS-52
r-e38/t80-190
r-e32/t82-272
a-p12/m50-105
r-e35/t89-296
r-e32/t82-86
r-e35/m50-354*
a-e35/m47-590**
r-e34/m50-216
a-e33/t80-272
r-e33/t89-174
r-e36/m47-260
r-e38/t80-550
r-e37/m49-104
r-e39/t80-178
a-e38/t82-550
r-e36/m59-112
II
III
IV
C3-2 / Alt-4
C3-3 / Alt-3
C3-4 / Alt-20
0,0
10,9
MH-08
MH-09
FOH-08
FOH-09
SOH-08
SOH-09
a-e33/t89-310
a-CyEM-162
23,0
r-e38/m50-206
27,3
r-p13/m59-320
144,5
r-CyEM-294
r-e35/m50-280
Acyltransf-2-snp
r-e38/t80-212
r-e36/m48-82
a-e32/t81-590
CyEM-128
r-e33/t89-338**
r-e32/t80-190
r-CyEM-56
CyEM-77
a-e35/m47-332
r-e32/t81-380
a-p13/m59-170
r-p12/m60-395**
r-e32/t81-460
r-e42/m50-590
a-e34/m50-282
C4H-snp
CyEM-190
r-p12/m62-106
r-p45/m59-116
r-CyEM-86
r-CELMS-03
r-CyEM-221
r-p12/m47-196
a-e35/t81-340
r-e33/t80-224
r-p13/m60-110
r-CyEM-231b
CyEM-282
r-e38/t80-390
CLIB-02
r-CELMS-15
r-e38/t80-450
CyEM-250
r-e32/t82-92
a-e38/t80-90
a-e32/t82-90
a-e33/t89-490
r-e32/t82-140
a-e32/t82-260
CELMS-42
a-e35/t80-238
r-e35/m50-220
a-e38/t82-638
r-e42/m50-176
a-e33/t89-402
r-p45/m60-690
a-CyEM-122
r-e38/m50-230
CELMS-13
r-p12/m60-116*
r-e34/m49-322
r-e38/m47-350
a-e38/m59-190
a-p13/m50-365
a-CyEM-284
a-CELMS-25
r-CyEM-94
a-e32/t82-124
r-p13/m61-272
a-p13/m62-410
r-CyEM-202
r-CyEM-7
CyEM-183
IX
X
C3-11 / Alt-12
0,0
0,3
2,7
0,0
6,6
8,4
r-CyEM-229
14,0
CyEM-64
18,7
20,1
21,1
r-e38/t80-250
CyEM-10
r-e39/t80-406
26,8
27,3
27,5
29,2
38,9
39,6
40,6
42,4
r-p13/m50-430
CyEM-34
r-CyEM-123
a-CyEM-148
a-e34/m49-108
CELMS-60
r-e33/t80-174
CyEM-108
50,7
51,2
a-p13/m62-174
r-e32/t81-122
55,2
57,7
59,6
a-p13/m62-170
r-p13/m62-164
r-CyEM-54b
62,5
64,1
CyEM-200
r-e38/t80-340
68,5
69,4
71,4
83,5
11,3
12,8
13,4
MH-08
MH-09
FOH-08
FOH-09 18,4
r-e37/m50-340
r-CyEM-233
r-CyEM-113
r-e38/t82-214
MH-09
FOH-09
SOH-09
r-CyEM-289
a-e32/t81-200
20,2
21,5
23,6
a-CyEM-247
a-p45/m59-402
a-CyEM-59
30,5
32,3
CyEM-260
r-e38/t82-600
35,6
36,4
37,8
r-p12/m62-340
r-e37/m61-136
a-e35/m48-650*
46,8
48,0
49,2
50,5
51,0
54,4
55,6
56,2
59,8
60,3
61,5
62,8
64,9
65,8
66,8
67,9
r-e38/m50-234
a-e37/m61-240
r-e39/t80-560
a-e37/m61-228
r-e35/m50-282
r-e36/m59-130
a-e39/t80-124
r-e35/t81-220
r-CyEM-266
a-e38/t82-306
r-e38/t80-252
r-e32/t80-474
r-e33/t89-280
CELMS-01
r-CELMS-45
r-CyEM-29
75,0
75,7
76,3
77,8
80,8
r-e38/m47-280
a-e32/t81-328
CyEM-199
r-CyEM-209
r-e33/t80-252
85,5
86,1
87,1
90,9
91,3
92,5
93,9
Acyltransf-3-snp
a-e32/t81-168
r-e36/m48-600
a-e32/t81-352
r-p13/m60-86
r-p13/m60-420
r-CyEM-210
99,4
100,2
HCT-snp
a-p13/m59-450
106,8
108,9
r-p12/m61-290
r-p12/m60-235
111,4
CELMS-10
118,3
119,9
a-e35/m49-206
r-p13/m61-192
125,0
a-p45/m60-102
135,6
r-CyEM-120
140,0
r-p13/m47-175
XI
0,0
a-p45/m60-420
12,0
r-e32/t82-160
21,1
21,6
24,1
25,5
26,4
a-e32/t82-158
r-e35/m47-228
r-e32/t80-266
r-p45/m60-428*
r-p45/m60-432
30,1
30,7
r-e32/t82-164
r-e33/t89-234
37,4
r-p13/m47-550
40,1
r-p13/m47-542
42,8
44,1
46,4
r-p12/m50-220
r-e38/t80-540
r-CyEM-244
50,1
51,3
52,7
CyEM-293
r-CyEM-300
a-CyEM-90
58,7
60,4
r-e38/m59-450**
r-e33/t80-232
74,2
a-e36/m48-326
80,2
r-e33/t89-154
86,5
88,4
88,5
91,5
r-e38/m59-214
r-CyEM-163
r-CyEM-72
102,6
r-e35/m48-222
107,8
r-e37/m50-172
r-CLIB-14
XII
C3-12 / Alt-6
0,0
r-e36/m48-640
5,1
7,4
9,0
r-e32/t82-420
r-e39/t80-206
r-cyre5/m49-352
C3-13+18 / Alt-14
0,0
r-e34/m49-250**
r-p45/m47-335
r-CyEM-37
r-CyEM-193
22,8
CELMS-04
26,8
26,9
a-e39/t80-86
r-CyEM-75
31,8
r-CyEM-126
35,3
CyEM-156
38,3
r-CLIB-04
41,7
42,8
r-CELMS-20
a-p12/m50-95
46,3
a-p13/m62-230
49,7
a-e35/t80-340
53,4
r-e39/t80-90
61,3
a-p45/m60-258
4,4
V
C3-5+-10 / Alt-1a+-1b
0,0
3,9
5,2
9,8
11,2
11,8
14,5
15,3
17,1
17,5
18,3
19,5
21,8
24,1
24,7
26,4
26,5
27,7
28,5
28,7
29,8
30,5
30,6
32,7
33,5
34,1
36,9
38,0
39,9
42,8
44,1
44,7
45,9
47,0
47,5
49,0
49,7
50,9
51,5
51,8
52,0
53,4
54,6
56,7
57,1
58,0
58,2
61,7
61,9
62,4
62,5
64,8
67,1
68,4
68,5
68,7
70,3
70,5
74,2
75,9
78,4
78,5
79,4
82,2
83,2
85,8
89,7
91,3
95,0
95,3
98,3
101,2
105,4
107,6
112,8
117,6
a-e38/m50-600
r-p45/m61-192
r-p45/m47-610
r-e35/m50-314**
a-e32/t82-64
r-e35/m47-580
r-cyre5/t89-255
a-p12/m50-295
a-e33/t80-200
r-e35/m62-140
r-e38/m47-198
r-e37/m61-316
r-p13/m59-195
r-e35/t80-280
a-CyEM-38
a-CELMS-59
r-CELMS-48
a-CyEM-99
r-e35/t81-68
r-CELMS-41
r-e33/t89-340
r-e33/t80-240
a-e38/t82-540
r-p45/m59-190
r-e38/t80-504
