Supplementary Table S1Literature data on QTLs detected on pepper chromosome P5 for resistance to P.capsici
Reference / Resistant parent / Mapping progeny (d) / P.capsici isolate / QTL name / Linked markers / LOD score / Confidence interval / R²Name / Origin
Lefebvre and Palloix (1996) (a) / Perennial / 114 DH (PY) / Pc101 (e) / France / NA / TG483 / NA / NA / 41 to 55%
Thabuis et al. (2003) / Vania (b) / 101 DH (HV) / Pc101 (e) / France / Pc5.1 / E38M61-139 / 6.9 to 26.0 / NA / 17 to 54%
Perennial / 114 DH (PY) / Pc101 (e) / France / Pc5.1 / E43M53-159 / 2.3 to 24.9 / NA / 10 to 74%
Pc5.2 / E33M53-Cp / 3.4 to 6.4 / NA / 6 to 26%
CM334 / 151 F2 (F2YC) / Pc197 (e) / France / Pc5.1 / E43M53-159 / 4.4 to 35.7 / NA / 21 to 70%
Pc5.2 / E36M47-183 / 15.3 / NA / 42%
Thabuis et al. (2004a) / CM334 / 450 BC (Morelos) / Pc101 (e) / France / Phyto.5.2 / E38M61-249/E38M61-220 / NA / NA / 16%
Thabuis et al. (2004b) / Perennial / 620 BC (BC1S1(DH285)) / Pc101 (e) / France / Pc5.1 / E43M53-159/ASC037 / NA / NA / 71%
Ogundiwin et al. (2005) / PI201234 / 94 RIL F7 (PSP-11xPI201234) / PC17E / Taiwan / Phyto-P / H03b909/Hpms2-23 / 2.5 / 7.0 cM / 16%
GPS1-1 / California / Phyto-P / H03b909/Hpms2-23 / 4.3 / 7.0 cM / 22%
CM334 / 94 F2 (JoeE.ParkerxCM334) / M / New Mexico / Phyto-U / J12b1480/E33M49-434 / 6.2 / 42.3 cM / 35%
Sugita et al. (2006) / AC2258 (b) / 176 DH (K9-11xAC2258) / Keihoku / Japan / Phyt-1 / M10E3-6 / 67.0 / 85.0 cM / 83%
Bonnet et al. (2007) / CM334 / 297 RIL F5 (F5YC) / Pc197 (e) / France / Pc5.1 / Mfvt_M02 / 14.3 to 33.9 / 10.0 cM / 20 to 53%
Pc5.2 / E41M61-348 / 11.5 / 5.0 cM / 24%
Minamiyama et al. (2007) / CM334 / 96 DH (ManganjixCM334) / P-5 / Japan / NA / CAMS420 / 10.6 to 16.1 / NA / 40 to 58%
Kim et al. (2008) / CM334 / 100 F2 (CM334xChilsungcho) / Pa23 / South Korea / NA / HpmsE015/pR5_93 / 2.2 to 2.4 / 30.0 cM / 8 to 9%
NA / CDI78/CDI25 / 4.6 to 10.5 / 9.3 cM / 19 to 42%
Truong et al. (2012) / YCM334 (c) / 126 RIL F8 (YCM334 x Tean) / 09-051 / South Korea / Ph051-5.1 / a015_7/a133_4 / 7.1 / 8.6 cM / 20%
Ph051-5.2 / a133_4/a170_1 / 13.4 / 8.4 cM / 34%
Ph051-5.3 / a015_7/a133_4 / 8.3 / 8.1 cM / 22%
Ph051-5.4 / a133_4/a170_1 / 15.4 / 8.3 cM / 37%
07-127 / South Korea / Ph0127-5.5 / a057-6/a133_4 / 16.6 / 4.1 cM / 40%
Ph0127-5.6 / a133_4/a170_1 / 21.6 / 6.2 cM / 47%
Ph0127-5.7 / a057_6/a119_7 / 20.6 / 4.7 cM / 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.
Supplementary Table S2Resistance/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
CM334 / R
YW / S
F6YC-009 / R
F6YC-017 / R
F6YC-034 / S
F6YC-038 / R
F6YC-055 / S
F6YC-125 / R
F6YC-247 / R
F6YC-277 / R
Vania / R
H3 / S
HV-021 / S
HV-023 / R
HV-038 / R
HV-040 / S
HV-057 / R
HV-122 / S
Perennial / R
YW / S
PY-238 / S
PY-253 / S
PY-255 / R
PY-260 / R
PY-279 / 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.
Supplementary Table S3List of pepper maps included in the chromosome P5 consensus map
(b) / Progeny size / Number of markers from chromosome P5 / Reference
1 / AC99-1 / C. annuum cv. “NuMex RNaky” x C. chinense PI 159234 / F2 / 75 / 11 / (Livingstone et al. 1999; Quirin et al. 2005)
2 / PY / C. annuum Perennial x C. annuum CM334 / DH / 114 / 21 / (Lefebvre and Palloix 1996; Thabuis et al. 2003); this paper
3 / HV / C. annuum H3 x C. annuum Vania / DH / 101 / 20 / (Thabuis et al. 2003); this paper
4 / F5YC / C. annuum cv. "Yolo Wonder" x C. annuum CM334 / RIL F5 / 297 / 43 / (Barchi et al. 2007); this paper
5 / CC / C. annuum CM334 x C. annuum Chilsungcho / F2 / 100 / 10 / (Kim et al. 2008)
6 / TH-1 / C. annuum cv. "TF68" x C. chinense cv. "Habanero" / F2 / 107 / 14 / (Yi et al. 2006)
7 / TH-2 / C. annuum cv. "TF68" x C. chinense cv. "Habanero" / F2 / 107 / 13 / (Lee et al. 2004)
8 / KA / C. annuum K9-11 x C. annuum cv. "AC2258" / DH / 176 / 24 / (Sugita et al. 2006)
9 / MC / C. annuum cv. "Manganji" x C. annuum CM334 / DH / 96 / 8 / (Minamiyama et al. 2007)
10 / AC99-2 / C. annuum cv. "NuMex RNaky" x C. chinense PI 159234 / F2 / 100 / 16 (c) / Sol Genomic Network
11 / FA03-1 / C. annuum cv. "NuMex Rnaky" x C. frutescens BG 2814-6 / F2 / 100 / 27 (c) / Sol Genomic Network; (Rao et al. 2003)
12 / YCT / C.annuum YCM334 RIL F6 x C.annuum cv. "Tean" / RIL F8 / 126 / 16 / (Truong et al. 2012)
13 / JC / C. annuum cv. "JEP" x C. annuum CM334 / F2 / 94 / 5 / (Ogundiwin et al. 2005; Quirin et al. 2005)
14 / FA03-2 / C. annuum cv. "NuMex Rnaky" x C. frutescens BG 2814-6 / F2 / 94 / 25 (c) / (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.
1
Supplementary Figure S1UWNJ 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.
1