Supplemental Figure 1. Alignment of Agpase Haplotypes, Based on Polymorphisms Found In

Supplemental Figure 1. Alignment of AGPase haplotypes, based on polymorphisms found in EST sequences from Shepody. The sequence shown represents the regions of exon 1 amplified by the LS031 primers. Locations of forward (LS031F), reverse (LS031R) and probe (LS031P) are indicated below the sequence. Polymorphisms are highlighted grey and bold.

Supplemental Figure 2. Alignment of TG689 haplotypes, based on sequences from potato lines with golden nematode resistant (haplotype 1) or susceptible (haplotypes 2 and 3) alleles (De Jong, unpublished data). Locations of forward (LS034F), reverse (LS034R) and probe (LS034P) are indicated below the sequence. Polymorphisms are highlighted grey and bold.

Supplemental Figure 3. Alignment of purple (Genbank accession AY675559) and non-purple (AY675560) f3’5’5’h haplotypes, as described in Jung et al. (2005). The sequence shown represents the regions of exon 2 amplified by the LS033 and LS129 primers. Locations of forward, reverse, and probe are indicated below the sequence. Polymorphisms are highlighted grey and bold. The ClaI site described in Jung et al. (2005) is at position 119.

Supplemental Figure 4. Alignment of yellow-flesh and white-flesh bch haplotypes, as described in Brown et al. (2006). Locations of forward (BCH100F), reverse (BCH100R), probe (LS032P), and two short amplicon assays (LS138 F/R and LS139 F/R) are indicated below the sequence. Polymorphisms are highlighted grey and bold.

Supplemental Figure 5. Individual probe genotype groups 1 – 16 based on the LS031P (AGPase) assay evaluated with DNA samples from 96 clones described in Supplemental Table 1.

Supplemental Figure 6. Individual probe group scans (1 – 14) based on amplicon scanning analysis of the LS031P (AGPase) assay evaluated with DNA samples from 96 clones described in Supplemental Table 1.

Haplotype_1 1 CACCTTCTTC TAACAATTGC ATCAATGAGA GAAGAAATGA TTCTACACGT GCAGTATCCA

Haplotype_2 1 CACCTTCTTC TAACAATTGC ATCAATGAGA GAAGAAATGA TTCTACACGT GCAGTATCCA

|------LS031F------>

61 GCAGAAATCT CTCATTTTCG TCTTCTCATC TCGCCGGAGA CAAGTTGATG CCTATATCGT

61 GCAGAAATCT CTCATTTTCG TCTTCTCATC TCGCCGGAGA CAAGTTGATG CCTGTGTCGT

|------LS031P------

121 CCTTACGTTC CCAAGGAGTC CGATTCAATG TGAGAAGAAG TTCATTGATT GTGTCGCCTA

121 CGTTACGTTC CCAAGGGGTC CGATTCAATG TGAGAAGAAG TCCATTGATT GTGTCGCCTA

-----|

181 AGGCTGTTTC TGATTCGCAG AATTCACAGA CAT

<----LS031R------|

Supplemental Fig. 1.

Haplotype_1 1 GGGCTTATCC TGGTTGAAGT AACTTGTGTG CCATGTCTAG ACAAACAAGA AATGAGAGAA

Haplotype_2 1 GGGCTTATCC TGGTTGAAGT AACTTGTGTG CTATGTCTAG ACAAACAGGA AATGAGAGAA

Haplotype_3 1 GGGCTTATCC TGGTTGAAGT AACTTGTGTG CTATGTCTAG ACAAACAAGA AATGAGAGAA

|------LS034F------> |------

61 GACATAAAAC TCTTGGTTAT AGCCTATAGG AGCCAGCTAC TTTACCGGAA AGTTTCCCAG

61 GACACAAAAC TCTTGGT------TATAGG AGCCAGATAC TTTACCGGAG AGTTCCCCAT

61 GACACAAAAC TCTTGGT------TATAGG AGCCAGCTAC TTTACCGGAA AATTTCCCAG

------LS034P------|

121 AATACTTATA GGATATCTTA TGTCAAA-TT T-CATTGAAG CAGTATTATT TTTTTTCTTG

121 AATA------CTTA TGTCAAAATT TTCAT-GATG CAGTATTATT TTTT--CTTG

121 AATACTTATA GGATATCTTA TGTCAAA-TT T-CATTGATG CAGTAT--TT TTTTTTCTTG

181 GAATTGGTGA AACAACACAT TCTATTG

<----LS034R------|

Supplemental Fig. 2.