a-e32/t81-258
r-p13/m62-210
r-CyEM-207
r-e38/t82-380
a-e32/t81-248
r-e36/m47-580
r-e35/t89-162
r-e38/t82-212
a-cyre5/t90-145
r-e35/m62-348
r-CyEM-9
a-e39/m50-186
a-CyEM-118
r-e38/m47-450
a-p12/m62-136
r-CLIB-12
a-e37/m61-204**
r-e42/m50-204
CyEM-175
a-e38/t80-230
r-CyEM-66
a-e42/m50-182
r-e34/m50-120
r-CyEM-13
r-e35/m47-140
CyEM-36
r-CELMS-33
a-p13/m60-108
r-p13/m47-330
r-CyEM-279
a-CyEM-76
a-p12/m62-256
r-e36/m48-164
a-e33/t80-302
CyEM-32
r-e39/m50-188
a-p13/m50-690
r-CyEM-63
r-CyEM-25
a-e36/m47-158**
r-e39/t80-480
a-p13/m47-335
r-p13/m50-150
r-e38/t82-176
a-e32/t80-220
r-e39/t80-330
a-e35/m62-238
CyEM-136
r-e36/m59-164
a-e32/t82-112
r-p13/m47-240
a-e34/m49-380*
r-e42/m50-520
124,2
a-e35/m62-138
130,3
132,5
a-e35/t89-244
a-e35/t89-252
VI
VII
C3-6 / Alt-18
C3-7 / Alt-5
0,0
7,5
12,1
14,4
a-p45/m62-370
a-CyEM-196
a-e38/m47-440
r-e35/m49-192
23,7
r-e32/t80-282
29,4
r-p45/m60-64
34,0
r-e32/t80-102
39,2
40,6
41,3
r-e35/m50-420
r-e38/t80-242
r-CyEM-158
46,2
a-CyEM-11
50,6
4CL-snp
55,9
a-CyEM-256
60,1
62,5
a-CyEM-69
a-p45/m61-150
68,5
a-e36/m48-410
75,6
r-p13/m59-164
90,1
105,1
VIII
C3-8+-14 / Alt-7+-10
0,0
r-e38/m47-530
0,0
a-p45/m50-590
3,5
a-e39/t80-78
2,9
4,6
a-e32/t80-76
r-e34/m50-404
7,4
r-e36/m59-334**
13,3
CyEM-80
18,2
19,2
a-e33/t89-510
r-e35/m62-220
25,3
26,2
27,7
a-e39/t80-224
r-e35/m62-432
r-e32/t81-468
33,3
r-e39/m50-270
37,3
a-p13/m50-90
43,7
44,1
r-e32/t82-206
a-CELMS-14
49,2
49,8
r-p12/m50-160
a-CyEM-197
53,8
55,5
57,4
a-p12/m60-118
r-e35/t89-312
a-e35/t80-200
61,5
63,5
r-p12/m60-125
r-CyEM-214
69,5
70,6
r-e32/t82-146
a-e39/m50-410*
73,5
r-CMAFLP-11
76,4
r-CyEM-47*
81,6
CyEM-112
86,6
r-p12/m47-670
92,3
r-CyEM-55
11,9
17,0
17,9
20,1
20,8
22,1
23,3
24,7
25,7
26,0
27,9
28,7
31,0
32,6
33,3
34,2
36,0
36,7
37,3
37,7
39,5
40,3
40,5
43,4
45,7
47,5
48,3
50,4
51,0
53,5
56,4
56,9
58,0
60,1
60,9
62,0
63,0
65,4
65,8
67,1
67,2
68,9
70,2
71,0
71,3
72,1
72,7
74,2
74,3
75,3
77,0
80,6
81,0
81,8
81,9
84,0
86,4
87,3
90,9
94,3
95,8
99,9
r-p12/m62-166
r-e38/m47-114
106,1
a-CMAFLP-07
a-p45/m50-280
r-e37/m50-290
CELMS-12
a-e32/t82-308
a-p45/m47-88
r-e35/t89-300
r-e35/t89-176
a-e35/t81-554
r-e35/t81-540
r-CyEM-195
r-CyEM-121
r-e32/t80-178
r-CyEM-188
CyEM-52
r-CyEM-220
CyEM-2
CyEM-236
a-e32/t82-148
r-e38/t82-490
r-CyEM-173
a-e35/m62-248
a-CyEM-110
r-e33/t89-232
r-e32/t81-250
a-p12/m47-315
r-e42/m50-298
r-e32/t81-136
CELMS-37
a-e35/m62-252
r-p12/m59-180
CELMS-02
a-p45/m47-250
a-e38/m59-102
a-e37/m49-146
r-e38/m47-400
r-e32/t81-340
a-p45/m60-122
a-p45/m60-68
r-p13/m60-100
r-p12/m62-100
a-e32/t80-226
r-e38/t82-680
r-CELMS-21
a-e35/t80-148
r-p12/m47-105
r-e35/t81-298
r-e33/t80-132
Acyltransf-1-snp
a-p13/m50-278
r-e35/t89-142
r-e35/m48-274
a-e35/t89-322
r-e34/m50-340
a-e35/t89-212
r-e38/m47-182
r-e36/m59-500
r-e34/m50-298
a-p45/m47-134
r-e36/m59-306**
r-e35/m48-186
r-cyre5/t87-320
r-p45/m47-288
MH-08
MH-09
r-e35/m48-158
108,3
r-CELMS-19
117,8
r-p12/m61-140
r-e37/m61-510
C3-9 / Alt-17
r-e32/t82-254
a-p13/m47-430
r-p13/m62-148
0,0
9,8
11,8
r-e38/m50-108
19,2
32,2
35,2
36,1
38,2
38,6
39,2
42,5
42,6
45,0
47,2
48,3
51,5
52,3
52,9
53,3
55,3
57,8
58,0
59,4
60,0
61,0
61,5
61,8
62,9
63,3
64,1
64,3
64,5
65,1
65,4
65,6
66,3
66,4
66,5
67,0
67,2
67,9
68,1
69,0
69,6
69,8
71,3
71,8
73,1
74,5
74,9
79,5
79,6
81,8
82,3
83,8
86,0
88,6
92,6
93,3
96,9
99,4
103,7
104,5
113,3
117,1
117,7
121,8
126,2
129,3
MH-08
MH-09
FOH-08
FOH-09
Page 7 of 15
a-e39/m50-360
a-e32/t82-256
r-CyEM-70*
CyEM-231*
15,7
17,2
20,3
23,3
24,4
25,9
26,9
29,4
30,2
31,4
34,1
35,2
37,8
39,4
40,8
44,6
46,9
48,0
49,8
51,6
53,6
54,4
55,2
56,4
57,7
60,0
61,1
61,2
62,8
63,4
63,7
64,5
65,1
66,2
67,5
70,0
71,8
72,5
74,0
r-e39/m50-690
r-e39/t80-190
r-e35/m49-320
r-e35/t81-272
r-e38/t82-662
r-e37/m49-278
r-p12/m62-245
r-e35/t81-560
r-CELMS-31
r-e38/t82-696
r-e35/t89-224
r-e35/t89-64
CyEM-218
r-e34/m49-178
r-CELMS-23
r-CyEM-174
r-e35/m47-136
a-e34/m50-130
a-e34/m49-90
r-e35/t81-680
a-e36/m47-148
r-e35/m50-302
a-e35/t80-144
r-e42/m50-90
a-e38/m50-274
a-CELMS-57
r-e42/m50-162
a-e35/m50-272
a-e33/t80-154
a-e32/t82-178
a-e36/m59-270
a-e39/t80-500
a-e35/t80-440
a-CyEM-16
a-e33/t89-492
a-p12/m59-228
r-p12/m61-530
a-e35/m62-198
a-CyEM-204
79,9
a-e38/m50-350
a-cyre5/m47-90
Figure 4 (See legend on next page.)
