Bingguang Xiao1, Katherine Drake2, Vijay Vontimitta3, Zhijun Tong1, Xueting Zhang1, Mei-yun Li1, Xiao-dong Leng1, Ramsey S. Lewis2

North Carolina State University in collaboration with

Yunan Academy of Tobacco Agricultural Sciences

Location of genomic regions contributing to Phytophthora nicotianae resistance in the tobacco

cultivar ‘Florida 301’

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Black Shank: Phytophthora nicotaiane

Wilting & yellowing of lower leaves Stem and root necrosis

Disking of the pith

Total loss of crop

Source: http://www.apsnet.org/edcenter/intropp/lessons/fungi/Oomycetes/Pages/BlackShank.aspx

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Economic Impact of Black Shank

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

5

2006 2007 2008 2009 2010

% C

rop

Lost

Flue Cured Tobacco Disease Loss Estimates

Black Shank Granville Wilt Tomato Spotted Wilt Mosaic Target Spot

In North Carolina: Average crop loss of 3% over

the last 5 years

Average dollar loss of 20.7 million over the last 5 years

Black shank accounts for 30% of total disease incidence

Source: NCSU Flue Cured Tobacco Disease Report, 2010

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Current Sources of Resistance

Exotic N. tabacum genes Alien Nicotiana genes Transferred from cigar

cultivars in 1931

Partial, non-race specific resistance

Possible negative correlation with yield and quality in flue-cured tobacco

Transferred from N. longiflora (Phl)and N. plumbaginifolia (Php) in the 1960’s

Complete resistance but to race 0

No resistance to race 1

Recent wide-scale planting of cultivars with the Php gene has led to race shifts Races that can overcome the

Ph resistance now prevail Fl 301 resistance

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NCSU Plant Breeding Objective

To develop a cultivar with intermediate to high levels of both race 0 and race 1 resistance while maintaining high yield and quality Better understand resistance provided by Fl 301 and how it

compares to the resistance provided by Beinhart 1000 How to more efficiently transfer this resistance to new cultivars

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Black Shank Resistance in Historical Lines

Year of End % Variety Release Survival Yellow Special 1943 6.2 Gold Dollar Pre 1940's 7.1 Virginia Bright Leaf Pre 1940's 8.6 Yellow Special A Pre 1940's 9.0 Jamaica Pre 1940's 9.3 Warne Pre 1940's 9.4 400 1942 10.6 White Stem Orinoco Pre 1940's 10.6 White Gold 1949 11.4 Golden Cure 1950 11.8 Hicks Broadleaf Pre 1940's 12.8 Virginia Gold 1947 13.4 McNair 30 1962 17.2 Golden Wilt 1949 19.4 Vesta 5 1952 27.1 Vesta 64 1940's 27.5 Coker 187-Hicks 1957 30.0 NC 2326 1964 31.3 NC55 1996 33.6 Dixie Bright 101 1949 36.5 Vesta 30 1940's 37.4 McNair 10 1960 37.4 Oxford 1 1942 41.2 SC 58 1959 42.0 K149 1990 42.7 Oxford 3 1942 43.5 Ox. 1-181 1948 43.6 Coker 319 1962 43.9 Coker 139 1954 47.0 Dixie Bright 244 1955 47.3 McNair 135 1970 50.5 Coker 258 1966 50.8 Coker 187 1956 52.2 Dixie Bright 102 1949 52.3 Virginia 115 1964 54.9 McNair 20 1962 55.0 K326 1982 56.9 McNair 944 1973 62.7 Speight G-28 1969 62.7 NC810 2001 65.5 Oxford 2 1942 65.8 NC606 1999 69.0 K 394 1984 70.1 Coker 298 1964 70.3 Oxford 207 1996 71.8 NC 82 1979 75.9 Florida 301 Source 76.8 K346 1990 78.6 Beinhart 1000 Source 91.5

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Black Shank Resistance Origin in Early Flue-Cured Varieties

Most US flue-cured tobacco cultivars are believed to have derived the majority of their black shank resistance alleles from Fl 301 via these early varieties

Variety Pedigree Year

Florida 301 BigCuba/LittleCuba 1931

Oxford 1, 2, 1-181 Fla301/3*VirginiaBrightLeaf 1943

Oxford 3 Fla301/3*WhiteStemOrinoco 1943

Oxford 4 Fla301/3*Warne 1943

Vesta 30 Fla301/3*Warne//YellowSpecial 1949

Vesta 64 Fla301/3*WhiteStemOrinoco//YellowSpecial 1949

Dixie Bright 101 TI448A/4*400//Oxford1/3/Fla301/3*400 1950

Dixie Bright 102 TI448A/4*400//Oxford1/3/Fla301/3*400 1950

Coker 139 GoldenCure/Oxford 1-181//GoldenWilt/DixieBright101 1954

Coker 187 GoldenWilt/Oxford 1-181 1956

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Possible Mechanisms of Inheritance of Fl 301 Resistance