Purple 1 CACCCTATGG ACCTCGTTGG AAGTTGCTAA GGAAATTGAG CAACTTACAG ATGCTAGGTG

Non-purple 1 CACCCTATGG ACCTCGTTGG AAGTTGCTAA GGAAATTGAG CAACTTACAC ATGCTAGGTG

|------LS033F--->

61 GAAAAGCCTT AGAAAATTGG GCCAATGTTC GTGCCAATGA GCTAGGTCAC ATGATAAAGT

61 GAAAAGCCTT AGAAAATTGG GCCAATGTTC GTGCCAATGA GCTAGGTCAC ATGCTAAAAT

61 |------LS033P------

|----LS129F------>

121 CGATGTTCGA TGCAAGCCAC GTGGGCGAAT GTGTGGTGAT TGCTGATATG TTGACGTTCG

121 CGATGTTCGA TGCAAGCCAG GAGGGCGAAT GTGTGGTGAT TGCTGATATG TTGACGTTTG

------|

<-----LS129R------|

181 CGATGGCAAA TATGATTGGT CAAGTGATGT TAAGTAAGAG AGTGTTCGT

<------LS033R-----|

Supplemental Fig. 3.

Yellow 1 AGTTCTGTTC TTCTCTCCGT TAACTCGCAA TTTTGGCGCA ATTTTGCTGT CTCGAAGAAA

White 1 AGTTCTGTTC TTCTCTCCGT TAACTCGCAA TTTTGGCGCA ATTTTGCTGT CTCGARGAAA

|------BCH100F------>

61 GCCGAGGTTG GCGGTTTGCT TTGTGCTGAA GAATGAGAAA TTGAATAGTA CTATCCAAAG

|-----

121 TGAGAGTGAA GTAATACAGG ATCAGATACA AGTAGAGATT AATGAGGAGA AGAGTTTAGC

121 TGAGTGTGAA GTAATACAGG ATCAGATACA AGTAGAGATT AATGAGGAGA AGAGTTTAGC

------LS032P------|

181 TGCCTGTTGG CTGGCGGAAA AATTGGCGAG GAAGAAATCG GAGAGGTTTA CTTATCTTGT

<------BCH100R------|

241 GGCGGCTGTC ATGTCTAGTT TAGGGATTAC TTCTATGGCG ATTTTGTCAG TTTATTACAG

241 GGCGGCTGWC ATGTCTAGTT TAGGGATTAC TTCTATGGCG ATTTTGTCGG TTTATTACAG

|-----LS138F------> <--

301 ATTTTCATGG CAAATGGAGG TACTAATTAA TTACTCCATT CTT-TTGCTT CTTCTTTCTT

301 ATTTTCATGG CAAATGGAGG TACTAATTAA TTACTCCATT CTTYTTCCT- CTTCTTTCTT

------LS138R---|

|--LS139F------>

361 AAGCTTAATC TTAAGCTTTT TGGATAGGGT GG

<------LS139R------|

Supplemental Fig. 4.

LS031P – Group 1

LS031P – Group 2

LS031P – Group 3

LS031P – Group 4

LS031P – Group 5

LS031P – Group 6

LS031P – Group 7

LS031P – Group 8

LS031P – Group 9

LS031P – Group 10

LS031P – Group 11

LS031P – Group 12

LS031P – Group 13

LS031P – Group 14

LS031P – Group 15

LS031P – Group 16

Supplemental Fig.5.