88,2
88,8
a-e35/t89-336
a-cyre5/m47-160
92,1
93,4
a-CyEM-219
a-e32/t80-152
97,6
a-CELMS-49
MH-08
MH-09
FOH-08
FOH-09
SOH-08
SOH-09
r-p45/m59-172
6,4
r-p12/m62-120
10,4
11,7
14,7
16,1
16,6
17,1
21,4
23,3
24,4
25,3
26,1
26,7
27,8
28,3
29,1
30,1
31,0
33,9
34,9
37,0
38,8
r-e42/m50-144*
a-e35/m62-144
r-e38/t82-288
a-e37/m49-196
a-e35/t81-86
r-e38/m59-178
r-p45/m60-76*
r-e35/t80-128*
r-e32/t80-170
r-e32/t82-182
a-e38/t82-406
r-p13/m50-98
r-p45/m50-390
r-e32/t80-260
CyEM-15
CyEM-155
r-e32/t81-372
r-e38/t80-430
CyEM-189
r-e33/t89-530
a-p12/m62-114
44,1
44,4
47,0
48,6
49,4
50,0
53,4
53,5
55,6
r-e38/m59-186
a-e38/m47-248
CyEM-106
r-CyEM-280
CyEM-135
r-CMAL-21
r-e33/t89-144
r-e34/m49-154
r-e36/m47-112
59,0
60,0
XIII
XIV
C3-15 / Alt-8
C3-16 / Alt-19
0,0
1,8
a-e37/m50-232
r-e36/m48-150
12,9
15,1
15,6
CyEM-48
a-e34/m49-272
r-CyEM-152
19,9
21,0
23,1
a-CyEM-153
r-CyEM-185
CyEM-286
25,8
r-e36/m47-248
32,4
34,4
34,9
36,8
38,8
a-e38/m50-170
CyEM-211
r-CyEM-24
r-p13/m50-140
CyEM-237
43,3
43,5
45,3
46,5
47,1
48,0
50,8
53,5
53,8
r-CyEM-127
a-e33/t80-178
CyEM-117
r-CMAL-110
a-e32/t82-510
r-CyEM-42
r-p45/m59-164
a-e33/t89-190
CyEM-240
a-e35/t80-540
r-CyEM-53
60,1
r-p12/m62-280
66,4
a-e32/t82-228
65,5
66,5
r-e33/t80-322
a-p12/m50-310**
69,3
70,1
71,6
r-CYEM-226
r-CyEM-181
a-CyEM-205
77,3
79,3
81,5
82,6
85,3
86,3
86,5
88,4
90,8
91,5
93,2
CyEM-73**
r-CyEM-169
r-CyEM-288
r-CyEM-145
CyEM-243
r-CyEM-8
a-e32/t80-338
r-CyEM-291
r-p45/m60-200
CyEM-178
CyEM-43
a-e35/m48-500
98,8
r-e32/t81-400
101,6
r-e32/t80-410
110,5
r-e32/t82-258
123,2
a-e35/m50-650
0,0
2,5
r-cyre5/t87-230
XV
C3-17 / Alt-9
XVI
XVII
C3-19 / Alt-21
C3-20 / Alt-15
0,0
r-e33/t80-280
0,0
Myb12-snp
4,5
r-CyEM-45
10,2
CyEM-225
7,1
a-CyEM-3*
9,9
a-CELMS-11
13,9
r-CyEM-19**
17,2
a-CyEM-227
21,1
23,2
a-e38/m50-500 21,5
r-CyEM-97
9,5
10,3
11,0
r-p45/m47-162 MH-08
MH-09
FOH-08
FOH-09
CELMS-39
SOH-08
CyEM-248
SOH-09
CyEM-144
C3H-snp
16,0
a-e35/m48-108
18,8
r-e36/m59-322
23,0
24,7
a-p13/m50-124
r-e35/t89-284
34,5
r-e38/m50-214
44,5
a-p12/m47-162
0,0
r-CyEM-172
6,9
r-e33/t89-166
11,6
13,9
r-e35/t80-660
r-p45/m61-248
16,9
19,0
19,3
21,7
23,9
25,5
27,6
28,3
31,1
r-p45/m61-102
a-e35/m62-280
r-CyEM-111
r-CyEM-246
r-e32/t81-188
r-e35/t80-98
r-CELMS-32
r-e35/t81-154
34,2
r-e38/m59-130
36,9
r-e35/t81-278
40,8
41,0
42,9
r-e35/m50-254
r-e32/t80-310
CyEM-93
46,9
49,3
50,9
r-p45/m50-220
54,6
r-e37/m61-262
r-p13/m60-148
r-e35/t89-198
a-e32/t81-82
5,4
15,0
r-cyre5/e35-70
r-CyEM-141
28,4
a-p13/m59-105
35,9
CyEM-277
39,3
r-e32/t82-294
43,0
r-e35/m50-230
29,6
r-p13/m47-188
33,2
34,2
35,4
37,5
r-CELMS-36
a-e38/t82-182
a-e32/t82-134
r-e32/t80-162
40,1
42,0
r-e33/t80-504*
r-CMAL-24**
46,1
48,3
48,4
49,8
51,8
53,6
53,7
54,8
56,7
58,8
60,2
62,9
64,4
66,6
68,8
70,5
r-e35/t89-310
r-CyEM-138
a-p13/m60-230
r-e32/t81-570
51,1
r-e35/t89-292
r-CELMS-24
CELMS-17
r-CyEM-146
HQTsnp359
r-e42/m50-242** 59,3
r-e36/m48-620
r-CyEM-107
r-e38/t80-496
r-p13/m61-340 66,7
r-CyEM-271
a-e35/m62-390
r-CELMS-44
76,5
77,6
a-e39/m50-240
CyEM-35
80,4
r-CyEM-20
83,8
r-CyEM-232
92,4
a-e37/m49-336
r-p13/m47-560
r-e35/m49-324
r-e35/m49-164
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 8 of 15
(See figure on previous page.)
Figure 4 Consensus genetic map of C. cardunculus. Marker names appear to the right of each LG, with map distances in cM to the left; 'r-'
and 'a-' indicate markers segregating only in, respectively, ‘Romanesco C3’ (C3) and ‘Altilis 41’ (Alt41). Arrows indicate the positions of earliness
QTL, named as follows: trait abbreviation (MH: main inflorescence; FOH: first order inflorescence; SOH: second order inflorescence) and harvest
season (08: “2008”, 09: “2009”).
and no better alignment than that of contig CL4773 was
detected. PBS1 was found to work as R gene against the
bacterial pathogen Pseudomonas syringae, where its
cleavage, operated by the pathogens’ effector AvrPphB,
triggers the signalling cascade, generating the host response (HR) [46]. Pseudomonas spp. together with other
endophytic bacteria may affect globe artichoke plants
both in field and during micropropagation [47] and the
CyEM-42 may be likely considered a reliable marker for
tagging a bacterial resistance trait in the species.
Our EST-SSR markers may be defined as functional
markers with the potential to target polymorphisms in
gene responsible for traits of interest and they can be
also particularly useful for constructing comparative
framework maps with other Asteraceae, giving the possibility to amplify ortholog genes and provide anchor loci.
The genetic basis of earliness
An evaluation of the variance for the three earlinessrelated traits established significant genotypic differences
(P < 0.05) between ‘Romanesco C3’ and ‘Altilis 41’
(Table 4). Thus, eMH in the former was 162 days in
“2009” and 178 days in “2008”, while in the latter the respective times were 218 and 223 days. All three traits
varied continuously among the F1 progeny (the distribution for eMH is shown in Figure 5); no progeny was as
early flowering as ‘Romanesco C3’, but a few were later
flowering than ‘Altilis 41’, due to transgressive segregation.
The mean eMH, eFOH and eSOH lay substantially above
the mid-parent value, suggesting semi-dominance for lateness. The low global level of heterozygosity characteristic
of the cultivated cardoon makes it possible that one or
more of the earliness QTL are in the homozygous state in
‘Altilis 41’, so that the presence of dominant alleles for lateness may contribute to later flowering across the whole
mapping population. The inter-trait correlations were
similar in both seasons, with the strongest correlation
linking eMH and eFOH (r > 0.80, P < 0.0001). The correlations between the two seasons were also strong, ranging
from 0.64 (P < 0.0001) for eMH to 0.49 (p < 0.001) for
eSOH (Table 5). Flowering and head harvesting time was
a little earlier in “2009” than in “2008” (7–8 days on
average), while performance was somewhat more
variable in “2009” (Table 4), probably reflecting the
difference between re-awakened and newly sown material. The broad sense heritability for eMH of 0.76
(Table 4) indicated the trait to be predominantly
under genetic control, but the rather lower heritabilities
shown by the traits eFOH and eSOH suggested that
the environment is quite influential in their
determination.
The KW test and SIM procedure identified, at first, six
QTL regions stable across years in the developed consensus map (Figure 4). Those on LGs I, XI and XVII
involved all three traits, those on LGs I and IX only
eMH and eFOH, and the one on LG VII solely eMH.
