Supplementary Table S1 Literature data on QTLs detected on pepper chromosome P5 for resistance to P. capsici
Reference
Lefebvre and
Palloix (1996) (a)
Thabuis et al.
(2003)
Thabuis et al.
(2004a)
Thabuis et al.
(2004b)
Ogundiwin et al.
(2005)
Sugita et al. (2006)
Bonnet et al.
(2007)
Minamiyama et al.
(2007)
Kim et al. (2008)
Truong et al.
(2012)
Resistant
parent
Perennial
Mapping progeny (d)
114 DH (PY)
P. capsici isolate
Name
Origin
Pc101 (e)
France
QTL name
Linked markers
LOD score
Vania (b)
Perennial
101 DH (HV)
114 DH (PY)
Pc101 (e)
Pc101 (e)
France
France
CM334
151 F2 (F2YC)
Pc197 (e)
France
CM334
450 BC (Morelos)
Pc101 (e)
Perennial
620 BC (BC1S1(DH285))
PI201234
94 RIL F7 (PSP-11xPI201234)
CM334
AC2258 (b)
CM334
94 F2 (JoeE.ParkerxCM334)
176 DH (K9-11xAC2258)
297 RIL F5 (F5YC)
CM334
96 DH (ManganjixCM334)
CM334
YCM334 (c)
NA
Confidence
interval
NA
NA
TG483
France
Pc5.1
Pc5.1
Pc5.2
Pc5.1
Pc5.2
Phyto.5.2
Pc101 (e)
France
PC17E
GPS1-1
M
Keihoku
Pc197 (e)
Taiwan
California
New Mexico
Japan
France
P-5
Japan
100 F2 (CM334xChilsungcho)
Pa23
South Korea
126 RIL F8 (YCM334 x Tean)
09-051
South Korea
07-127
South Korea
R²
41 to 55%
6.9 to 26.0
2.3 to 24.9
3.4 to 6.4
4.4 to 35.7
15.3
NA
NA
NA
NA
NA
NA
NA
17 to 54%
10 to 74%
6 to 26%
21 to 70%
42%
16%
Pc5.1
E38M61-139
E43M53-159
E33M53-Cp
E43M53-159
E36M47-183
E38M61-249/E38M61220
E43M53-159/ASC037
NA
NA
71%
Phyto-P
Phyto-P
Phyto-U
Phyt-1
Pc5.1
Pc5.2
NA
H03b909/Hpms2-23
H03b909/Hpms2-23
J12b1480/E33M49-434
M10E3-6
Mfvt_M02
E41M61-348
CAMS420
2.5
4.3
6.2
67.0
14.3 to 33.9
11.5
10.6 to 16.1
7.0 cM
7.0 cM
42.3 cM
85.0 cM
10.0 cM
5.0 cM
NA
16%
22%
35%
83%
20 to 53%
24%
40 to 58%
NA
NA
Ph051-5.1
Ph051-5.2
Ph051-5.3
Ph051-5.4
Ph0127-5.5
Ph0127-5.6
Ph0127-5.7
HpmsE015/pR5_93
CDI78/CDI25
a015_7/a133_4
a133_4/a170_1
a015_7/a133_4
a133_4/a170_1
a057-6/a133_4
a133_4/a170_1
a057_6/a119_7
2.2 to 2.4
4.6 to 10.5
7.1
13.4
8.3
15.4
16.6
21.6
20.6
30.0 cM
9.3 cM
8.6 cM
8.4 cM
8.1 cM
8.3 cM
4.1 cM
6.2 cM
4.7 cM
8 to 9%
19 to 42%
20%
34%
22%
37%
40%
47%
48%
NA: Not available
(a) While this QTL was not linked to any chromosome by Lefebvre and Palloix (1996), the linked RFLP marker TG483 was later mapped to chromosome P5
(Lefebvre et al. 2002).
(b) Thabuis et al. (2003) indicated that Vania was issued from a recurrent selection including in its genealogy PM217 that is derived from PI201234. Sugita et al.
(2006) indicated that AC2258 was derived from PI201234.
