Post on 09-Feb-2021
Genetic and QTL mapping of Fusarium wilt (FOV) race 1 & race 4 resistance in cotton for breeding
Mauricio Ulloa, USDA‐ARS, WICS Shafter
Bob Hutmacher, Dept. Plant Science, UC‐Davis, Shafter
Mike Davis, Dept. of Plant Pathology, UC Davis
Steve Wright, UC Cooperative Extension, Tulare
Phil Roberts and Congli Wang, Dept. Nematology, UC Riverside
• FOV Plant Symptoms:• Wilting, yellowing, and necrosis of leaves.
• Internally, the xylem is dark brown [vascular root stain (VRS)].
Plant Material & Tests
Used two Mapping Populations:• F2 Pima‐S7 x ‘Acala NemX’ • RIL Upland TM‐1 x Pima 3‐79
RIL Population evaluated in:• Three greenhouse artificial inoculated tests ( 4 –
5 plants in a CRD)• One known infested race 1 FOV field test ( 5
plants, two reps, RCBD)
FOV race 1 assays
• Used disease severity index (DSI) of leaves, and vascular stem and root staining [VRS (Scale 0 ‐5)].
• Disease was monitored on plants at different days after inoculation (dai) 9, 12, 14, 16, 19, 23, and 24.
• QTL used mean phenotypic scores of dai from the various experiments.
Greenhouse TestSeeded RIL Population
race 1 FOV infection days after Inoculation (dai)
race 1 FOV Seedling Inoculation
Plant InfectionDisease severity index (DSI) of leaves, (scale 0 – 5)
Vascular stem and root staining (VRS)
DSI = 0 DSI = 2 ‐ 3 DSI = 5
VRS = 0 VRS = 2 ‐ 3 VRS =5
Field Assay
Field Assay
2006 Day 9 UC Riverside 139 2.84 1.372006 Day 14 139 3.68 1.232006 Day 23 139 4.56 0.88
2007 Day 12 UC Riverside 138 1.24 0.992007 Day 14 138 2.68 1.142007 Day 16 138 3.48 1.002007 Day 19 138 3.89 0.952007 Day 23 138 4.24 0.90
2008 Day 24 UC Kearney 137 2.52 1.08
Field Test Shafter CA RIL No Mean SD
2007 Day 67 after planting 113 1.61 0.71
2007 Day 67 % Survival 113 85.74 13.37
2007 Day 146 % Survival 113 27.39 19.36
0
10
20
30
40
50
60
70
80
12 Days 14 Days 16 Days 19 Days 23 Days
Nu
mb
er o
f RIL
s
Days after Inoculation (dai)
Disease Severity Index (DSI)
0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0
3-79
TM-1 3-79 TM-1
3-79 TM-1
F1s ranged from 2.3 to 4.3 (Pima S-7 x Acala NemX)
Genotype/Population
Expected Ratios R:H:S & R:S
Observed ratio R:S χ2 P‐value
Parents
Pima S7 All R 38:5
Acala NemX All S 5:39
F1 All S 6:60
F2 33:100 (1:3) 31:102 0.203 NS
Parents
Upland TM1 All S 0:5
Pima 3‐79 All R 4:1