LS031P – Group 1 scans

LS031P – Group 2 scans

LS031P – Group 3 scans

LS031P – Group 4 scans

LS031P – Group 5 scans

LS031P – Group 6 scans

LS031P – Group 7 scans

LS031P – Group 8 scans

LS031P – Group 9 scans

LS031P – Group 10 scans

LS031P – Group 11 scans

LS031P – Group 12 scans

LS031P – Group 13 scans

LS031P – Group 14 scans

Supplemental Fig. 6.

Supplemental Table 1. Select information about tuber characteristics and potato cyst nematode resistance for 95 clones in the multi-line screening plate.

Genotype / Female / Male / Skinb / Fleshc / PCN_Ro1d
AC Belmont / Raritan / F51013 / WH / WH / S
AC Brador / F61101 / F60034 / WH / LY / ND
AC Domino / Blue Mac / AM66-42 / PUR / WH / R
AC RedIsland / Brigus / Redsen / RED / CR / S
AC Sunbury / Raritan / Agitato / WH / Y / R
AF186-2 / Chipbelle / Norchip / WH / WH / R
AM66-42 / (VTn)2 62-33-3 / MPI 40.1465/6 / WH / CR / R
Aminca / Resy / Amaryl / WH / Y / R
Anson / F53018 / Mira / PUR SPL / CR / S
AWN86514-2 / KSA195-96 / Ranger Russet / WH / WH / ND
Barbara / MPI 64.956/68 / AM62-740 / PUR SPL / Y / R
Belleisle / SSRBP 834c (29) / F47024 / WH / WH / ND
BL 61 74 167 / Y 2020 / BL 54 121 / WH / LY / ND
Brigus / G64-124-5P / SJ62-26-14 / PUR / LY / S
Brodick / 7683 A 12 / 8898 AC 14 / RED SPL / LY / S
Caribe / F55066 / USDA X96-56 / PUR / CR / S
Cariboo / 1256A(23) / MN113-1 / RED SPL / WH / S
Chieftain / LA1354 / IA1027-18 / RED / WH / S
Chipbelle / Wauseon / Lenape / WH / CR / R
Conestoga / G7063 / G6652 / WH / WH / ND
CS7232-4 / Wauseon / B6503-2 / WH / WH / ND
Cupids / N150-3 / Wauseon / WH / CR / R
Delcora / Cebeco 60-15-5 / Désirée / RED / Y / S
Désirée / Urgenta / Depesche / RED / LY / S
Dorita / N-44 / Libertas / WH / CR / S
Exploits / N1614-5 / N69-478 / WH / CR / R
F00044 / Coastal Russet / F74070 / WH / WH / S
F00069 / Barbara / Cupids / WH / CR / MR
F00074 / Barbara / Redsen / RED / CR / MR
F01030 / F87084 / Stirling / WH / CR / S
F01031 / Stirling / Redsen / RED / CR / ND
F01065 / Torridon / AC RedIsland / RED / LY / ND
F02004 / J101K06 / F65089 / WH / Y / ND
F02005 / J101K27 / F66011 / WH / Y / ND
F02006 / J101K27 / Lenape / WH / WH / ND
F02007 / J101K27 / Lenape / WH / CR / ND
F02008 / J101K27 / Lenape / WH / CR / ND
F51013 / Houma / USDA X96-56 / WH / WH / ND
F51043 / USDA 46952 / F43026 / WH / WH / ND
F58089 / B381-2 / MN113-1 / WH / WH / ND
F61010 / Raritan / Cariboo / RED SPL / WH / ND
F61019 / F45019 / Cariboo / WH / WH / ND
F64073 / Sable / F51043 / WH / WH / ND
F66094 / F51043 / Dorita / WH / WH / ND
F67127 / Houma / F47024 / WH / WH / ND
F67128 / Ontario / F51043 / WH / WH / ND