Simply inherited and controlled by recessive alleles Clayton, 1958

Partially dominant and influenced by modifiers Moore & Powell, 1959

Polygenic and additive Smith & Clayton, 1948; Crews

et al., 1964; Chaplin, 1966 Fl 301 in a race 1 black shank field in Rocky Mount, NC

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Beinhart 1000 QTL Study

Beinhart 1000 is a cigar line with a high level of black shank resistance

In 2012 a study was conducted to identify QTL associated with the black shank resistance in Beinhart 1000 using a limited number of microsatellite markers (Vontimitta and Lewis, 2012)

QTL identified here may be of value to cultivar development efforts

Beinhart 1000 beside a susceptible line in a race 1 black shank field in Rocky Mount, NC

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Objectives

To gain increased understanding of the mechanism of inheritance of black shank resistance in Fl 301

To identify microsatellite markers associated with Fl 301 genomic regions contributing to this resistance

To compare genomic regions contributing to resistance in Fl 301 to those previously found to be associated with resistance in Beinhart 1000

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Methods

Develop mapping population RIL population from Fl 301 x Hicks (a black shank susceptible

variety)

Evaluate for resistance Field – NC black shank disease nurseries at 3 locations in 2008 Greenhouse – Yuxi, China

Analyze data Linkage analysis to generate a map Multiple interval mapping to identify significant QTL

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Fl 301 x Hicks RIL Population

x

Fl 301 Hicks

F1 x

F2 x

F2:3 x

F3:4 x

F4:5 x

F5:6

F2 x

F2:3 x

F3:4 x

F4:5 x

F5:6

F2 x

F2:3 x

F3:4 x

F4:5 x

F5:6

F2 x

F2:3 x

F3:4 x

F4:5 x

F5:6

122 F5:6 Recombinant Inbred Lines

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Disease Evaluation Field Evaluation Greenhouse Evaluation

Evaluated in 3 locations in NC in 2008 in black shank disease nurseries RCBD with 3 reps 12-plant plots AUDPC was calculated for each plot

Evaluated in a GH in Yuxi, China in soil inoculated with P. nicotianae race 0 infested rice grains RCBD with 3 reps 8-plant experimental units AUDPC was calculated for each unit

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Genotyping and Linkage Map Generation

Parental lines were screened for polymorphisms at ~5700 microsatellite marker loci 5.95% were found to be polymorphic

Genotyped the 122 RIL lines with the

polymorphic markers 341 primer pairs → 373 polymorphic

microsatellite bands

373 polymorphic markers were classified into 24 linkage groups using JoinMap Groups based on a LOD score of 2.0 – 10.0 Kosambi’s mapping function used to order

marker and predict genetic distances

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QTL Identification

Composite interval mapping and multiple interval mapping were performed on field and greenhouse data separately using Windows QTL Cartographer V2.5

Composite interval mapping was used only to provide an initial model for multiple interval mapping QTL with LOD greater than 3.2

for field data and 3.4 for greenhouse data from CIM were kept for the first model in MIM

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AUDPC

0

5

10

15

20

25

30

# o

f RIL

s

AUDPC

Field AUDPC Histogram

Fl 301 Hicks K346

0

5

10

15

20

25

30

# o

f RIL

s AUDPC

Greenhouse AUDPC Histogram

Fl 301

Hicks

ANOVA indicated highly significant differences for AUDPC among 122 RILs

Fl 301 at the end of distribution for low AUDPC while Hicks is much higher

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Linkage Map

373 polymorphic markers mapped, map length: 1176 cM 34 markers not linked LG numbers align with Bindler et al. (2011) map

PT51859(2)0.0

PT1279(4)20.6

PT30061(2)27.9

TM1058234.4TM1037340.5

PT30350(2)49.4

TM1009362.1

2

TME07070.0TM103783.7TM101595.4PT60302(3)6.3TM109817.4PT20286(3)12.4TM1017319.4

TM1017548.4

3

TM109120.0

TM1085717.9

TM1097730.9TM1077132.7TM1080034.2TM1038236.8TME098038.2TME041244.9

TM1072155.0

PT1140(4)61.9

TM10476a72.1TM10476b74.7TM1082178.7

TM1091488.0

TM11213a96.3

TM10681120.6

4a

TM108930.0

TME052320.0

PT30167(4)33.5TM1005238.1TM1086041.0TM1086547.3TME098151.5TME072454.5PT61323b(4)57.5TM1006961.2PT5154963.4TM1095771.4TM1093572.7TM1005178.0