RIL (2007) Day 14 41:97 (1:3) 35:103 1.379 NS
(1:1) 35:103 18.03 0.001
Upland TM1 All S 0:4
Pima 3‐79 All R 1:3
RIL (2008) Day 24 52:78 (1:3) 34:103 17.83 0.001
52:78 (1:1) 68:69 4.94 0.05
Race 1 FOV Inheritance in Pima by Acala and Upland by Pima Cottons
LocusTM1 allele
Mean3‐79 allele
Mean K*† P value
24 SSRs Identified 2.88 ‐ 3.10 1.70 – 2.35 8.2 – 22.5 0.01
SSR Markers and QTLs for FOV race 1 Resistance based on Vascular Stem and Root
Staining
Nine Chromosomes: 01, 06, 08, 09, 11, 12, 15, 16, and 19
†Kruskal‐Wallis analysis (K*) test ‐ nonparametric 1‐way ANOVA
C I R 2 0 3 _ 2 4 0 b0 . 0G h 0 3 2 _ 1 1 6 / 9 74 . 5
B N L 2 5 6 9 _ 1 6 4 / 1 6 91 0 . 9G h 0 3 9 _ 1 3 1 / 1 1 91 5 . 3
N A U 5 2 6 9 _ 1 5 0 / 1 5 52 5 . 8
M U S B 0 7 5 4 _ 3 5 9 h4 5 . 4
B N L 3 8 1 2 _ 2 4 7 / 2 9 56 3 . 2
M U S S 2 7 5 _ 2 2 3 b7 8 . 1
B N L 2 8 8 4 _ 1 7 7 / 1 9 38 9 . 2
M U S B 0 7 8 0 - 1 3 5 / 1 3 20 . 0N A U 1 3 3 6 _ 1 6 3 / 1 5 94 . 3M U S S 1 3 0 _ 2 5 7 - 2 5 14 . 9N A U 1 1 6 4 _ 1 7 4 / 1 6 95 . 7
N A U 3 6 0 5 _ 2 2 2 / 2 2 71 3 . 8N A U 1 0 3 7 _ 2 1 3 / 2 2 11 4 . 9N A U 4 9 0 0 _ 1 4 8 / 1 4 21 7 . 0B N L 3 2 5 51 9 . 4M U S B 0 4 2 2 _ 3 3 02 2 . 0M U S B 0 1 0 0 - 1 0 4 / 9 42 4 . 2M U S S 2 5 0 b2 4 . 6N A U 3 7 0 8 _ 2 3 7 / 2 2 83 0 . 0
N A U 0 8 9 13 7 . 8N A U 0 9 5 4 _ 2 0 8 / 2 0 03 9 . 1N A U 1 3 0 2 _ 2 1 6 / 2 0 34 3 . 7M U C S 1 1 34 6 . 4N A U 3 4 9 9 _ 2 7 0 / 2 8 54 7 . 5
M U S S 0 2 20 . 0
B N L 2 5 9 08 . 8
M U S S 0 8 31 4 . 3
B N L 1 4 1 42 1 . 4M U S S 1 8 1 _ 1 8 3 / 1 8 42 2 . 9
N A U 1 0 4 6 _ 2 3 1 / 2 2 62 9 . 1M U C S 0 3 1 _ 2 6 . 0 h3 3 . 1G h 2 4 73 5 . 2B N L 1 3 1 73 6 . 9G h 4 8 44 1 . 4N A U 1 0 0 94 4 . 1M U C S 0 8 04 5 . 8M U S S 2 6 64 8 . 7G h 1 1 85 2 . 3N A U 3 9 6 7 _ 2 6 2 b5 3 . 1G h 4 9 55 4 . 8M U S S 5 7 9 _ 1 7 3 / 1 7 15 7 . 3N A U 1 3 6 0 _ 2 2 3 / 2 1 56 1 . 2M U S S 5 4 76 4 . 4B N L 1 6 7 26 6 . 8M U S S 1 1 0 _ 2 7 5 / 2 7 76 9 . 0M U S S 3 1 67 2 . 6M U C S 3 2 57 6 . 4
M U S B 0 4 0 4 _ 3 6 5 h0 . 0
C I R 0 0 3 _ 1 3 2 / 1 3 51 3 . 3
M U S B 0 8 4 9 _ 2 4 8 b1 8 . 6M U S B 0 8 2 7 _ 3 2 6 / 3 2 22 2 . 8B N L 3 5 9 2 _ 2 0 7 / 1 9 92 6 . 5B N L 1 4 0 8 _ 2 0 7 / 1 9 72 9 . 4N A U 1 0 1 4 _ 2 7 6 b3 1 . 9M U S B 1 2 7 8 _ 3 9 9 b3 3 . 5M U S B 0 8 2 3 _ 2 2 7 / 2 3 53 6 . 7M U S B 1 1 6 3 _ 2 8 8 b3 8 . 3M U S B 1 0 3 5 _ 4 2 5 h4 0 . 2M U S S 0 9 2 _ 3 1 4 / 3 1 84 4 . 5
