Identification of quantitative trait loci for resistance to shoot fly in maize. Yogesh Vikal

1. Identification of quantitative trait loci
for resistance to shoot fly in maize
13th Asian Maize Conference on “Maize for Food, Feed, Nutrition and Environmental Security”
Yogesh Vikal, Arshpreet Kaur, Jawala Jindal, Kirandeep
Kaur, Ashanpreet Singh, Princepal Singh and Tosh Garg
Punjab Agricultural University, Ludhiana

2. Spring maize - high yield potential and it fits in the
short window of rice-potato-maize cropping system.
Insect-pest attack- major cause for yield instability
Shoot fly : serious pest known to damage the crop
Sixteen shoot fly species have so far been recorded on
maize in Africa and Asia (Panwar and Sarup 1985).
A. naqvii Steyskal (Muscidae: Diptera) is prevalent in
North India (Sandhu and Kaushal 1976, Singh and
Kanta, 2004).
Yield loss upto 45% (Jindal 2013)
The crop losses (%) in maize due to maize shoot fly in Punjab
Spring season crop losses (%)
Maize shoot fly,
Atherigona naqvii
End Jan. Mid Feb. End Feb. Mean*
32.95 38.44 42.02 37.80
SHOOT FLY: Atherigona naqvii

3. Management of shoot fly
eggs
• Gaucho (imidacloprid) 600 FS @ 6ml/
kg of seed
• The treated seed should be used
within 14 days of the treatment
Seed treatment
• Furadan 3G (carbofuran) @ 5 kg/acre
at the time of sowingEmergence
Host Plant Resistance

4. OBJECTIVES
Studies on genetics of shoot fly
resistance in CM143 maize inbred
line
Mapping QTL for the component
traits associated with shoot fly
resistance using SSR markers
Mechanism of shoot fly resistance

5. PLANT MATERIALS
INBRED LINE PEDIGREE
CM143(female) JS2×J3022
CM144(male) Tarun×MS1Y
F2:3 PROGENIES

6. Traits
Egg Count
Leaf Injury
Dead heart

7. Leaf Glossiness
A(1) A(5)
11
B(1) B(5)
LS Pigmentation

8. C(1) C(5)
Seedling Vigor
Leaf length Leaf width Leaf area Stem girth

9. Parents/
Population
Mean Egg Count
5 DAE 10 DAE 15 DAE
CM143 6.0±0.12 13.0±0.23 20±0.21
CM144 9.5±0.22 21.0±0.11 38.50±0.19
F2:3 families 7.64±0.13 17.59±0.08 28.36±0.16
Mean egg count of parents and F2:3 families at different times

10. Parents/
Populati
on
Leaf injury (%)
7 DAE 14 DAE 21 DAE
Range Mean Range Mean Range Mean
CM143 0.0-10.0 7.0±0.114 0.0-15.0 13.0±0.167 15.0-25.0 18.0±0.10
CM144 0.0-15.0 12.0±0.126 25.0-35.0 27.0±0.118 35.0-45.0 41.0±0.23
F2:3
families
0.0-20.0 10.295±0.13 10.0-45.0 22.80±0.23 15.0-55.0 32.7±0.19
CD 12.492 CV 19.24
Dead heart (%)
CM143 0.0-5.0 1.0±0.216 5.0-10.0 7.0±0.109 10.0-15.0 13.0±0.13
CM144 0.0-10.0 4.0±0.109 15.0-20.0 18.0±0.094 25.0-30.0 28.0±0.12
F2:3
families
0.0-10.0 2.425±0.30 5.0-25.0 12.16±0.13 10.0-35.0 18.9±0.14
CD 10.734 CV 31.97
The percentage of leaf injury and dead heart data
on F2:3 families and parents at different times