Table 3 CyEM markers with Gene Ontology annotation for stimuli response-related terms
Level
N° of loci
GO:0050896
GO ID
response to stimulus
Term
2
17
CyEM-008, CyEM-030, CyEM-42, CyEM-054, CyEM-057, CyEM-070,
CyEM-072, CyEM-093, CyEM-120, CyEM-135, CyEM-145, CyEM-150,
CyEM-152, CyEM-218, CyEM-229, CyEM-259, CyEM-266
GO:0009628
response to abiotic stimulus
3
13
CyEM-008, CyEM-030, CyEM-054, CyEM-070, CyEM-093, CyEM-120,
CyEM-135, CyEM-145, CyEM-150, CyEM-152, CyEM-218, CyEM-229, CyEM-259
GO:0042221
response to chemical stimulus
3
4
CyEM-093, CyEM-218, CyEM-229, CyEM-266
GO:0006950
response to stress
3
15
CyEM-008, CyEM-030, CyEM-054, CyEM-057, CyEM-070, CyEM-072,
CyEM-093, CyEM-120, CyEM-135, CyEM-145, CyEM-150, CyEM-152,
CyEM-229, CyEM-259, CyEM-266
GO:0009266
response to temperature stimulus
4
5
CyEM-008, CyEM-054, CyEM-093, CyEM-145, CyEM-150
GO:0006970
response to osmotic stress
4
8
CyEM-030, CyEM-070, CyEM-093, CyEM-120, CyEM-135, CyEM-152,
CyEM-229, CyEM-259
GO:0010033
response to organic substance
4
3
CyEM-093, CyEM-229, CyEM-266
GO:0009409
response to cold
4
5
CyEM-008, CyEM-054, CyEM-093, CyEM-145, CyEM-150
GO:0009651
response to salt stress
5
8
CyEM-030, CyEM-070, CyEM-093, CyEM-120, CyEM-135, CyEM-152,
CyEM-229, CyEM-259
Redundancy occurs since each available GO-level of annotation was considered.
Locus Name
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 9 of 15
Table 4 Earliness of the parental lines (‘C3’: ‘Romanesco C3’, ‘Alt 41’: ‘Altilis 41’) and their F1 progeny in “2008” and
“2009”
Precocity trait
Parents 1
Year
F1 population
2
C3
A41
Mean
Range
s.e.
Main head (eMH)
2008
178 a
223 b
212.9
202-238
0.518
2009
162 a
218 b
206.1
190-235
0.694
First order heads (eFOH)
2008
185 a
229 b
221.3
209-248
0.456
2009
180 a
224 b
214.0
198-239
0.828
2008
198 a
239 b
232.6
214-267
0.695
2009
192 a
237 b
225.7
207-246
0.897
Second order heads (eSOH)
h2B
0.76
0.61
0.54
Means followed by different letters within the same row are significantly different at P < 0.05.
2
s.e. : standard errors; h2B: broad sense heritability based on two years’ data.
1
‘Romanesco C3’ and ‘Altilis 41’ maps were used separately for QTL validation, the percentage of phenotypic
variance explained by some of the QTL differed from
that predicted by the analysis based on the consensus
The seventh QTL cluster on LG II involved all three
traits, but was only expressed in “2009” (Figure 4). On
the whole, seven chromosomal regions scattered over six
LGs of the consensus map were identified. When the
50
Main head 2008
30
A41
20
238
232
229
235
229
226
226
223
220
217
214
211
208
205
0
C3
202
10
178
Numbers of F1 genotypes
(eMH-08)
40
40
(eMH-09)
30
20
A41
235
232
223
220
217
214
211
208
205
202
199
196
193
0
C3
190
10
162
Numbers of F1 genotypes
Main head 2009
Earliness of head production (days)
Figure 5 Distribution of the harvesting time of the main head among 154 F1 individuals in “2008” and “2009”. Parental means (‘C3’:
‘Romanesco C3’, A41: ‘Altilis 41’) indicated by arrows.
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 10 of 15
Table 5 Correlations between the three earliness traits
measured in the ‘Romanesco C3’ x ‘Altilis 41’ F1
population in “2008” and “2009”
Precocity trait
Year
eMH
eMH
2008
0.64***
eFOH
eSOH
eFOH
eSOH
0.84***
0.69***
2009
0.86***
0.76***
2008
0.54***
0.66***
2009
0.72***
2008
0.49**
2009
**P < 0.001; ***P < 0.0001.
map (data not shown), perhaps reflecting the structure
and size of the segregating progeny and the existence of
different allelic interactions [48]. However, all seven
QTL regions were detectable by applying the SIM
method to the parental maps, and further analysed with
the MQM procedure. QTL identified in each map and
season are shown in Table 6 and graphically reported in
Figure 6. Only three of the seven QTL regions were detectable in both parental maps, presumably these regions
were heterozygous in both parental lines. The other four
were only detectable in one of the two maps, suggesting
that one parent was homozygous in the critical region
(Figure 6). Across all three traits, a total of 25 QTL was
detected, of which 19 were stable across both growing
seasons, with the other six expressed only in “2009”.
With respect to eMH, two of the QTL were heterozygous in both parents, three only in ‘Romanesco C3’ and
two just in ‘Altilis 41’. The largest effect stable eMH
QTL in ‘Romanesco C3’ mapped to LG C3_1 in the
neighbourhood of the SSR locus CELMS_40, named
eMH.C3_1. This QTL was responsible for 38-48% of the
phenotypic variation and was associated with an additive
effect of 10–12 days. The other four QTL in ‘Romanesco
C3’ mapped to LGs C3_9, _8, _12 and _2, and accounted
individually for between 6-10% of the phenotypic variance; eMH.C3_2 was only detected in “2009”. The largest stable QTL detected in ‘Altilis 41’ (eMH.Alt_2),
Table 6 Characteristics of the earliness QTL detected using the ‘Romanesco C3’ (C3) and the ‘Altilis 41’ (A41) maps
Precocity trait
Main head (eMH)
Map
C3
LG
QTL
2008
Locus
First order head (eFOH)
C3
3.6
rCELMS-40
105.1 14.7
47.9 −10.5 3.3
CyEM_10
29.8
3.4
7.6
−4.0
−4.3
CyEM_2
81.8
3.6
6.8
−3.5
6.6
−3.6
e35/m50-302
47.2
3.3
6.1
−3.1
-
-
-
e32/t81-380
58
3.9
13
6.4
CyEM_10
29.8
4.8
10.5
eMH.C3_8
CyEM_173
81.0
4.1
8.9
e39/m50-690
41.2
3.6
-
-
Alt_2
eMH.Alt_2
e38/m47-158
64.3
6.2
41.4
−8.9 3.2
e38/m47-158
64.3
7.9
32.9 −10.9
Alt_2 eMH.Alt_2b
p12/m62-150
29.3
3.6
10.7
−5.3
p12/m62-150
29.3
3.3
8.9
−5.7
Alt_15 eMH.Alt_15
CyEM_248
20.9
3.3
8.9
4.2
CyEM_144
20.3
3.2
7.1
5.1
-
-
e32/t82-90
35.4
3.4
9.8
5.2
rCyEM_223
106.1 7.6
29.9 −10.5
Alt_4
eMH.Alt_4
C3_1
eFOH.C3_1
C3_9
eFOH.C3_9
3.3
3.4
C3_2
eFOH.C3_2
Alt_2
eFOH.Alt_2 3.0
Alt_15 eFOH.Alt_15
Alt_6
eFOH.Alt_6
Alt_4
eFOH.Alt_4
C3_1
eSOH.C3_1
3.4
C3_12 eSOH.C3_12
A41
−4.5
eMH.C3_9
Alt_2 eFOH.Alt_2b
Second order head (eSOH) C3
38.1 −11.6
C3_8
eMH.C3_2
cM LOD % var Add
105.1 9.62
C3_9
C3_2
Locus
rCELMS-40
eMH.C3_1
C3_12 eFOH.C3_12
A41
cM LOD % var Add GW
C3_1
C3_12 eMH.C3_12
A41
2009
GW
C3_2
eSOH.C3_2
Alt_2
eSOH.Alt_2 3.1
Alt_15 eSOH.Alt_15
Alt_6
eSOH.Alt_6
Alt_4
eSOH.Alt_4
-
-
104.0 8.9
31.0
−7.1 3.1
CyEM_10
29.8
3.8
8.1
−4.1
CyEM_10
29.8
3.5
6.6
−5.1
e39/m50-690
41.2
3.4
5.6
−3.1
e35/m50-302
47.2
3.1
5.5
−4.8
−4.3
e33/t89-430
-
-
-
-
e42/m50-176
55.0
3.2
5.1
e38/m47-158
64.3
7.2
25.6
−6.7 3.0
-
e38/m47-158
64.3
6.3
26.7 −10.2
aCyEM_12
20.5
3.6
11.0
3.8
p12/m62-164
32.1
3.4
8.3
CyEM_248
20.9
3.2
9.1
3.3
CyEM_144
20.3
3.6
7.8
5.3
cyre5/m47-160 1.5
3.0
8.3
3.1
cyre5/m47-160 1.5
3.0
5.7
3.4
-
-
-
-
e38/t80-630
99.7
7.1
32.2
−9.7 3.2
e35/m50-302
47.2
3.4
15.1
-
-
-
-
e38/m47-158
64.3
4.9
19.0
−7.6 3.2
CyEM_248
20.9
3.1
5.9
3.1
cyre5/m47-160 1.5
3.1
7.4
3.9
-
-
-
-
-
-
−5.4
e33/t89-490
36.0
3.0
6.3
4.2
e32/t81-98
98.0
5.6
22.4
−9.8
−7.1
e35/m50-302
47.2
3.4
18.0
−9.2
-
e38/m50-108
59.2
3.2
7.8
5.2
e38/m47-158
64.3
6.3
21.4
−8.2
CyEM_144
20.3
3.5
9.1
6.4
cyre5/m47-160 1.5
3.2
6.1
4.1
3.2
5.9
4.1
e33/t89-490
36.0
Each QTL name is formed by the abbreviated form of the trait followed by the relevant LG. The table indicates genome-wide LOD thresholds (GW) as determined
by a permutation test at P ≤ 0.05, the closest linked markers (Locus) and their map location (cM), the estimated LODs at the QTL peak (LOD), the proportions of
the total variance explained (% var), and the additive effects (Add).