M U C S 3 9 9 _ 2 1 9 / 2 2 44 9 . 1
M U S B 1 0 1 5 _ 2 9 7 b5 5 . 0
M U S B 0 6 4 1 _ 3 0 2 h6 7 . 2M U S B 1 0 0 0 _ 3 5 6 / 3 0 86 9 . 3
B N L 0 5 8 0 _ 2 7 4 h0 . 0
B N L 2 9 8 6 _ 1 6 5 / 1 7 11 0 . 2
B N L 3 0 0 8 _ 1 4 4 / 1 5 51 5 . 3G h 2 9 5 _ 9 6 / 8 41 7 . 8
M U C S 5 9 4 _ 2 4 0 b2 6 . 8G h 3 4 5 _ 1 2 2 / 1 1 33 0 . 3
M U C S 6 1 6 _ 0 / 2 3 74 0 . 8
M U S B 0 8 1 2 _ 4 3 4 / 3 9 74 7 . 0
N A U 0 9 2 20 . 0
C I R 3 7 36 . 1N A U 3 6 5 0 _ 2 5 6 h9 . 9
N A U 5 2 7 3 _ 2 5 8 b1 6 . 0
N A U 2 5 0 3 _ 2 4 0 / 2 1 72 5 . 3N A U 1 2 2 1 _ 2 3 2 / 2 3 82 6 . 9G h 1 0 9 _ 1 1 9 / 1 0 83 1 . 5N A U 2 8 1 6 _ 1 7 0 / 1 7 83 1 . 9B N L 3 3 4 7 _ 1 7 7 / 1 7 03 3 . 7B N L 8 5 2 b3 7 . 8B N L 0 8 2 7 _ 1 8 6 / 1 9 03 9 . 3B N L 1 6 7 1 _ 1 8 7 / 1 6 14 3 . 2B N L 1 6 7 1 _ 1 8 2 / 1 7 34 7 . 9
N A U 2 2 3 2 _ 1 8 1 h5 4 . 1
Chromosome 6 Chromosome 9 Chromosome 16
Chromosome 8 Chromosome 11 Chromosome 19
QTL =
MGG 2011
MUCS594_269b0.0MUSB0812_452h0.6
MUCS616_256b10.7
M1E731.1BNLl3008_150/13933.3Gh295_86/10034.3M-CAA_E-AGC-16935.5
M-CAA_E-AAC-8540.2
Gh345_116/12642.8
Fov148.5
Fov1-C1652.0MUSB0812_412/40152.3
BNL0580_274h0.0
BNL2986_165/17110.2
BNL3008_144/15515.3Gh295_96/8417.8
MUCS594_240b26.8
Gh345_122/11330.3
MUCS616_0/23740.8
Fov1-C1646.9MUSB0812_434/39747.0
Chromosome 16
F2 (Pima‐S7 x NemX) Population
RIL (TM1 x Pima 3‐79) Population
Major QTLs were detected : QTL on chromosome 6 explained from 8.0 to 22.3% of variation in DSI with additive effect ranging from 0.33 to 0.51. QTL on chromosome 8 explained from 8.8 to 10.6% of DSI variation with additive effect ranging from 0.31 to 0.33. QTLs on chromosome 11 (two) explained from 9.0 to 14.2% of DSI variation with an additive effect averaging 0.39 − 0.43. QTL on Chromosome 19explained 13% of DSI variation with an additive effect of 0.46.
QTL explained 27% of DSI variation with an additive
effect of 0.77.
QTL explained 31% of VRS variation with an additive
effect of 0.72.
LOD > 6
Mapping Fusarium wilt (FOV) race 1 resistance summary
A set of 24 SSR markers indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five. Breeding targets.
The single recessive locus (Fov1), previously identified in F2 (Pima‐S7x NemX) mapped to chromosome 16 and co‐located with the Fov1 and QTL in the TM1 x 3‐79 RIL. Breeding target.