11. Distribution of F2:3 families
Progress curve for parental lines and of F2:3 families at 7, 14 and 21 DAE
A
B

12. Parents/
Population
Seedling
vigor
Leaf
glossiness
leaf sheath
pigmentation
Leaf
wetness
Leaf length Leaf
width
Leaf area
Stem
girth
CM143 1.5±0.137 2±0.216 1±0.122 2±0.16 11.56±0.12 1.69±0.2 19.53±0.1 2.07±0.2
CM144 4.25±0.836 4.5±0.228 4±0.202 4.5±0.18 13.04±0.17 1.87±0.1 24.38±0.2 1.76±0.1
F2:3 families 2.182±0.19 2.706±0.06 1.659±0.311 3.28±0.12 12.00±0.17 1.71±0.1 20.53±0.1 1.98±0.2
CD 1.333 1.028 1.001 1.094 2.098 0.379 8.157 4.76
CV 30.78 19.15 30.22 16.82 7.54 10.56 15.64 11.54
Mean values of parents and F2:3 families for various morphological
characters after shoot fly infestation

13. 13 10
15
57
53
62
22
32
18
8 5 5
0
10
20
30
40
50
60
70
Seedling Vigour Leaf Glossiness Pigmentation
%agedistributionofF2:3families
R MR MS S
Distribution of F2:3 families into different classes
CM143
CM143
CM143
CM144
CM144
CM144

14. Variables SV LG LSW Pigm LL LW LA SG LI DH EC
SV 1 0.752
< 0.0001
0.739
< 0.0001
0.709
< 0.0001
-0.103
0.289
-0.087
0.373
0.008
0.932
-0.008
0.935
0.669
< 0.0001
0.669
< 0.0001
0.668
< 0.0001
LG 1 0.831
< 0.0001
0.725
< 0.0001
-0.068
0.489
-0.079
0.417
0.042
0.664
0.088
0.368
0.737
< 0.0001
0.692
< 0.0001
0.738
< 0.0001
LSW 1 0.694
< 0.0001
-0.121
0.215
-0.166
0.088
-0.023
0.810
0.079
0.419
0.769
< 0.0001
0.701
< 0.0001
0.752
< 0.0001
Pigm 1 -0.165
0.090
-0.183
0.060
-0.099
0.309
0.040
0.684
0.702
< 0.0001
0.658
< 0.0001
0.702
< 0.0001
LL 1 0.736
< 0.0001
0.854
< 0.0001
0.342
0.000
-0.027
0.783
0.022
0.819
-0.019
0.849
LW 1 0.855
< 0.0001
0.318
0.001
-0.035
0.720
-0.010
0.918
-0.036
0.712
LA 1 0.371
< 0.0001
0.113
0.248
0.131
0.180
0.100
0.307
SG 1 0.217
0.024
0.148
0.129
0.204
0.035
LI 1 0.824
< 0.0001
0.891
< 0.0001
DH 1 0.936
< 0.0001
EC 1
Phenotypic correlation coefficients of southern leaf blight (SLB) measures among recombinant
inbred lines from the cross of LM5 x CM140 population, with p values

15. Genotyping of F2 Population
Parental polymorphism
with 701 SSR markers was
accomplished and 228
polymorphic markers were
identified.
199 SSR markers were
analysed on mapping
population.
A total of 125 SSR
markers exhibited
Mendelian segregation.
74 SSR markers showed
segregation distortion.
Five of the SSR markers
did not showed linkage
with their respective
linkage group.
umc 1886
bnlg 1189
phi 026

16. qlength1.1
qwidth1.1
qwidth1.2
Qgloss1.3
qlength2.3
qwidth2.1
qarea2.3
qSV2.1
qwidth4.2
qpigm4.1
qgirth4.1
qSV6.1
qgirth9.1
qDH9.1
qEC9.1
SV QTL
length QTL pigm QTL
area QTL
width QTL
gloss QTL
girth QTL
DH QTL
EC QTL
Traits
qgirth9.2
LI QTL
LW QTL
qLI1.2
qLW2.2
Genetic linkage map showing distribution of 120 SSR markers on maize
chromosomes and QTL mapping for component traits of shoot fly resistance