4b

TM101020.0

TM105889.3TM1089416.6PT30361a(4)19.7PT30361b(4)22.2

4c

TM108910.0

TM1133411.2PT30111(24)14.1TM1133215.9PT61321(5)20.2

TM1093231.9

5

PT50951a(6)0.0TM103726.7TME042312.3PT20287(6)25.8TM1073127.2TM1110634.1TM1085436.1TM1092337.2TM1107639.7TM11213b39.8TM1078944.3PT20172(6)46.6TM1111048.5PT20372(6)49.4TM1026849.7PT30183(6)50.0TM1116552.5PT50951b(6)54.5TM1013657.0TM1090157.5TM1008960.4TME082361.9TM1113366.4TM1047067.4TM1092269.0TM1117771.1TM1091775.0PT30202(3)80.2TM1044590.8

6TM108810.0TM111742.2TM104086.0PT30005(7)11.0TM1086415.0TME042718.4TM1094819.9TM1081722.8PT1078(10)24.3TM1111429.3PT55341(7)29.4TM1088732.0TM1094633.6PT30218(7)34.7PT53795(7)35.0PT30395(7)36.1TME043736.6TM1002738.6PT51405(7)40.7PT52753(7)41.4PT53518(7)42.5TME014144.2TME016346.1PT61512(7)49.2PT40009(7)55.6PT30174(7)62.0PT30165(7)65.1TM1087665.2

7

TM105810.0PT40005(18)7.4PT60231(18)16.3TM1058426.9TME013731.1TM1084639.1PT30142(18)42.5TM1124146.5TM1117152.5PT30485(8)54.8TM1065456.6TM1039057.7TME012559.7TM1096960.7TM1060162.0PT20391(8)63.8TM1101665.1TM10142a67.1TM1042870.0TM1021171.8TM10142b74.7TM1035878.2PT30351(8)80.3TM1119986.6TM1071995.3TM1061797.9

8

TM103590.0

TM106067.9

PT30110(9)24.8TM1096429.7PT30200(18)33.0TM1049537.5TM1078743.8TM1115146.1

TM1106258.1TM1065763.5

TM1013771.3

9/18

TM112330.0

PT30137(11)6.5

TM1115717.8TM10525b21.2TM10525a21.7PT30480(11)25.0PT30417(11)31.1

PT30168a(13)44.4

11a

PT1199(1)0.0

TM1098814.2

PT20383(11)25.3TME029332.4TME026134.7PT60046(11)38.5

PT30420(11)47.8

11b

TM109300.0

PT30459(12)9.1TM1032412.9

TM1035332.3TM1120236.3TM1113838.1TM1100140.6TM1038143.1TME011947.9TM1086250.6TM1013852.4TM1108355.0TME008259.0TM1102962.7PT30412(12)69.4

TME044384.7

12

PT30346a(15)0.0

PT30346b(15)15.7

PT20343(15)26.1

TM1032733.4PT61373(15)39.2PT30124(15)41.8

TM1055854.7TM1092955.7TM1044460.2PT52061(15)62.6TM1083867.3

TM1108877.8

PT30224(15)93.3

15

PT55333(5)0.0

TM110277.2

TM1090928.8TM1044329.7

TM1015740.1TM1067945.6TM10595a50.6TME079255.4TM10595b60.8TM1112066.1

PT20196(16)73.0PT20289(16)77.1TM1015381.4TM1102386.4

TM1113992.7

PT30316(16)100.2

TME0022108.1

PT20275(16)115.8

16

TM105190.0

TM1062423.4TM1130926.2TM1062127.7TM1062328.5TM1061929.6TME090031.4TME090132.3TM1084035.1TM1052037.0TM1081147.1TM1120647.8TM1025352.4TM1025557.8TM1109759.6TM1058964.9TM1025668.0TM1112573.2TM1021683.1PT30173(17)88.8PT55392(17)89.9PT30159(17)92.3TM1037198.9PT30314(17)100.2TM10816104.4