(c) YCM334 is an F6 RIL derived from the cross Yolo Wonder x CM334 developed at INRA Montfavet France (Bonnet et al. 2007).
(d) Progeny size, population type (DH: doubled haploids, RIL: recombinant inbred lines, F2: second generation progeny, BC: backcross progeny), name of the
cross in brackets.
(e) Names of INRA strains were formerly S101 and S197.
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Supplementary Table S2 Resistance/susceptibility allele configuration at QTL Pc5.1 for resistance against P. capsici in the 19 progeny lines and parental lines
assessed for the resistance spectrum
Plant Genotype
CM334
YW
F6YC-009
F6YC-017
F6YC-034
F6YC-038
F6YC-055
F6YC-125
F6YC-247
F6YC-277
Vania
H3
HV-021
HV-023
HV-038
HV-040
HV-057
HV-122
Perennial
YW
PY-238
PY-253
PY-255
PY-260
PY-279
Pc5.1
R
S
R
R
S
R
S
R
R
R
R
S
S
R
R
S
R
S
R
S
S
S
R
R
S
R: alleles of the markers within the QTL CI are associated with resistance in the progeny.
S: alleles of the markers within the QTL CI are associated with susceptibility in the progeny.
2
Supplementary Table S3 List of pepper maps included in the chromosome P5 consensus map
(a)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
Map
identifier
AC99-1
PY
HV
F5YC
CC
TH-1
TH-2
KA
MC
AC99-2
FA03-1
YCT
JC
FA03-2
Parental cross
C. annuum cv. “NuMex RNaky” x C. chinense PI 159234
C. annuum Perennial x C. annuum CM334
C. annuum H3 x C. annuum Vania
C. annuum cv. "Yolo Wonder" x C. annuum CM334
C. annuum CM334 x C. annuum Chilsungcho
C. annuum cv. "TF68" x C. chinense cv. "Habanero"
C. annuum cv. "TF68" x C. chinense cv. "Habanero"
C. annuum K9-11 x C. annuum cv. "AC2258"
C. annuum cv. "Manganji" x C. annuum CM334
C. annuum cv. "NuMex RNaky" x C. chinense PI 159234
C. annuum cv. "NuMex Rnaky" x C. frutescens BG 2814-6
C.annuum YCM334 RIL F6 x C.annuum cv. "Tean"
C. annuum cv. "JEP" x C. annuum CM334
C. annuum cv. "NuMex Rnaky" x C. frutescens BG 2814-6
Cross
type
(b)
Progeny
size
Number of
markers from
chromosome P5
F2
DH
DH
RIL F5
F2
F2
F2
DH
DH
F2
F2
RIL F8
F2
F2
75
114
101
297
100
107
107
176
96
100
100
126
94
94
11
21
20
43
10
14
13
24
8
16 (c)
27 (c)
16
5
25 (c)
Reference
(Livingstone et al. 1999; Quirin et al. 2005)
(Lefebvre and Palloix 1996; Thabuis et al. 2003); this paper
(Thabuis et al. 2003); this paper
(Barchi et al. 2007); this paper
(Kim et al. 2008)
(Yi et al. 2006)
(Lee et al. 2004)
(Sugita et al. 2006)
(Minamiyama et al. 2007)
Sol Genomic Network
Sol Genomic Network; (Rao et al. 2003)
(Truong et al. 2012)
(Ogundiwin et al. 2005; Quirin et al. 2005)
(Wu et al. 2009)
(a) Order of projection: the markers on individual maps of chromosome P5 were iteratively projected onto the reference P5 map of Livingstone et al. (1999) in the
order presented in this table.
(b) F2: second generation progeny, DH: doubled haploids, RIL: recombinant inbred lines.
(c) We used only markers that were regularly distributed and improved the anchorage between maps of chromosome P5 containing resistance QTLs to P. capsici.
3
4
Supplementary Figure S1 UWNJ phenetic tree reflecting genomic similarities between the four P. capsici isolates,
Pc101, Pc107, Pc197 and Pc204, based on the Jaccard coefficient using 97 AFLP markers and 28 SSR markers
Root branching of the outgroup is indicated by the point on the main branch. Bootstrap values are shown.
5