Portis et al. BMC Research Notes 2012, 5:252
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C3_12
C3_2
0,0
29,3
32,1
61,5
58,1
59,2
eSOH.C3_2(09)
eFOH.C3_2(09)
eMH.C3_2(09)
eSOH.C3_12(09)
eSOH.C3_12(08)
eFOH.C3_12(09)
eFOH.C3_12(08)
eMH.C3_12(09)
eMH.C3_12(08)
Alt_15
C3_8
0,0
9,3
14,1
0,0
Alt_4
19,0
21,2
21,9
5,2
6,9
29,8
32,3
11,8
36,1
17,2
19,0
23,9
26,0
28,0
30,7
32,3
33,5
34,1
35,4
36,0
37,0
37,6
39,4
41,2
46,2
49,1
42,2
49,3
50,4
51,6
61,0
67,6
69,5
72,3
74,0
60,0
63,9
66,3
79,4
81,4
13,1
18,1
23,2
24,2
20,3
20,9
30,6
32,6
35,5
36,4
40,5
42,2
43,4
44,3
45,7
46,5
47,2
48,6
50,5
52,2
55,0
24,9
60,1
62,3
65,5
68,0
70,9
55,6
70,8
54,3
eSOH.Alt_2(09)
eSOH.Alt_2(08)
eFOH.Alt_2(09)
eFOH.Alt_2(08)
eMH.Alt_2(09)
eMH.Alt_2(08)
49,9
14,8
16,8
20,5
22,0
24,3
26,7
27,9
29,3
30,0
30,7
31,1
32,1
33,6
36,2
38,6
40,4
46,1
39,2
41,7
42,6
45,3
57,7
55,3
57,7
58,1
0,0
40,2
eMH.C3_8(09)
eMH.C3_8(08)
16,8
19,2
20,5
50,3
52,1
8,0
C3_9
eFOH.C3_9(09)
eFOH.C3_9(08)
eMH.C3_9(09)
eMH.C3_9(08)
4,1
6,0
8,6
11,9
47,2
0,0
1,5
0,0
2,5
eSOH.Alt_4(09)
eFOH.Alt_4(09)
eMH.Alt_4(09)
0,0
37,9
38,9
41,2
43,8
Alt_6
eSOH.Alt_6(09)
eSOH.Alt_6(08)
eFOH.Alt_6(09)
eFOH.Alt_6(08)
Alt_2
13,5
15,9
18,2
20,9
22,8
24,8
26,7
28,9
30,2
32,8
35,0
0,0
2,8
8,6
9,1
11,3
15,2
16,6
21,0
21,5
22,5
24,7
25,8
27,7
28,6
30,8
32,3
34,2
34,7
36,0
36,2
38,3
39,7
40,2
40,3
40,9
42,1
42,6
43,0
43,1
43,6
44,1
44,7
45,6
46,3
47,3
47,8
48,2
51,7
54,9
58,0
58,5
59,2
63,5
65,3
67,5
82,9
eSOH.Alt_15(09)
eSOH.Alt_15(08)
eFOH.Alt_15(09)
eFOH.Alt_15(08)
eMH.Alt_15(09)
eMH.Alt_15(08)
5,2
7,1
eMH.Alt_2b(09)
eMH.Alt_2b(08)
0,0
3,8
4,9
6,7
8,6
13,3
14,3
15,8
17,2
18,6
19,3
19,9
21,6
25,5
28,9
31,3
33,8
38,6
40,2
41,3
43,3
46,7
48,5
50,3
52,3
55,3
58,2
61,3
63,8
64,9
65,3
70,3
72,0
73,7
74,7
76,8
82,7
83,4
84,1
85,7
88,6
89,9
91,9
93,8
94,9
96,5
97,2
98,0
99,1
99,7
100,1
101,2
102,7
102,9
103,1
103,3
104,0
105,1
106,1
107,2
107,8
109,5
110,4
111,9
113,8
114,6
116,6
119,5
121,6
124,3
128,5
130,5
140,9
eFOH.Alt_2b(09)
eFOH.Alt_2b(08)
eSOH.C3_1(09)
eSOH.C3_1(08)
eFOH.C3_1(09)
eFOH.C3_1(08)
eMH.C3_1(09)
eMH.C3_1(08)
C3_1
Page 11 of 15
81,0
81,8
82,7
84,6
90,0
90,9
94,9
99,8
63,5
80,2
104,0
84,7
107,5
64,3
66,6
68,1
72,2
96,1
75,9
77,7
90,4
Figure 6 Location of earliness QTL for the main head (MH), the first order head (FOH) and the second order head (SOH). Only those LGs
(‘Romanesco C3’ LGs shown in yellow, ‘Altilis 41’ ones in blue) harbouring QTL are shown. Black and green bars represent 1-LOD support intervals
for each QTL detected in, respectively, “2008” and “2009”.
homologous to the ones detected in the same region of the
‘C3’ map, explained from 33-41% of the phenotypic variance and was associated with an additive effect of 9–11 days.
A second QTL, eMH.Alt_4, was detectable only in “2009”,
but its location suggested it to be identical with eMH.C3_2
(Figure 6). Further two minor QTL present on LGs Alt_2
and _15 accounted for, respectively, 8% and-11% of the
variance. Globally, the QTL identified in the ‘Romanesco
C3’ and ‘Altilis 41’ maps accounted for, respectively, 74%
and 62% of the phenotypic variance for main head harvesting time in “2008”.
Six eFOH QTL were detected, three of which were
represented in both parental maps, one on just the
‘Romanesco C3’ map, and the other two on just the ‘Altilis 41’ map. Five of the six QTL mapped to a region
where a eMH QTL was also located, with overlapping
LOD confidence intervals but with an overall lower
phenotypic effect. The exception was eFOH.Alt_6
(Table 6, Figure 6). As for eMH, the largest effect QTL
mapped to LGs C3_1 and Alt_2 in the neighbourhood of
CyEM_223. Based on the “2009” data, the set of eFOH
QTL accounted for 47% (‘Romanesco C3’) and 54%
(‘Altilis 41’) of the variation.
Only four eSOH QTL were uncovered, due to the
reduced heritability of this trait (h2B = 0.54, Table 4). All
four co-localized with eFOH QTLs, with an overall
lower phenotypic effect (Table 6, Figure 6), with the largest effect QTL mapping to the cluster on C3_1 and
Alt_2. Based on the “2009” data, the set of eSOH QTL
accounted for 48% (‘Romanesco C3’) and 43% (‘Altilis
41’) of the variation.
Conclusions
We have reported here an extension of the C. cardunculus genetic map by introducing SSR loci sited within
genic sequence. The integration of 139 of these loci has
significantly improved the resolution and accuracy of the
maps. Given that the genome size of the species is
~1.08Gbp [49], the mean equivalence between the physical and genetic length in this species is of the order of
1 cM to 670 kbp. Thus the mean physical separation of
the mapped markers is around 2.2Mbp. On this basis,
most gene sequences should lie within about 1Mbp of
the nearest marker, although this value makes the nonvalid assumption that recombination sites are randomly
distributed along the length of the chromosomes.