17

TM110260.0

TME00658.4

TM1100521.1TM1103026.5TME049128.3

TM1077437.9

TM10530a50.4

TM1113556.7TME041462.5

PT30289(19)74.2

TM1060381.0TM1120484.4

TM1110491.5TM1018196.1

19

TM103490.0

TME0324b9.1TME0324a14.1

TM1038633.3PT20149(20)35.6TM1101939.6PT30416(20)43.0

20

TM10966a0.0

TM10966b8.3

PT30355(21)22.8TM1098023.4TM1088227.8TM1098730.9TM1099731.4PT30186(21)36.0TM10530b41.9TM1043146.9TM1092650.1

TM1040461.2TM1086862.5TM1098964.2TM1040369.7

PT30257(21)79.1

21

TM109240.0

TME043610.2

TME044824.1TM1036831.6TM1116134.4TM1085036.5

PT30473(22)50.7TM1033754.0PT20242(22)55.7

TM1116666.8PT20213(22)71.7

TM1094290.0

22

TM108280.0TM111050.5

TM1013513.3TM1081415.6

PT30408(23)24.4

PT30380(23)47.2TM1025251.4TM1055753.0

TM1078664.6PT20192(23)73.6TM1018077.1PT20445(23)77.8TM1041379.8TM1013482.9TM1092891.6

23

TM108840.0TME04660.5

PT6030819.3TME074425.4TM1097026.6PT40035(24)27.6PT52633(24)28.6TM1120733.3PT30114(24)34.4PT51624(24)36.3PT61153(24)38.9

TME073468.6

24

)

)

PT55251(24)0.0

TM1035016.8

TM1015643.7TM1097948.1PT30028(13)51.0TM1079453.4PT30095(13)65.2TM1097667.1TM1084968.2TM1103668.4TME041068.9TM1072570.2TM1115373.0PT30034(13)73.2TM1110175.1

13

TM103920.0TM105521.9

TM1098312.1

PT30274(14)23.1TM1056227.5TM1014529.7TME052229.9PT61323a(4)32.5

TM1058549.2PT30053(14)50.2TM1114854.2

14

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11 QTL Identified in both field and greenhouse models 7 of the field QTL were also identified using the GH data 3 major QTL Explained ~35% of the phenotypic variation combined

Other QTL were all minor Each explained <7% of variation

Fl 301 Black Shank Resistance QTL

TM108810.0TM111742.2TM104086.0PT3000511.0TM1086415.0TME042718.4TM1094819.9TM1081722.8PT107824.3TM1111429.3PT5534129.4TM1088732.0TM1094633.6PT3021834.7PT5379535.0PT3039536.1TME043736.6TM1002738.6PT5140540.7PT5275341.4PT5351842.5TME014144.2TME016346.1PT6151249.2PT4000955.6PT3017462.0PT3016565.1TM1087665.2

Field

GH

0 5

10

15

PMI LG 7 TM109120.0

TM1085717.9

TM1097730.9TM1077132.7TM1080034.2TM1038236.8TME098038.2TME041244.9

TM1072155.0

PT114061.9

TM10476a72.1TM10476b74.7TM1082178.7

TM1091488.0

TM11213a96.3

TM10681120.6

Field GH

0 2 4 6

PMI LG 4

TM108840.0TME04660.5

PT6030819.3TME074425.4TM1097026.6PT4003527.6PT5263328.6TM1120733.3PT3011434.4PT5162436.3PT6115338.9

TME073468.6

Field

GH

0 2 4 6 8

PMI LG 24

Explained 17% variation Explained 13% variation

Explained 9% variation

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Fl 301 Black Shank Resistance QTL Effect (AUDPC)‡

LOD value

% Phenotypic Variance

Explained Linkage Left Right Position Green- Green- Green-

QTL Group† Marker Marker (cM) Field house Field house Field house 1 7 PT30174 PT30165 62.02 -45.09 -49.69 8.79 11.70 16.9 18.6 2 24 TME0466 PT60308 9.53 -32.09 -44.93 3.52 7.04 9.2 15.3 3 4 TM10552 TM10983 4.94 -28.05 -47.39 3.17 8.17 6.0 10.7 4 3 TM10173 TM10175 23.44 - -28.71 - 4.06 - 5.6 5 6 TM10470 TM10922 67.38 -28.24 -21.03 4.19 2.60 7.1 5.3 6 4 TM10821 TM11213a 83.75 -24.96 -35.95 2.79 5.02 4.2 6.9 7 11 PT30137 TM11157 10.56 41.27 - 5.96 - 6.6 - 8 19 TM11026 TME0065 1.01 21.20 31.84 2.14 4.77 3.4 6.3 9 24 PT51264 PT61153 37.29 -26.29 - 2.60 - 6.1 -

