Table S1 Molecular markers used in this study

Marker / Primer sequence (5'-3')a
CONTIG9303 / CAAGGTTCTTGGTCCACATGC
CAGTTACCACAGGCTTACCAG
CONTIG6473 / GGAGAAGGCGCTAACAACGG
CGTTCTCTCATCGGAAGGTAGC
7890upSNP_2 / GTGGGGTTTAGTTTGAAGTTGG
CCATCACTAACCTACACACTC
SNP002466_2 / GGTGCTTCTTCATTGATGGCC
CCAATCCATCCTCTGAAAATCC
Phyto5NBS1 / TTGATAGCCCCTGGTAAAGA
GGGCAAACTTATAGTGGTG
Phyto5SAR / GGCACAACAATAGTCACAACGG
GAGACTAAGAAAGTTGGACGCC
Phyto5NBS2_1 / GCAGCAACTGCGGCACATTG
GTCCCACTCTAGGGGTTATGTTC
Phyto5NBS2_2 / CCCAGAGCAACATAACAATAGAC
GGAACAGCAATAATCGCCAGA
CONTIG1820 / GCAAGGAGAAATCAACAGAGCC
AATACAAAGAACGCAGTAGGAGGG
907783 / GACTCCATTTTCATGTTAGCGTGC
CTTGCACCTGGTAAACAACGC
IB1556 / TGAAGCAAGAGCCTGGTACG
TGAACCATTCACTCGCACCT
IB1558 / TGGCTGAAACCAGGAGGTCT
TACCGATCTGGATGCGTCAC
CONTIG1896 / CATAACACAACCCAATTGCAGAACC
GTCCTACACTTGTTACAGCTGCC
KS14035C05 / GCACGAGGAGATAGGTCAAATG
CATTGGCTGAAGTTGAACTCCG
CONTIG5473 / TACACTAGGGACGATGAGCAG
GTAGTCCCTCTTCAATTTCCC
KS17024G04 / GCACGAGGGCTGCTCAGTCG
GGCTGGAGGCGTCTGTTTCGC
KS17054F01 / CGAAGATGACAGATTTGGATGGG
CATACCTGGTTCTCCGTTTGC

a For each marker, the forward primer is listed above the reverse primer.

Table S2 Candidate genes for P. capsici resistance in scaffold194 linked to the major QTL

Location (kbp) / Annotation / E value /
55.0 / partial putative RLK protein / 8.00E-59
138.2 / partial putative RLK protein / 2.00E-34
161.1 / partial putative NBS-LRR / 1.00E-71
162.2 / partial putative NBS-LRR / 1.00E-107
166.9 / partial putative RLK protein / 2.00E-83
389.5 / partial putative RLK protein / 3.00E-54
395.9 / putative NBS-LRR / 0
528.4 / partial putative RLK protein / 1.00E-58
648.6 / partial putative RLK protein / 7.00E-10
819.0 / partial putative RLK protein / 2.00E-69
823.5 / partial putative RLK protein / 1.00E-62
829.4 / partial putative RLK protein / 8.00E-71
1050.3 / partial putative RLK protein / 1.00E-13
1258.3 / partial putative RLK protein / 5.00E-29
1264.3 / partial putative RLK protein / 1.00E-18
1374.3 / partial putative RLK protein / 2.00E-38
1414.3 / partial putative RLK protein / 1.00E-40
1464.3 / partial putative RLK protein / 2.00E-32
1485.3 / partial putative RLK protein / 1.00E-66
1503.3 / partial putative RLK protein / 3.00E-31
1634.3 / partial putative RLK protein / 9.00E-25
1798.3 / partial AIG-like protein / 3.00E-18
1820.9 / partial putative NBS-LRR / 2.00E-82
1942.0 / partial putative RLK protein / 9.00E-36
1956.3 / partial putative RLK protein / 2.00E-17
1961.5 / partial putative RLK protein / 1.00E-11
2005.4 / partial putative RLK protein / 4.00E-37
2058.7 / SAR8.2A / 8.00E-117
2140.4 / partial putative RLK protein / 3.00E-20
2149.8 / partial putative RLK protein / 8.00E-06
2361.0 / partial putative RLK protein / 3.00E-18
2390.5 / partial putative RLK protein / 4.00E-07
2415.4 / partial putative RLK protein / 8.00E-08
2480.1 / partial putative RLK protein / 2.00E-76
2936.4 / partial putative RLK protein / 3.00E-57
2939.6 / partial putative NBS-LRR / 2.00E-100
2957.0 / partial putative NBS-LRR / 5.00E-91
2961.1 / putative NBS-LRR / 0
3054.2 / partial putative RLK protein / 8.00E-68
3165.3 / partial putative RLK protein / 3.00E-21
3168.7 / partial putative NBS-LRR / 0.057
3243.9 / partial putative RLK protein / 3.00E-105
3260.7 / partial putative RLK protein / 3.00E-126
3372.1 / partial putative RLK protein / 1.00E-74