17. Component
Trait
QTL Marker interval Bin LOD
score
Phenotypic
variance
(%)
Additive
effect
Dominance
effect
Gene
Action
Leaf width
qwidth1.1 bnlg1614-bnlg1083 1.02-1.02 3.68 9.32 0.0526 0.0314 PD
qwidth1.2 bnlg1083-umc1073 1.02-1.03 4.27 9.94 0.0595 0.0194 PD
qwidth2.1 bnlg1092-bnlg1338 2.01-2.01 2.65 8.16 0.05 0.0031 A
qwidth4.2 umc1667-umc2290 4.08-4.11 3.18 11.26 -0.0457 0.0312 PD
Leaf length
qlength1.1 bnlg1178-bnlg1803 1.02-1.02 4.67 4.25 0.1162 0.2853 OD
qlength2.2 umc1884-umc1233 2.05-2.05 2.94 10.85 -0.1465 0.0236 A
Leaf area
qarea1.1 bnlg1178-bnlg1803 1.02-1.02 6.28 8.48 0.3731 0.6358 OD
qarea2.2 umc1884-umc1233 2.05-2.05 2.55 9.82 -0.3392 0.1158 PD
Leaf injury qLI1.2 bnlg1083-umc1568 1.02-1.02 3.14 11.96 0.1143 - A
Leaf surface
wetness
qLW2.1 bnlg2277-bnlg2248 2.02-2.03 3.22 7.30 -0.018 - A
Leaf
glossiness
qgloss1.3 umc1306-bnlg100 1.09-1.09 2.62 12.98 0.0501 -0.0614 D
Marker intervals showing putative QTLs for shoot fly resistance
component traits

18. Component
Trait
QTL Marker interval Bin
LOD
score
Phenotypic
variance (%)
Additive
effect
Dominance
effect
Gene
Action
Leaf sheath
pigmentation
qpigm4.1 bnlg1621b-bnlg1189 4.07-4.07 3.08 7.58 0.1207 0.0439 OD
Seedling
vigour
qSV2.1 bnlg1338-bnlg2248 2.01-2.03 2.73 9.8 -0.0432 0.1402 OD
qSV6.1 bnlg238-phi077 6.00-6.01 2.80 9.7 0.0340 -0.1229 OD
Oviposition qEC9.1 umc1420-umc1258 9.03-9.03 4.09 18.49 -2.881 0.8197 OD
Dead heart qDH9.1 umc1420-umc1258 9.03-9.03 3.49 15.03 -0.0393 0.0040 A
Stem girth
qgirth9.1 umc1258-umc2134 9.03-9.05 2.65 7.26 -0.1722 -0.2282 OD
qgirth9.2 phi236654-umc1789 9.05-9.06 4.27 10.5 -0.1118 -0.5880 OD
qgirth4.1 bnlg1621-bnlg1189 -4.07 3.47 9.8 0.0670 -0.3669 OD
Marker intervals showing putative QTLs for shoot fly resistance
component traits

19. QTL likelihood plot of chromosome 9
showing putative QTL qDH9.1 and qEC9.1
QTL likelihood plot of chromosome 1 showing
putative QTL for qLL1.1, qLW1.1 and qLA1.1

20. Antixenosis
Antibiosis
Tolerance
Three fold basis Resistance based insect plant
inter action according to Painter (1951) is
Resistance Mechanism