Shortening the life cycle is seen as an important breeding goal in terms of both globe artichoke’s economic
value, and the ease of exploiting cultivated cardoon as
an energy crop [13,14]. The newly developed consensus as
well as the parental genetic maps can accelerate the process
of tagging and eventually isolating the genes underlying
Portis et al. BMC Research Notes 2012, 5:252
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earliness in both the domesticated C. cardunculus forms.
We have shown that a cluster of large effect QTL
resides on the homologous LGs C3_1 and Alt_2, and
this clearly represents a reasonable candidate for marker assisted breeding. The critical genetic interval
contains two SSR loci (CELMS_40 and CyEM_223),
either of which is well-placed to serve as an indirect
selection criterion for earliness. Before such a genotypic selection programme can be implemented, however, a validation of the presence and importance of
the QTL needs to be conducted using different genetic backgrounds and in other relevant environments
[50,51]. To date, this study represents the first attempt to
identify QTL in C. cardunculus, which is the necessary
preliminary step for implementing marker-assisted selection for quantitative traits. Beyond tagging, mapping also prepares the ground for positional cloning,
which will enable the molecular basis of trait variation to be identified.
Methods
Plant material and SSR analysis
The 178 informative CyEM markers identified by Scaglione et al. [22] were used to genotype a set of 94 F1 hybrid (randomly selected from 154 true hybrids as
described by Portis et al. [17] from the cross’Romanesco
C3’(globe artichoke; female parent) x ‘Altilis 41’ (cultivated cardoon; male parent). A 7 ng aliquot of genomic
DNA from each mapping population individual was
amplified in a 10 μl reaction containing 1x PCR buffer,
1 mM MgCl2, 0.5U Taq DNA polymerase (Qiagen Inc.,
Venlo, Netherlands), 40nM 5’-labelled (FAM, HEX or
TAMRA) forward primer, 40 nM unlabelled reverse primer and 0.2 mM dNTP. A touchdown cycling regime
was applied, consisting of an initial denaturation of 94°C/
2.5 min, followed by nine cycles of 94°C/30s, 63°C/30s
(decreasing by 0.7°C per cycle), 72°C/60s, and 30 further
cycles of 94°C/30s, 57°C/30s, 72°C/60s. Where only weak
amplification was achieved, the MgCl2 concentration was
raised to 1.5 mM and the final annealing temperature was
lowered to 55°C. The amplicons were separated on an
ABI3730 capillary DNA sequencer (Applied Biosystem
Inc., Foster City, CA, USA). Internal ROX-labelled GS500
size standards were included in each capillary. The
output was analysed by GeneMapper v3.5 software
(Applied Biosystems).
Linkage analysis and parental maps construction
The CyEM genotypes of the 94 mapping population
individuals were combined with previous genotypic data
based on 605 AFLP, 27 S-SAP and 56 other SSRs [17],
along with ten SNP from genes underlying caffeoylquinic
acid synthesis (reported by Comino et al. [18] and
Menin et al. [19]). JoinMap v4.0 [52] was used to
Page 12 of 15
generate two separate linkage maps (one for each parent) using the double pseudo-testcross mapping strategy
[53]. The markers fell into three classes: maternal testcross markers segregating only in ‘Romanesco C3’
(expected segregation ratio 1:1); paternal testcross markers segregating only in ‘Altilis 41’ (1:1); and intercross
markers segregating within both parents (either 1:2:1 or
1:1:1:1). Differences between observed and expected segregation ratios were tested by χ2, and only markers deviating if at all only slightly from expectation
(χ2α=0.1 < χ2 ≤ χ2α=0.01) were used for map construction and
the estimation of genetic distances, when their presence
did not alter surrounding marker order in the LG. Heavily distorted loci (χ2 > χ2α=0.01), along with those associated with 30 or more missing values, were excluded.
LGs were established on the basis of an initial LOD
threshold of 6.0. Locus order and distances between loci
were established using the following parameter set: Rec =
0.40, LOD = 1.0, Jump = 5. Map distances were converted to cM using the Kosambi mapping function [54].
Where a locus order discrepancy arose between a pair of
parental LGs, the marker order of the ‘1:1:1:1’ segregating SSR and the marker order of SNP markers were
taken as the ‘fixed order’. Once the framework maps had
been established, additional loci were subsequently
added and some LGs merged by lowering the LOD
threshold to 5.0. On the resulting maps, loci suffering
from slight segregation distortion have been identified
with either one (χ2α=0.1 < χ2 ≤ χ2α=0.05) or two (χ2α=0.05 <
χ2 ≤ χ2α=0.01) asterisks. The ‘Romanesco C3’ LGs are labelled LG_C3, and the ‘Altilis 41’ ones LG_Alt, using the
numbering system suggested by Portis et al. [17].
Consensus map construction
A genotypic data set based on all the available markers
was then used to construct a consensus map. Here, the
loci belonging to two segregation classes ‘1:2:1’ (the
same pair of alleles segregating in each parent), and
‘1:1:1:1’ (different alleles segregating in each parent) were
used as ‘bridge markers’. The most likely locus order
was established from a comparison of the ‘C3’, ‘Alt’ and
consensus LGs, and where these differed substantially
from one another, the most likely order was assumed to
be one associated with the lowest χ2 value (estimating
goodness-of-fit) and the lowest mean χ2 contribution for
all loci. LGs were established on the basis of an initial
LOD threshold of 5.0 and numbered according to C3
maps LGs order.
Sequence annotation
Annotation of mapped sequences was carried out using
the Blast2Go software [55]. The best twenty BlastX
results were retrieved by querying the nr protein database at NCBI. Gene Ontology terms were retrieved
Portis et al. BMC Research Notes 2012, 5:252
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accordingly to software capabilities and transferred to
our sequences, adopting an annotation threshold of 55.
Additional GO terms were obtained performing InterPro
scan for conserved motif, using all available databases.
ANNEX function was used to obtain further GO terms
which are implicit on the base of electronically annotated ones.
Earliness evaluation and QTL analysis
The mapping population (154 F1 progeny of the cross
‘Romanesco C3’ (var. scolymus) x ‘Altilis 41’ (var. altilis)),
along with six clones of each parental line, was cultivated at the University of Catania's experimental station
(37°25’N; 15°30’E; 10 m a.s.l) and evaluated over the two
growing seasons 2007–2008 (hereafter referred to as
“2008”) and 2008–2009 (“2009”). In “2008”, seedlings at
the three true leaf stages (about 40 days after germination) were transferred to the field in mid September,
while in “2009”, the growing season was initiated by applying drip irrigation to field capacity in mid August.
Earliness was scored either as the number of days between transplanting (“2008”) or awakening (“2009”) and
harvesting of both the main (eMH trait) and first and
second order heads (obtained from the ramification of
the main stem: eFOH and eSOH traits). Population
means, standard deviations, distribution histograms and
trait correlations were calculated using R software [56].
Analyses of variance were based on treating each growing season as an independent replicate. The broad sense
heritability was given by the expression h2B = σ2g/(σ2g + σ2e/y),
where σ2g represented the genetic variance and σ2e the error
variance. Correlations between traits were estimated using
Pearson’s coefficient.
In the initial step of the QTL analysis, the consensus
map was used to assign putative locations by performing
a Kruskal-Wallis (KW) non-parametric test in conjunction with a simple interval mapping procedure (SIM)
[57], applying the cross-pollination algorithm implemented within MapQTL v4.0 software [58]. Next, the two
separate parental maps were employed for a re-analysis
based on the BC1 algorithm, using both SIM and multiple QTL mapping (MQM) [59]. Markers lying within a
putative QTL region and associated with the highest
LOD score were used as co-factors. For the MQM, a
backward elimination procedure was applied to select
the appropriate co-factors (significantly associated with
each trait at P < 0.02). The LOD thresholds for QTL significance were confirmed by a permutation test consisting of 1,000 replications, which implies a genome-wide
significance level of 0.05 [60]. Only those QTL associated with a LOD greater than either the genome-wide
threshold or the LG threshold were considered. 1-LOD
support intervals were determined for each LOD peak
[61]. The additive effect and the proportion of the
Page 13 of 15
overall phenotypic variance associated with each QTL
and all QTL together were estimated from the MQM
model. Linkage maps and QTL position were drawn
using MapChart [62].
Competing interests
The authors declare that they have no competing interests.