Breeding for Race 4 Fusarium wilt (FOV) Disease Resistance
Fusarium wilt (FOV) Symptoms
Plant InfectionResistant < 2.0 & Susceptible > 2.0
Disease severity index (DSI) of leaves, (scale 0 – 5)
Vascular stem and root staining [VRS (scale 0 ‐ 5)]
DSI = 0 DSI = 2 ‐ 3 DSI = 5
VRS = 0 VRS = 2 ‐ 3 VRS = 5
Race 4 FOV Disease ResistanceResistant & Susceptible
Resistant & F1 Progeny
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
NMSI
1601
8810
DP-74
4Ph
yto-81
0RPh
yto-80
0OA
-353
PS-7
A1_9
A1_1
8A1
_52
A2_3
1A2
_72
A2_8
0A2
_241
D_65
D_70
F_DamageV_Stain
Identification of Resistant Sources from Early EvaluationsPima Cottons and Accessions
PS: R2 = 0.56 &
h2 = 0.61
F_Damage: R2 = 0.58 &
h2 = 0.64
VRS: R2 = 0.63 &
h2 = 0.70
VRS
VRS
Sca l e
Race 4 FOV Inheritance Ulloa et al (2006)
Pima by Pima Crosses
Root top Vascular Stain Evaluation
Vascular Root Staining Fusarium wilt (FOV)
0.000.501.001.502.002.503.003.504.004.505.00
Phyto
gen 7
2
Pima S
-7Ph
ytoge
n 800
SJ-07
P-FR0
1SJ
-07P-F
R02
SJ-07
P-FR0
3SJ
-07P-F
R04
Cultivars
Roo
t Sta
inin
g
S40 FOV race 1 & RKNKern FOV race R4Fresno FOV race R4
Plant Percentage Survival
Percentage Survival Rate Fusarium wilt (FOV)
0.010.020.030.040.050.060.070.080.090.0
100.0
Phyto
gen 7
2
Pima S
-7Ph
ytoge
n 800
SJ-07
P-FR
01SJ
-07P-
FR02
SJ-07
P-FR
03SJ
-07P-
FR04
Cultivars
Perc
enta
ge S40 FOV race 1 & RKNKern FOV race R4Fresno FOV race R4
Four Pima Germplasm Lines Jointly Released by USDA-ARS, Univ. of California, & NMSU
SJ-07P-FR01
SJ-07P-FR02
SJ-07P-FR03
SJ-07P-FR04
Continuing efforts for releasing additional germplasm with improved Yield, Fiber, and Pest Resistance
0.00
400.00
800.00
1,200.00
1,600.00
2,000.00
2,400.00
2,800.00
3,200.00
3,600.00
4,000.00
Seed Cotton Lint Yield
Pima New Releases USDA-ARS and Univ. of CA. (R. Percy, R. Hutmacher, S. Wright, and M. Ulloa)
LB per Acre
0.00
0.50
1.00
1.50
2.00
2.50
F_Damage
V_Stain
Identification of Resistant Sources from Early EvaluationsAcala and Upland Cottons
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
4.50
5.00
AU‐1107
AU‐5367
AU‐5491
AU‐6103
Ark0001‐01
‐03
Ark0002‐03
‐02
Ark0008‐22
‐10
Ark0012‐03
‐08
Ark0015‐06
‐11
GA2
004089
GA2
004230
GA2
004303
GA2
006128
LA05307029
LA05307061
LA05307083
LA05307094
0149
‐17 ne
0147
‐22 ne
0020
‐31 ne
0028
‐16 ne
8921
‐2‐2‐14‐13
‐11
04PST‐246
04PST‐250
04‐PST‐275
Acala 1517
‐99
NM 03012
PD03011
PD03025
PD04012
PD99041
TAM B182‐34
DP 393
FM 958
Phytogen
72
SG 105
Pima‐S7
Phytogen
800
SJ‐07P
‐FR0
1
SJ‐07P
‐FR0
2
SJ‐07P
‐FR0
3
SJ‐07P
‐FR0
4
Shafter FOV race 1 & RKN Kern FOV race 4 Fresno FOV race 4
Vascular Root Staining [scale 0 = no staining to 5 = plant death]
AL AR GA LA MS MS NM SC TX Checks CA
RBTN Entries in 2008
0
10
20
30
40
50
60
70
80
90
100
AU‐5491
AU‐5367
AU‐6103
AU‐1107
Ark0012‐03
‐08
Ark0015‐06
‐11
Ark0002‐03
‐02
Ark0001‐01
‐03
Ark0008‐22
‐10
GA2
004230
GA2
004089
GA2
004303
GA2
006128
LA05307029
LA05307061
LA05307083
LA05307094
0149
‐17 ne
0147
‐22 ne
0020
‐31 ne
0028
‐16 ne
8921
‐2‐2‐14‐13
‐11
04PST‐250
04‐PST‐275
04PST‐246
Acala 1517
‐99
NM 03012
PD99041
PD04012
PD03025
PD03011
TAM B182‐34
DP 393
FM 958
SG 105
Phytogen
72
Pima‐S7
Phytogen
800
SJ‐07P
‐FR0
1
SJ‐07P
‐FR0
2
SJ‐07P
‐FR0
3
SJ‐07P
‐FR0
4
Shafter FOV race 1 & RKN Kern FOV race 4 Fresno FOV race 4
AL AR GA LA MS MS NM SC TX Checks CA
Percent of Plant Survival [scale 0 to 100 %]
RBTN Entries in 2008
QTL mapping & breeding resistance to FOV race 4
1200 genome-wide markers analyzed
Populations from Upland-by-Upland, Upland-by-Pima, and Pima-by-Pima cottons.