21. S.No Bins Reporting SLB QTLs Trait Populations References
1
1.07-1.08, 1.10, 2.09, 5.00-5.01, 5.07-5.08,
6.01-6.02, 6.05-6.06, 7.03, 7.05-7.06, 8.00-
8.01, 9.02-9.04
Meditterean corn borer
RILs (B73 × CML103) Samayoa et al
(2015)
2 1.02, 1.06, 1.12, 3.05, 8.05, 9.04 Meditterean corn borer
RILs (EP39 x EP42)
(B73 x Mo17)
Ordas et al (2009,
2010)
3
1.05, 1.07-1.08, 3.09, 5.03, 5.05, 6.07, 8.05,
9.03, 10.08
European corn borer
F2:3 families (D06 ×
D408)
Bohn et al (2000)
4
1.01-1.02, 1.06, 1.07-1.08, 2.03-2.04, 2.05,
2.07, 2.08, 3.01, 3.04, 3.06, 3.07-3.08, 4.01,
5.04, 5.05, 7.02-7.03, 7.04, 8.03, 8.08, 9.01,
9.03-9.05, 10.04
European corn borer
F2:3 families & RILs
(H99 x Mo17) & (B73 x
B52)
Schon et al (1993);
Cardinal et al
(2001, 2006);
Cardinal and Lee
(2005)
5
1.01, 1.02, 1.11, 2.07, 3.02, 3.04, 3.05, 4.01-
4.02, 4.03, 5.02, 5.03, 5.07, 6.01, 6.05, 7.01-
7.03, 7.05, 8.03, 8.04-8.05, 9.00, 9.08, 10.03,
10.06
European corn borer
F2:3 families & RILs
(B73 x De811)
Krakowsky et al
(2002, 2004)
6
1.01, 1.02, 1.07, 2.04, 3.09, 5.03, 5.04, 5.05,
5.07, 6.06-6.07, 7.04, 7.05, 8.04-8.05, 10.04
European corn borer
F2:3 families and test
cross progeny (D06 ×
D408)
Papst et al (2004)
7
1.01, 1.06, 1.11, 2.01, 2.09, 4.01. 4.06, 5.05,
5.08, 6.00, 6.02, 6.07, 8.03, 8.06, 9.02
European corn borer
F2:3 families (B73 x
Mo47)
Jampatong et al
2002)
Summary of location of insect pest resistance QTL in maize

22. S.No Bins Reporting QTLs Trait Populations References
8
1.01-1.02, 1.03-1.04, 1.06, 1.07, 1.08,
1.10,1.11, 2.02, 3.05, 3.07-3.09, 4.04,
5.02, 5.04, 5.05-5.06, 5.07, 6.02, 6.04-
6.05, 6.06, 7.02-7.03, 7.04-7.05, 8.02,
8.03, 8.05, 8.06-8.08, 9.02, 9.03, 9.04,
9.05-9.06, 10.03-10.06
South western
corn borer
F2:3 families & RILs
(CML139 x Ki3; CML67 x
CML131; CML67 x
CML204; Mp704 x Mo17;
Mp708 x A619)
Bohn et al (1997);
Khairallah et al (1998);
Groh et al (1998a);
Willcox et al (2002);
Brooks et al (2005,
2007)
9
1.01, 1.08, 2.04, 2.05, 4.01, 9.01, 9.02,
10.01
Asian corn borer
F2:3 families (Mc37 x
Zi330)
Xia et al (2010)
10
1.02, 1.03, 1.05, 1.09. 1.11, 2.02, 2.08,
5.02, 5.04, 5.07, 6.02, 6.07, 7.02, 7.03,
7.04, 8.03, 9.03, 9.05, 9.07, 10.04
Fall army worm
F2:3 families (Mp704 x
Mo17; Mp708 x A619)
Brooks et al (2005,
2007)
11
1.02, 1.07, 2.05, 2.09, 3.06-3.07, 4.03,
4.08, 6.00, 5.03, 5.05, 6.05, 7.01-7.02 ,
8.06, 9.07, 10.04, 10.06-10.07
Maize weevil
F2:3 families
(CML290 × Muneng-8128
C0 HC1-18-2-1-1)
García-Lara et al
(2009); Castro Alvarez
et al (2015)
12
1.03, 1.06, 1.07, 1.11, 2.02-2.03, 3.05,
5.04, 5.05-5.06, 5.07, 7.02, 7.03, 7.04,
9.02-9.03, 9.04, 9.05-9.06, 10.04
Sugarcane borer
F2:3 families
(CML131 x CML67)
Bohn et al (1996,
1997); Groh et al
(1998b)
13 1.04, 2.02, 2.09, 4.06, 6.01, 6.06, 10.04 Corn ear worm
F2:3 families
(GE37 x FF8) Byrne et al (1998)
Summary of location of insect pest resistance QTL in maize