F69090 / F62014 / F61101 / RED / LY / ND
F73068 / B6516-19 / F58050 / WH / WH / ND
F74070 / Raritan / Agitato / WH / Y / R
F79070 / Agitato / F58050 / WH / LY / R
F83065 / F66041 / AF186-2 / WH / WH / R
F87031 / Wischip / F66011 / WH / WH / ND
F87084 / S62/47/1 / Cupids / WH / WH / R
F88042 / F66041 / AF186-2 / WH / CR / R
F89098 / Wischip / F73068 / WH / WH / ND
F91031 / F81109 / CS 7232-4 / WH / CR / ND
F93102 / Coastal Russet / B6503-2 / WH / WH / ND
F94001 / Grand Falls / F58050 / WH / WH / ND
F95031 / AC Novachip / Conestoga / WH / WH / ND
F96001 / B6503-2 / ND6993-13 / WH / WH / ND
F97015 / Wischip / F66011 / WH / WH / ND
F97050 / F87084 / NYL235-4 / WH / CR / R
F98021 / J101K27 / Wischip / WH / WH / ND
F99009 / Atlantic / ND860-2 / WH / CR / ND
F99041 / Frontier Russet / Russette / WH / CR / S
F99058 / N1618A / N1653-7 / PUR / CR / R
Favorita / ZPC 50-35 / ZPC 55-37 / WH / Y / S
GreenMountain / Excelsior / Dunmore / WH / WH / S
Houma / Charles Downing / Katahdin / WH / WH / S
Hunter / F48023 / SSRBP 834c (29) / WH / WH / S
J101K06 / J101 / Katahdin / RED SPL / WH / ND
Jemseg / Sable / F55069 / WH / WH / ND
Kennebec / B127 / USDA X96-56 / WH / WH / S
Lenape / Delta Gold / B3672-3 / WH / WH / ND
Monona / B1268-46 / B1299-15 / WH / WH / S
N0634-7 / S62/47/1 / 694/3 / WH / Y / R
N1322-27 / S62/47/1 / Cupids / WH / CR / S
N1598-1 / Brigus / Cupids / WH / CR / R
N1598-9 / Brigus / Cupids / WH / LY / R
ND2008-2 / unknown / unknown / WH / CR / ND
ND860-2 / ND78-3 / ND9583-1 / WH / WH / ND
Norvalley / Norchip / ND860-2 / WH / CR / ND
Red Beauty / Cayuga / ND-1 / RED / WH / ND
Reddale / Erik / Chieftain / RED / WH / ND
Rideau / Viking / P177-13R / RED / WH / ND
Rochdale Gold / AC Chaleur / Agitato / WH / Y / S
Saco / USDA 41956 / USDA X96-56 / WH / WH / S
Sebago / Chippewa / Katahdin / WH / WH / S
Serrana Inta / B2.63 / MPI 59.703/21 / WH / Y / ND
Shepody / Bake-King / F58050 / WH / WH / S
Snowden / Lenape / Wischip / WH / WH / S
Stirling / 8318 (6) / 8204 (4) / WH / CR / S
Sunrise / Wauseon / B6563-2 / WH / WH / R
Torridon / 8372a (17) / G5833-5 / WH / LY / S
Urgenta / Furore / Katahdin / RED / Y / S
W5281.2a / PUR / - / -
Yema de Huevoa / - / Y / -

a Diploid clones

b WH, white; PUR, purple; SPL, splashed; -, not included in dfr or f3’5’5’h test

c WH, white; CR, cream; LY, light yellow; Y, yellow; -, not included in bch test

d R, resistant; MR, moderately resistant; S, susceptible; ND, not determined; -, not included in TG689 test.

Supplemental Table 2. HRM group information for 95 clones in the multi-line screening plate.