Table S3 Validation of scaffold194 markers by testing commercial F1 hybrids

No. / Cultivar / Company / Genotype by Markera / Phenotype by P. capsici isolateb
Phyto5NBS1 / Phyto5NBS2_1 / Phyto5NBS2_2 / MY-1 / KPC-1 / JHAI1-7 / KPC-7
1 / PR shinnara / Nongwoo / H / H / H / 0 / 0 / 0 / 0
2 / Tantandaemok / Nongwoo / H / R / R / 0 / 0 / 0 / 0
3 / Dokyachungchung / Syngenta / H / H / H / 0 / 0 / 0 / 6
4 / Ilsongjeong / Syngenta / H / H / H / 0 / 0 / 0 / 23
5 / Giribbarksoo / Syngenta / H / H / H / 0 / 0 / 0 / 35
6 / PR power / Nongwoo / H / H / H / 0 / 0 / 3 / 33
7 / PR awoollim / Nongwoo / H / H / H / 0 / 0 / 5 / 25
8 / Bakjangdaeso / Syngenta / H / H / H / 0 / 0 / 5 / 91
9 / Muhanjilju / Syngenta / H / H / H / 0 / 0 / 7 / 3
10 / Chunnyunmannyun / Syngenta / H / H / H / 0 / 0 / 7 / 25
11 / PR kummaek / Nongwoo / H / H / H / 0 / 0 / 10 / 35
12 / PR sangsaeng / Nongwoo / H / H / H / 0 / 0 / 15 / 55
13 / PR yeoljeong / Nongwoo / H / H / H / 0 / 0 / 15 / 67
14 / PR hongdukkae / Koregon seed / H / H / H / 0 / 0 / 50 / 57
15 / PR manitta / Nongwoo / H / H / H / 0 / 5 / 7 / 42
16 / Shinsegae / Sakata korea / H / H / H / 0 / 5 / 8 / 0
17 / Man sahyeongtong / Syngenta / H / H / H / 0 / 5 / 14 / 92
18 / Anjeonbelt / Sakata korea / H / H / H / 0 / 5 / 44 / 30
19 / Ilinja / Syngenta / H / H / H / 0 / 7 / 16 / 58
20 / Gungyeilhak / Syngenta / H / H / H / 0 / 10 / 0 / 10
21 / Ildeongkongshin / Syngenta / H / H / H / 0 / 10 / 0 / 25
22 / PR mansei / Nongwoo / H / H / H / 0 / 10 / 2 / 63
23 / Taesan / Nongwoo / H / H / H / 0 / 10 / 52 / 100
24 / PR jangwonkubje / Koregon seed / H / H / H / 0 / 10 / 70 / 82
25 / PR ukmankem / Koregon seed / H / H / H / 0 / 23 / 22 / 47
26 / Seonkuja / Syngenta / H / H / H / 0 / 24 / 8 / 60
27 / PR daechon / Nongwoo / H / H / H / 0 / 40 / 18 / 52
28 / Dokbulwang / Sakata korea / H / H / H / 0 / 43 / 42 / 83
29 / Kangryukjosangkun / Nongwoo / H / H / H / 0 / 48 / 73 / 93
30 / PR sun / Nongwoo / H / R / S / 0 / 50 / 65 / 100
31 / Josangshintop / Nongwoo / H / H / H / 0 / 52 / 72 / 48
32 / PR hwanhosung / Takii Korea / H / H / H / 1 / 10 / 14 / 24
33 / Hongmeein / Nongwoo / H / H / H / 1 / 10 / 19 / 81
34 / PR keosang / Koregon seed / H / H / H / 1 / 22 / 13 / 50
35 / Katakuruma / Sakata korea / H / R / R / 2 / 3 / 18 / 25
36 / Hanpansung / Nongwoo / H / R / S / 2 / 80 / 100 / 100
37 / PR sanghanga / Koregon seed / H / H / H / 2 / 9 / 27 / 51
38 / PR bulrocho / Koregon seed / H / H / H / 2 / 17 / 27 / 63
39 / PR kukgadaepyo / Koregon seed / H / H / H / 2 / 28 / 45 / 83
40 / PR sadaecheonwang / Koregon seed / H / H / H / 2 / 32 / 26 / 57
41 / Subiyeok / Sakata korea / H / H / H / 2 / 32 / 22 / 89
42 / PR jijon / Koregon seed / H / H / H / 3 / 14 / 32 / 42
43 / PR bultina / Koregon seed / H / H / H / 3 / 24 / 30 / 54
44 / Baerodda / Nongwoo / H / H / H / 4 / 37 / 18 / 45
45 / Youkganghongjangkun / Koregon seed / H / H / H / 4 / 20 / 21 / 43
46 / PR heemangchan / Koregon seed / H / H / H / 5 / 30 / 65 / 80
47 / Kemmedal / Koregon seed / H / H / H / 6 / 30 / 27 / 87
48 / Bulsechul / Sakata korea / H / H / H / 8 / 10 / 2 / 33
49 / PR youkbalsan / Koregon seed / H / H / H / 11 / 33 / 55 / 76