FBCX-2 Shorty PS 6 3-79 DP 744 Uzbekistan A1
Nem_ARS X X X X X
FBCX-2 X X X
Shorty X X X XPS 6 X X X XPS 7 X X X X X X
DP 744 X X X XTM 1 X X XA2 X
Parents, Crosses, & Progeny for FOV & Root-knot nematode Research
0
20
40
60
0 1 2 3 4 50
20
40
60
0 1 2 3 4 5
Num
ber o
f R
ILs
0
20
40
60
80
0 1 2 3 4 5
0
10
20
30
40
0 1 2 3 4 5
0
20
40
60
0 1 2 3 4 5
0
20
40
60
0 1 2 3 4 5
A
Num
ber o
f Pl
ants
Num
ber o
f R
ILs
Num
ber o
f R
ILs
Num
ber o
f Pl
ants
Num
ber o
f Pl
ants
TM-1
Pima-S6F1
Pima-S6
F1
B
C
Shorty
Pima-S6Shorty
D
E
F
TM-1Pima 3-79
Pima 3-79TM-1
Pima 3-79
TM-1
FOV 4 Screens for VSR in F2 and RILs
VRS Scale VRS Scale
VRS Scale
VRS Scale VRS Scale
VRS Scale
MUSB0255_228/2640.0Gh465_1161.9Gh272_134/1244.3GH237_102/1116.9
GH171_248/23411.2
MUSS354_3970.0
Fov4-C146.0
BNL0834_150/14326.9
CIR2921_49/19045.5
BNL3932_249/23652.0
CIR228_20165.7
A
BNL3347_172/1590.0
Gh109_107/9411.0
NAU2816_176/8414.9
NAU1221_233/24120.1
BNL1671_19329.1
NAU2232_159h38.4
BNL1690_128/14142.3
Gh537_174/1650.0
Gh224_111/1048.6
BNL3103_192/21012.9NAU3092_163/15815.1
BNL2691_304/29023.0
A
Chromosome 8
Chromosome 14
Chromosome 19
Chromosome 25
Fig 2
Major QTLs =Detected on three populations:RIL TM-1 x Pima 3-79 (A)F2 TM-1 x Pima-S6 (B)F2 Shorty x Pima-S6 (C)
Minor QTLs = Detected on at least two populations:
A B C
BC A B
C
A B
Major QTL for FOV1 QTL on chromosome 16 explained from 27 to 31% of variation in DSI & VRSwith additive effect ranging from 0.72 to 0.77.QTL on chromosome 6 explained from 8.0 to 22.3% of variation in DSI with additive effect ranging from 0.33 to 0.51. QTL on chromosome 8 explained from 8.8 to 10.6% of DSI variation with additive effect ranging from 0.31 to 0.33. QTLs on chromosome 11 (two) explained from 9.0 to 14.2% of DSI variation with an additive effect averaging 0.39 − 0.43. QTL on Chromosome 19 explained 13% of DSI variation with an additive effect of 0.46.
Major QTL for FOV4 QTL on chromosome 8 explained from 5 to 19% of variation in DSI & VRS.QTL on chromosome 14 explained from 18 to 80% of variation in DSI with additive effect ranging from 0.36 to 1.58; and 76% of variation for DSI and 1.10 additive effect. QTL on chromosome 19 explained 72% of VRS variation with dominant effect ranging of 1.80. QTLs on chromosome 25 explained from 15% of VRS variation and 1.80 additive effect .
Different QTL for Resistance to Race 1 and Race 4