Genotype / LS031_groupb / LS030_groupc / LS033_P / LS138_group / LS034_H1
AC Belmont / 38 / 21 - / - / a / -
AC Brador / 15 / 19 - / - / b / -
AC Domino / 44 / 12 ++ / ++ / a / +
AC RedIsland / 15 / 10 ++ / - / b / -
AC Sunbury / 21 / 2 + / - / b / +
AF186-2 / 12 / 1 + / - / a / +
AM66-42 / 12 / 1 + / - / a / +
Aminca / 35 / 16 ++ / - / b / +
Anson / 30 / 25 +++ / - / a / -
AWN86514-2 / 4 / 1 + / - / a / -
Barbara / 24 / 2 + / - / b / +
Belleisle / 38 / 7 + / - / a / -
BL 61 74 167 / 10 / 26 +++ / - / b / -
Brigus / 8 / 10 ++ / - / b / -
Brodick / 36 / 10 ++ / - / a / -
Caribe / 8 / 22 - / - / a / -
Cariboo / 20 / 25 +++ / - / a / -
Chieftain / 1 / 2 + / - / a / -
Chipbelle / 8 / 30 + / - / a / +
Conestoga / 23 / 1 + / - / a / -
CS7232-4 / 33 / 30 + / - / a / +
Cupids / 21 / 6 + / - / a / +
Delcora / 1 / 2 + / - / b / -
Désirée / 1 / 11 ++ / - / b / -
Dorita / 30 / 17 - / - / a / -
Exploits / 38 / 12 ++ / - / a / +
F00044 / 21 / 28 +++ / - / a / -
F00069 / 5 / 6 + / - / a / -
F00074 / 23 / 10 ++ / - / a / -
F01030 / 6 / 3 + / - / a / -
F01031 / 42 / 11 ++ / - / a / -
F01065 / 41 / 13 ++ / - / b / -
F02004 / 16 / 27 +++ / - / b / -
F02005 / 18 / 4 + / - / b / -
F02006 / 31 / 35 - / - / a / -
F02007 / 26 / 24 - / - / a / -
F02008 / 13 / 35 - / - / a / -
F51013 / 14 / 17 - / - / a / -
F51043 / 9 / 2 + / - / a / -
F58089 / 20 / 1 + / - / a / -
F61010 / 39 / 7 + / - / a / -
F61019 / 34 / 9 + / - / a / -
F64073 / 21 / 11 ++ / - / a / -
F66094 / 20 / 3 + / - / a / -
F67127 / 3 / 18 - / - / a / -
F67128 / 9 / 18 - / - / a / -
F69090 / 25 / 10 ++ / - / b / -
F73068 / 1 / 1 + / - / a / -
F74070 / 21 / 2 + / - / b / +
F79070 / 12 / 25 +++ / - / b / +
F83065 / 33 / 20 - / - / a / +
F87031 / 12 / 11 ++ / - / a / -
F87084 / 36 / 15 ++ / - / a / +
F88042 / 15 / 1 + / - / a / +
F89098 / 26 / 20 - / - / a / -
F91031 / 33 / 36 - / - / a / +
F93102 / 1 / 31 - / - / a / -
F94001 / 29 / 2 + / - / a / -
F95031 / 1 / 1 + / - / a / -
F96001 / 15 / 29 + / - / a / -
F97015 / 20 / 4 + / - / a / -
F97050 / 36 / 8 + / - / a / ++
F98021 / 30 / 5 + / - / a / -
F99009 / 37 / 34 ++ / - / a / -
F99041 / 12 / 17 - / - / a / -
F99058 / 43 / 14 ++ / + / a / +
Favorita / 34 / 4 + / + / b / -
GreenMountain / 19 / 20 - / - / a / -
Houma / 11 / 2 + / - / a / -
Hunter / 8 / 13 ++ / - / a / -
J101K06 / 11 / 26 +++ / - / a / -
Jemseg / 16 / 2 + / - / a / -
Kennebec / 20 / 20 - / - / a / -
Lenape / 13 / 36 - / - / a / -
Monona / 8 / 17 - / - / a / -
N0634-7 / 27 / 25 +++ / - / b / +
N1322-27 / 20 / 13 ++ / - / a / -
N1598-1 / 36 / 10 ++ / - / a / +
N1598-9 / 20 / 1 + / - / b / +
ND2008-2 / 12 / 33 ++ / - / a / -
ND860-2 / 10 / 29 + / - / a / -
Norvalley / 40 / 23 - / - / a / -
Red Beauty / 38 / 2 + / - / a / -
Reddale / 2 / 10 ++ / - / a / -
Rideau / 26 / 1 + / - / a / -
Rochdale Gold / 8 / 3 + / - / c / -
Saco / 2 / 20 - / - / a / -
Sebago / 1 / 2 + / - / a / -
Serrana Inta / 7 / 2 + / - / d / +
Shepody / 28 / 12 ++ / - / a / -
Snowden / 22 / 35 - / - / a / -
Stirling / 17 / 17 - / - / a / -
Sunrise / 9 / 1 + / - / a / ++
Torridon / 3 / 17 - / - / b / -
Urgenta / 2 / 1 + / - / c / -
W5281.2a / 32 ++++ / ++
Yema de Huevoa / d