50 / PR manjangilchi / Koregon seed / H / H / H / 16 / 53 / 37 / 60
51 / PR bulmyul / Koregon seed / H / H / H / 16 / 57 / 99 / 93
52 / Hot / Koregon seed / H / H / H / 42 / 83 / 100 / 100
53 / PR machom / Koregon seed / H / H / H / 49 / 90 / 100 / 100
54 / Shintongil / Koregon seed / H / H / H / 50 / 60 / 100 / 100
55 / Hongjangkun bigarim / Koregon seed / H / H / H / 94 / 80 / 97 / 100
56 / Meeting / Sakata korea / S / H / H / 0 / 5 / 25 / 76
57 / Jjang / Monsantokorea / S / S / S / 2 / 10 / 40 / 82
58 / Hankaram / Monsantokorea / S / S / S / 12 / 17 / 42 / 82
59 / Hongiljeom / Monsantokorea / S / S / S / 14 / 32 / 52 / 88
60 / Heemangbong / Nongwoo / H / H / H / 0 / 0 / 3 / 35
61 / Papipedepimang / Takii Korea / H / R / R / 5 / 87 / 100 / 100
62 / Morningput / Syngenta / H / H / H / 14 / 83 / 100 / 97
63 / Papi yellow / Takii Korea / S / R / R / 53 / 100 / 100 / 100
64 / Super manitta / Nongwoo / S / H / H / 55 / 80 / 95 / 100
65 / Dangchan / Nongwoo / S / H / H / 58 / 100 / 100 / 100
66 / Hanbando / Nongwoo / S / H / H / 87 / 100 / 100 / 100
67 / Bukang / Monsantokorea / S / R / R / 98 / 100 / 100 / 100
68 / Youngyangmat / Nongwoo / S / H / H / 100 / 90 / 100 / 100
69 / Newwavepimang / Koregon seed / S / R / R / 100 / 100 / 100 / 100
70 / Johyang / Monsantokorea / S / H / H / 100 / 100 / 100 / 100
71 / Chammani / Nongwoo / S / H / H / 100 / 100 / 100 / 100
72 / Kemhyang / Syngenta / S / H / H / 100 / 100 / 100 / 100
73 / Kangryuktaeyang / Nongwoo / S / S / S / 17 / 70 / 100 / 100
74 / Dabotab / Monsantokorea / S / S / S / 65 / 100 / 100 / 100
75 / Chamjoeun / Nongwoo / S / S / S / 70 / 100 / 95 / 100
76 / Ohbok / Nongwoo / S / S / S / 72 / 50 / 92 / 100
77 / Kembit / Syngenta / S / S / S / 80 / 100 / 98 / 97
78 / Hongjinju / Nongwoo / S / S / S / 83 / 100 / 100 / 98
79 / Maekomdalkom / Syngenta / S / S / S / 83 / 100 / 100 / 100
80 / Mansukgun / NHseed / S / S / S / 85 / 100 / 100 / 100
81 / Daechon / Nongwoo / S / S / S / 90 / 70 / 100 / 100
82 / Daedelbo / Takii Korea / S / S / S / 90 / 100 / 97 / 100
83 / Chukje / Syngenta / S / S / S / 90 / 100 / 100 / 100
84 / Manitta / Nongwoo / S / S / S / 92 / 100 / 100 / 100
85 / Gukbo / Monsantokorea / S / S / S / 93 / 100 / 100 / 100
86 / Euddeum / Monsantokorea / S / S / S / 94 / 100 / 100 / 100
87 / Hanson / Syngenta / S / S / S / 94 / 100 / 100 / 100
88 / Jinmi / Nongwoo / S / S / S / 95 / 100 / 100 / 90
89 / Wanggun / Koregon seed / S / S / S / 95 / 100 / 100 / 100
90 / Matkkalchan / NHseed / S / S / S / 95 / 100 / 100 / 100
91 / Hongbosuk / Monsantokorea / S / S / S / 97 / 100 / 100 / 70
92 / Hongshimii / Koregon seed / S / S / S / 97 / 100 / 100 / 100
93 / Hangwoon / Syngenta / S / S / S / 97 / 100 / 100 / 100
94 / Daejangbu / Syngenta / S / S / S / 99 / 93 / 100 / 100
95 / Imkemnim / Koregon seed / S / S / S / 99 / 100 / 100 / 100
96 / Bulmat / Syngenta / S / S / S / 100 / 93 / 100 / 100
97 / Ongolchan / Koregon seed / S / S / S / 100 / 100 / 100 / 100
98 / Boochon / Monsantokorea / S / S / S / 100 / 100 / 100 / 100
99 / Shinjokwang / Monsantokorea / S / S / S / 100 / 100 / 100 / 100
100 / Gangkun / Nongwoo / S / S / S / 100 / 100 / 100 / 100