Authors' contributions
SL and SK planned and supervised the experimental work; GM and RM
cultivated the C. cardunculus parental accessions and the F1 individuals and
performed earliness trait evaluation over the two growing seasons; DS and
AA performed the genotyping of the progenies; EP and DS carried out
linkage analyses and map construction; EP performed QTL analysis; SL and
EP supervised the drafting of the manuscript. All authors read and approved
the final manuscript.
Acknowledgements
This research was supported by grants from: (i) the National Science
Foundation Plant Genome Research Program (No. 0421630), (ii) the Georgia
Research Alliance, (iii) the University of Georgia Research Foundation, and (iv)
by MIPAAF (Ministero delle Politiche Agricole, Alimentari e Forestali - Italy)
through the CYNERGIA (“Costituzione e valutazione dell’adattabilita’ di
genotipi di Cynara cardunculus per la produzione di biomassa e biodiesel in
ambiente mediterraneo”) project .
Author details
1
Di.Va.P.R.A. Plant Genetics and Breeding, University of Torino, via L. da Vinci
44, I-10095, Grugliasco, Torino, Italy. 2Dipartimento di Scienze delle
Produzioni Agrarie e Alimentari (DISPA) – sez. Scienze Agronomiche,
University of Catania, via Valdisavoia 5, I-95123, Catania, Italy. 3Department of
Crop and Soil Sciences and Center for Applied Genetic Technologies,
University of Georgia, 111 Riverbend Rd,
30602, Athens, GA, USA. 4Monsanto Company, Woodland, CA, USA.
Received: 30 April 2012 Accepted: 10 May 2012
Published: 23 May 2012
References
1. Basnitzki J, Zohary D: Breeding of seed planted artichoke. Plant Breeding
Reviews 1994, 12:253–269.
2. Schutz K, Kammerer D, Carle R, Schieber A: Identification and
quantification of caffeoylquinic acids and flavonolds from artichoke
(Cynara scolymus L.) heads, juice, and pomace by HPLC-DAD-ESI/MSn.
Journal of Agricultural and Food Chemistry 2004, 52(13):4090–4096.
3. Lombardo S, Pandino G, Mauromicale G, Knödler M, Carle R, Schieber M:
Influence of genotype, harvest time and plant part on polyphenolic
composition of globe artichoke [Cynara cardunculus var. scolymus (L.)
Fiori]. Food Chemistry 2010, 119:1175–1181.
4. Pandino G, Courts F, Lombardo S, Mauromicale G, Williamson G:
Caffeoylquinic acids and flavonoids in the immature inflorescence of
globe artichoke, wild cardoon, and cultivated cardoon. Journal of
Agricultural and Food Chemistry 2010, 58:1026–1031.
5. Pandino G, Lombardo S, Mauromicale G, Williamson G: Phenolic acids and
flavonoids in leaf and floral stem of cultivated and wild Cynara
cardunculus L. genotypes. Food Chemistry 2011, 126:417–422.
6. Lattanzio V, Kroon PA, Linsalata V, Cardinali A: Globe artichoke: a functional
food and source of nutraceutical ingredients. Journal of Functional Foods
2009, 1(2):131–144.
7. Menin B, Comino C, Portis E, Moglia A, Cankar K, Bouwmeester H, Lanteri S,
Beekwilder J: Genetic mapping and characterization of the globe
artichoke (+)-germacrene A synthase gene, encoding the first dedicated
enzyme for biosynthesis of the bitter sesquiterpene lactone
cynaropicrin. Plant Science 2005, 190:1–8
8. Cravotto G, Nano G, Binello A, Spagliardi P, Seu G: Chemical and biological
modification of cynaropicrin and grosheimin: a structure-bitterness
relationship study. Journal of the Science of Food and Agriculture 2005,
85:1757–1764.
9. Fritsche J, Beindorff C, Dachtler M, Zhang H, Lammers J: Isolation,
characterization and determination of minor artichoke (Cynara scolymus
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
L.) leaf extract compounds. European Food Research and Technology 2002,
215:149–157.
Foti S, Mauromicale G, Raccuia S, Fallico B, Fanella F, Maccarone E:
Possible alternative utilization of Cynara spp. I. Biomass, grain yield
and chemical composition of grain. Industrial Crops and Products 1999,
10:219–228.
Ierna A, Mauromicale G: Cynara cardunculus L. genotypes as a crop for
energy purposes in a Mediterranean environment. Biomass and Bioenergy
2010, 34:754–760.
Encinar J, Gonzalez J, Rodriguez J, Tejedor A: Biodiesel fuels from
vegetable oils: Transesterification of Cynara cardunculus L. oils with
ethanol. Energy and Fuels 2002, 16(2):443–450.
Portis E, Acquadro A, Longo A, Mauro R, Mauromicale G, Lanteri S:
Potentiality of Cynara cardunculus L. as energy crop. Journal of
Biotechnology 2010, 150:165–166.
Acquadro A, Portis E, Scaglione D, Mauro RP, Campion B, Falavigna A,
Zaccardelli R, Ronga D, Perrone D, Mauromicale G, et al: Cynara
cardunculus L.: From Vegetable to Energy Crop. In Proceedings of the Joint
Meeting AGI-SIBV-SIGA. Società Italiana di Genetica Agraria (ed): 2011,
http://www.geneticagraria.it/Abstract_2011/5C_12.pdf
Lanteri S, Acquadro A, Comino C, Mauro R, Mauromicale G, Portis E: A first
linkage map of globe artichoke (Cynara cardunculus var. scolymus L.)
based on AFLP, S-SAP, M-AFLP and microsatellite markers. Theoretical
and Applied Genetics 2006, 112(8):1532–1542.
Acquadro A, Lanteri S, Scaglione D, Arens P, Vosman B, Portis E: Genetic
mapping and annotation of genomic microsatellites isolated from globe
artichoke. Theoretical and Applied Genetics 2009, 118:1573–1587.
Portis E, Mauromicale G, Mauro R, Acquadro A, Scaglione D, Lanteri S:
Construction of a reference molecular linkage map of globe artichoke
(Cynara cardunculus var. scolymus). Theoretical and Applied Genetics 2009,
120:59–70.
Comino C, Hehn A, Moglia A, Menin B, Bourgaud F, Lanteri S, Portis E: The
isolation and mapping of a novel hydroxycinnamoyltransferase in the
globe artichoke chlorogenic acid pathway. BMC Plant Biology 2009, 9:30.
Menin B, Comino C, Moglia A, Dolzhenko Y, Portis E, Lanteri S:
Identification and mapping of genes related to caffeoylquinic acid
synthesis in Cynara cardunculus L. Plant Science 2010, 179(4):338–347.
Lanteri S, Portis E, Acquadro A, Mauro RP, Mauromicale G: Morphology and
SSR fingerprinting of newly developed Cynara cardunculus genotypes
exploitable as ornamentals. Euphytica 2012, 184:311–321.
Sonnante G, Gatto A, Morgese A, Montemurro F, Sarli G, Blanco E, Pignone
D: Genetic map of artichoke x wild cardoon: toward a consensus map
for Cynara cardunculus. Theoretical and Applied Genetics 2011,
123(7):1215–1229.
Scaglione D, Acquadro A, Portis E, Taylor C, Lanteri S, Knapp S: Ontology
and diversity of transcript-associated microsatellites mined from a globe
artichoke EST database. BMC Genomics 2009, 10:454.
Lorieux M, Goffinet B, Perrier X, Deleon D, Lanaud C: Maximum-likelihood
models for mapping genetic markers showing segregation distortion. 1.
Backcross populations. Theoretical and Applied Genetics 1995, 90:73–80.
Lorieux M, Perrier X, Goffinet B, Lanaud C, Deleon D: Maximum-likelihood
models for mapping genetic markers showing segregation distortion. 2.
F2 populations. Theoretical and Applied Genetics 1995, 90:81–89.
Bradshaw H, Villar M, Watson B, Otto K, Stewart S, Stettler R: Molecular
genetics of growth and development in Populus. 3. A genetic-linkage
map of a hybrid poplar composed of RFLP, STS and RAPD markers.
Theoretical and Applied Genetics 1994, 89(2–3):167–178.
Pekkinen M, Varvio S, Kulju K, Karkkainen H, Smolander S, Vihera-Aarnio A,
Koski V, Sillanpaa M: Linkage map of birch, Betula pendula Roth, based on
microsatellites and amplified fragment length polymorphisms. Genome
2005, 48(4):619–625.
Rodzen J, May B: Inheritance of microsatellite loci in the white sturgeon
(Acipenser transmontanus). Genome 2002, 45:1064–1076.