10 22 TM10386 PT20149 33.62 -22.69 -27.36 2.49 3.15 3.7 5.2 11 9 TM10606 PT30110 13.86 - 30.96 - 3.46 - 4.4 12 20 TME0324a TM10386 15.11 -25.30 - 3.21 - 4.3 - 13 8/18 TM10368 TM11161 26.94 -26.29 - 3.92 - 4.2 - 14 8/18 TM10358 PT30351 78.25 - -20.93 - 2.88 - 1.7 15 11 TM1025a PT30480 22.69 - 31.84 - 4.99 - 1.2

1 x 10 -7.71 - 0.33 - 0.4 - 1 x 12 -12.46 - 0.77 - -0.9 - 1 x 15 - -27.13 - - - 5.0 2 x 10 -27.94 - - 3.59 4.6 - 4 x 6 - 14.00 - 0.95 - 0.5 7 x 8 -29.93 - 3.29 - 5.0 - 8 x15 - -25.33 - 3.13 - 1.3

12 x 13 23.59 - 2.69 - 2.0 - † Linkage groups correspond to those published by Bindler et al. (2011). ‡ Negative effect indicates that the favorable allele affecting AUDPC was derived from Florida 301. A positive effect indicates that the favorable allele wsa derived from Hicks.

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Fl 301 vs Beinhart 1000

TM10

881

0.0

TM11

174

2.2

TM10

408

6.0

PT30

005

11.0

TM10

864

15.0

TME0

427

18.4

TM10

948

19.9

TM10

817

22.8

PT10

7824

.3TM

1111

429

.3PT

5534

129

.4TM

1088

732

.0TM

1094

633

.6PT

3021

834

.7PT

5379

535

.0PT

3039

536

.1TM

E043

736

.6TM

1002

738

.6PT

5140

540

.7PT

5275

341

.4PT

5351

842

.5TM

E014

144

.2TM

E016

346

.1PT

6151

249

.2PT

4000

955

.6PT

3017

462

.0PT

3016

565

.1TM

1087

665

.2

Field

GH0

5

10

15

PMI L

G 7

Beinhart 1000 x Hicks Florida 301 x Hicks

Explained 25% variation Explained 17% variation

The QTL with the largest effect in both the Beinhart 1000 and Fl 301 mapping populations was that found on LG 7 Both confidence intervals are positioned over marker locus PT30174 Identifying this QTL in a second population further validates its

importance to black shank resistance in N. tabacum

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The QTL identified on LG 15 in the Beinhart 1000 population was not identified in the Fl 301 population This QTL is linked to 2 genes influencing the accumulation of cis-abienol and sucrose

esters on the leaf surface Fl 301 doesn’t accumulate these compounds to a measurable degree on its leaf surface

This QTL could partially explain the significant difference in resistance between these two lines If so, it is highly unlikely that this variation exists in US flue-cured or burley

germplasm

PMI L

G 1

5 X

0

5

10

15

20

PT30

346

0.0

PT20

343

0.9

PT51

164

4.5

PT61

373

10.7

PT30

124

cis-

abie

nol

12.6

PT55

091

15.3

PT60

146

17.0

PT50

962

25.5

PT51

311

35.0

PT61

362

PT52

061

40.4

BMVS

EPT

2031

5PT

3020

943

.1

PT30

354

50.5

PT60

668

72.2

PT30

223

92.2

PT30

224

93.1

PT30

272

98.8

Final Percent Disease

AUDPC

Disease Index

Abl

BMVS

E Explained 20% variation

Fl 301 vs Beinhart 1000 Beinhart 1000 x Hicks Florida 301 x Hicks 20

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Conclusions Fl 301 resistance is of the classic polygenic type Controlled by a combination of a few genes with large effects and a

greater number of genes with small to intermediate effects Fl 301 and Beinhart 1000 share the QTL on LG 7 which

contributes to the highest % of variation explained in both populations We would predict this QTL is in most varieties possessing Fl 301 type

resistance The QTL on LG 15 identified is probably unique to the Beinhart

1000 population This genetic variation likely is NOT in current varieties DNA markers associated with this region could be useful for precisely

transferring this unique variation to desired genetic backgrounds Fine mapping these regions with additional markers to more

precisely pinpoint markers associated with the resistance will aid in marker-assisted backcrossing and selection

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Altria Client Services Philip Morris International Yunan Academy of Tobacco Agricultural Sciences NCSU Center for Applied Tobacco Genetics

Acknowledgements

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