a Diploid clones

bRefer to Supplemental Table 3 for details of LS031 (AGPase) HRM groups

cRefer to Table 4 for details of LS030 (dfr) HRM groups

Supplemental Table 3. Probe and scan groups based on high-resolution DNA melting of 95 clones with AGPase (LS031) assay.

HRM_Group / N / Probe_Group / Scan_Group / Tm_62 / Tm_67 / Tm_71 / Tm_75
1 / 7 / 1 / a / 1 / 1 / 2
2 / 3 / 1 / b / 1 / 1 / 2
3 / 2 / 1 / c / 1 / 1 / 2
4 / 1 / 1 / d / 1 / 1 / 2
5 / 1 / 1 / e / 1 / 1 / 2
6 / 1 / 1 / f / 1 / 1 / 2
7 / 1 / 1 / g / 1 / 1 / 2
8 / 6 / 2 / a / 1 / 2 / 1
9 / 3 / 2 / b / 1 / 2 / 1
10 / 2 / 2 / c / 1 / 2 / 1
11 / 2 / 2 / d / 1 / 2 / 1
12 / 6 / 3 / a / 2 / 1 / 1
13 / 2 / 3 / b / 2 / 1 / 1
14 / 1 / 3 / c / 2 / 1 / 1
15 / 4 / 4 / a / 1 / 3
16 / 2 / 4 / b / 1 / 3
17 / 1 / 4 / c / 1 / 3
18 / 1 / 4 / d / 1 / 3
19 / 1 / 4 / e / 1 / 3
20 / 7 / 5 / a / 2 / 2
21 / 5 / 6 / a / 3 / 1
22 / 1 / 6 / b / 3 / 1
23 / 2 / 7 / a / 1 / 3
24 / 1 / 7 / b / 1 / 3
25 / 1 / 7 / c / 1 / 3
26 / 3 / 8 / a / 2 / 2
27 / 1 / 8 / b / 2 / 2
28 / 1 / 8 / c / 2 / 2
29 / 1 / 8 / d / 2 / 2
30 / 2 / 9 / a / 3 / 1
31 / 1 / 9 / b / 3 / 1
32 / 1 / 9 / c / 3 / 1
33 / 3 / 10 / a / 2 / 2
34 / 2 / 10 / b / 2 / 2
35 / 1 / 10 / c / 2 / 2
36 / 4 / 11 / a / 1 / 3
37 / 1 / 11 / b / 1 / 3
38 / 4 / 12 / a / 3 / 1
39 / 1 / 13 / a / 4
40 / 1 / 13 / b / 4
41 / 1 / 14 / a / 4
42 / 1 / 14 / b / 4
43 / 1 / 15 / a / 1 / 1 / 2
44 / 1 / 16a / a / 2.5 / 1.5

a Probe group 16 is intermediate between probe groups 5 and 6.