Shaw P, Turan C, Wright J, O'Connell M, Carvalho G: Microsatellite DNA
analysis of population structure in Atlantic herring (Clupea harengus),
with direct comparison to allozyme and mtDNA RFLP analyses. Heredity
1999, 83:490–499.
Van Oosterhout C, Hutchinson W, Wills D, Shipley P: MICRO-CHECKER:
software for identifying and correcting genotyping errors in
microsatellite data. Molecular Ecology Notes 2004, 4:535–538.
Page 14 of 15
30. Arens P, Odinot P, Vanheusden A, Lindhout P, Vosman B: GATA repeats
and GACA repeats are not evenly distributed throughout the tomato
genome. Genome 1995, 38(1):84–90.
31. Bhattramakki D, Dong J, Chhabra A, Hart G: An integrated SSR and RFLP
linkage map of Sorghum bicolor (L.) Moench. Genome 2000,
43(6):988–1002.
32. Gill G, Wilcox P, Whittaker D, Winz R, Bickerstaff P, Echt C, Kent J,
Humphreys M, Elborough K, Gardner R: A framework linkage map of
perennial ryegrass based on SSR markers. Genome 2006,
49(4):354–364.
33. Jones E, Dupal M, Dumsday J, Hughes L, Forster J: An SSR-based genetic
linkage map for perennial ryegrass (Lolium perenne L.). Theoretical and
Applied Genetics 2002, 105(4):577–584.
34. McCouch S, Teytelman L, Xu Y, Lobos K, Clare K, Walton M, Fu B, Maghirang
R, Li Z, Xing Y, et al: Development and mapping of 2240 new SSR
markers for rice (Oryza sativa L.). DNA Research 2002, 9(6):199–207.
35. Ramsay L, Macaulay M, Ivanissevich S, MacLean K, Cardle L, Fuller J, Edwards
K, Tuvesson S, Morgante M, Massari A, et al: A simple sequence repeatbased linkage map of barley. Genetics 2000, 156(4):1997–2005.
36. Fishman L, Kelly AJ, Morgan E, Willis JH: A genetic map in the Mimulus
guttatus species complex reveals transmission ratio distortion due to
heterospecific interactions. Genetics 2001, 159(4):1701–1716.
37. Lyttle T: The Genetics and Evolutionary Biology of Meiotic Drive Preface. American Naturalist 1991, 137(3):281–282.
38. Xu Y, Zhu L, Xiao J, Huang N, McCouch S: Chromosomal regions
associated with segregation distortion of molecular markers in F-2,
backcross, doubled haploid, and recombinant inbred populations in rice
(Oryza sativa L). Molecular and General Genetics 1997, 253:535–545.
39. Faris J, Laddomada B, Gill B: Molecular mapping of segregation distortion
loci in Aegilops tauschii. Genetics 1998, 149:319–327.
40. Lu H, Romero-Severson J, Bernardo R: Chromosomal regions associated
with segregation distortion in maize. Theoretical and Applied Genetics 2002,
105(4):622–628.
41. Kleinhofs A, Kilian A, Maroof M, Biyashev R, Hayes P, Chen F, Lapitan N,
Fenwick A, Blake T, Kanazin V, et al: A molecular, isozyme and
morphological map of the barley (Hordeum vulgare) genome. Theoretical
and Applied Genetics 1993, 86(6):705–712.
42. Ky C, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon
S, Noirot M: Interspecific genetic linkage map, segregation distortion and
genetic conversion in coffee (Coffea sp.). Theoretical and Applied Genetics
2000, 101:669–676.
43. Taylor D, Ingvarsson P: Common features of segregation distortion in
plants and animals. Genetica 2003, 117:27–35.
44. Lanteri S, Saba E, Cadinu M, Mallica G, Baghino L, Portis E: Amplified
fragment length polymorphism for genetic diversity assessment in
globe artichoke. Theoretical and Applied Genetics 2004, 108(8):1534–1544.
45. Portis E, Barchi L, Acquadro A, Macua J, Lanteri S: Genetic diversity
assessment in cultivated cardoon by AFLP (amplified fragment length
polymorphism) and microsatellite markers. Plant Breeding 2005, 124
(3):299–304.
46. Shao F, Merritt P, Bao Z, Innes R, Dixon J: A Yersinia effector and a
Pseudomonas avirulence protein define a family of cysteine proteases
functioning in bacterial pathogenesis. Cell 2002, 109(5):575–588.
47. Penalver R, Duranvila N, Lopez MM: Characterization and pathogenicity of
bacteria from shoot tips of the globe artichoke (Cynara-scolymus L).
Annals of Applied Biology 1994, 125(3):501–513.
48. Cabezas JA, Cervera MT, Ruiz-Garcia L, Carreno J, Martinez-Zapater JM: A
genetic analysis of seed and berry weight in grapevine. Genome 2006,
49(12):1572–1585.
49. Marie D, Brown S: A cytometric exercise in plant DNA histograms, with 2
C-values for 70 species. Biology of the Cell 1993, 78(1–2):41–51.
50. Melchinger AE, Utz HF, Schon GC: QTL analyses of complex traits with
cross validation, bootstrapping and other biometric methods. Euphytica
2004, 137(1):1–11.
51. Cloutier S, Ragupathy R, Niu ZX, Duguid S: SSR-based linkage map of flax
(Linum usitatissimum L.) and mapping of QTLs underlying fatty acid
composition traits. Molecular Breeding 2011, 28(4):437–451.
52. Van Ooijen JW: JoinMapW v.4, Software for the calculation of genetic linkage
maps in experimental populations. Wageningen, Netherlands: Kyazma BV;
2006.
Portis et al. BMC Research Notes 2012, 5:252
http://www.biomedcentral.com/1756-0500/5/252
Page 15 of 15
53. Weeden N: Approaches to mapping in horticultural crops. In Gressho. PM
(ed) Plant genome analysis.: CRC Press Boca Raton; 1994:57–68.
54. Kosambi D: The estimation of map distances from recombination values.
In.Ann Eugen 1944, 12:172–175.
55. Conesa A, Gotz S, Garcia-Gomez J, Terol J, Talon M, Robles M: Blast2GO: a
universal tool for annotation, visualization and analysis in functional
genomics research. Bioinformatics 2005, 21(18):3674–3676.
56. R Development Core Team: R: a language and environment for statistical
computing Version 2.11.1. Vienna, Austria: R Foundation for Statistical
Computing (ed), 2008, ISBN 3-900051-07-0, URL http://www.R-project.org.
57. Lander ES, Botstein D: Mapping mendelian factors underlying
quantitative traits using RFLP linkage maps. Genetics 1989,
121(1):185–199.
58. Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C: MapQTL 4.0: Software for
the calculation of QTL positions on genetic maps. Wageningen, The
Netherlands: Plant Research International (ed); 2002.
59. Jansen RC, Stam P: High-resolution of quantitative traits into multiple loci
via interval mapping. Genetics 1994, 136(4):1447–1455.
60. Churchill GA, Doerge RW: Empirical threshold values for quantitative trait
mapping. Genetics 1994, 138(3):963–971.
61. Van Ooijen JW: Accuracy of mapping quantitative trait loci in
autogamous species. Theoretical and Applied Genetics 1992,
84(7–8):803–811.
62. Voorrips R: MapChart: Software for the graphical presentation of linkage
maps and QTLs. Journal of Heredity 2002, 93(1):77–78.
63. Acquadro A, Portis E, Lanteri S: Isolation of microsatellite loci in artichoke
(Cynara cardunculus L. var. scolymus). Molecular Ecology Notes 2003,
3(1):37–39.
64. Acquadro A, Portis E, Lee D, Donini P, Lanteri S: Development and
characterization of microsatellite markers in Cynara cardunculus L.
Genome 2005, 48(2):217–225.
65. Acquadro A, Portis E, Albertini E, Lanteri S: M-AFLP-based protocol for
microsatellite loci isolation in Cynara cardunculus L. (Asteraceae).
Molecular Ecology Notes 2005, 5(2):272–274.
66. Sonnante G, Carluccio A, De Paolis A, Pignone D: Identification of
artichoke SSR markers: molecular variation and patterns of diversity in
genetically cohesive taxa and wild allies. Genetic Resources and Crop
Evolution 2008, 55(7):1029–1046.
doi:10.1186/1756-0500-5-252
Cite this article as: Portis et al.: Genetic mapping and identification of
QTL for earliness in the globe artichoke/cultivated cardoon complex.
BMC Research Notes 2012 5:252.
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