a Marker genotypes. R: resistant homozygote, H: resistant heterozygote, S: susceptible homozygote. Resistant and susceptible genotypes are indicated by blue and red, respectively.

b Resistance phenotypes based in inoculation with four P. capsici isolates of different virulence (MY-1: lowest virulence, KPC-1 and JHAI1-7: medium virulence, KPC-7: highest virulence). The degree of disease incidence is scored from 0 to 100. 0-25 (blue) and 26-100 (red) are considered to represent resistant and susceptible phenotypes, respectively.

Fig. S1. Wilting symptoms of pepper plants infected by P. capsici. P. capsici isolate JHAI1-7 was used as inoculum for Phytophthora root rot resistance screening. Resistance and susceptibility were scored based on severity of wilting at 10 d post-inoculation (dpi) using the following index: 0 = symptomless, 1 = mild wilt in leaves or stems (< 25% of wilt), 2 = severe wilt in leaves or stems (< 50% of wilt), 3 = death. As the number of disease index was higher, the leaves of infected plants were more wilted.

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Fig. S2 Sequence alignment of markers from four P. capsici-resistant and four P. capsici-susceptible cultivars. Markers Phyto5SAR (A), Phyto5NBS2_1 (B) and Phyto5NBS2_2 (C) are shown. Arrows indicate forward and reverse primers. Polymorphisms between resistant and susceptible cultivars are highlighted with rectangles. For genotyping, Phyto5NBS2_1 was converted into a CAPS marker using MluCI, with which only susceptible cultivars were cleaved, and Phyto5SAR and Phyto5NBS2_2 were analyzed by HRM.

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