23. Bin Gene ID Description Functional role
1.09 Zm00001d033420 MYB-related transcription Anthocyanin synthesis
LG Zm00001d033375
ubiquitin carboxyl-terminal hydrolase 15-
like
jasmonic acid mediated signaling pathway
Zm00001d031359 reactive oxygen species modulator 1-like
ROS play in cellular physiology to ascertain their
position in the life of the plant.
Zm00001d029658 TPA: glycosyl hydrolase family 10 Biotic, abiotic stresses and cell wall remodeling
Zm00001d030026 peroxidase 44-like involved in lignin biosynthesis
1.02-
1.03
Zm00001d028168 Glycosyl hydrolase family 10 expressed Biotic, abiotic stresses and cell wall remodeling
LW Zm00001d028115
inactive TPR repeat-containing
thioredoxin TTL3-like
Involved in osmotic and salt stress tolerance.
May play a role in the control of meristematic
cell size during osmotic stress
4.07 Zm00001d053166 auxin response factor 15-like
transcriptional factors that bind specifically to
the DNA sequence 5'-TGTCTC-3' found in the
auxin-responsive promoter elements (AuxREs).
Zm00001d053522
Biotic, abiotic stresses and cell wall
remodeling
disease resistance RPS2-like
6.0-6.01 Zm00001d035425
cell death,pentose-phosphate shunt, non-
oxidative branch,vegetative to
reproductive phase transition of meristem
TPA: ribose-5-phosphate isomerase
SV Zm00001d036036 protect the cell from oxidative damage glutathione S-transferase
Zm00001d048047
probable cyclic nucleotide-gated ion
channel 6
development and as a ‘guard’ in defense against
biotic and abiotic challenges
A list of the putative candidate genes QTL intervals for shoot fly resistance in maize

24. Bin Gene ID Description Functional role
9.03 Zm00001d045551 probable phosphatase 2C 13
regulators of various signal transduction
pathways
Zm00001d046039 target of Myb 1
play roles in a number of developmental and
stress-responsive: Zea mays C1 involved in
anthocyanin biosynthesis by encoding c-myb-
like transcription factor
Zm00001d046344 Extracellular sulfatase Sulf-1 regulate growth factor signaling
Zm00001d046625 TPA: glycosyl hydrolase family 10
Biotic, abiotic stresses and cell wall
remodeling
Zm00001d046710 myosin heavy chain PCR43
beta-myosin heavy chain expression on
cardiac function during stress
Zm00001d046938 leucine-rich repeat kinase family
structure, function, and signal transduction
pathways
Zm00001d047015 TPA: cytochrome P450 superfamily
these proteins are important for the
biosynthesis of several compounds such as
hormones, defensive compounds and fatty
acids
9.03-9.05 Zm00001d047981 glutamate decarboxylase 1-like
plays a major role in GABA synthesis in plants
under normal growth conditions and in
response to stress
9.05-9.06 Zm00001d045551 probable phosphatase 2C 13
regulators of various signal transduction
pathways
A list of the putative candidate genes QTL intervals for shoot fly resistance in maize

25. QTLs
Maize
Chr.No.
Synteny with
Sorghum Chr.
qgirth9.2 Zm9 Sb1
qgirth9.1
Zm9 Sb10
Zm9 Sb1
qDH9.1,qEC9.1 Zm9 Sb10
qSV6.1
Zm6 Sb7
Zm6 Sb8
Zm6 Sb9
Zm6 Sb10
qwidth4.1 Zm4 Sb4
qpigm4.1, qgirth4.1 Zm4 Sb4
qLSW2.1 Zm2 Sb6
qarea2.1,qlength2.1
Zm2 Sb6
Zm2 Sb5
Zm2 Sb2
qSV2.1 Zm2 Sb6
qLI1.1 Zm1 Sb1
qwidth1.2 Zm1 Sb1
qwidth1.1 Zm1 Sb1
qarea1.1,qlength1.1 Zm1 Sb1
qgloss1.2 Zm1 Sb1

26. Numerous studies have been conducted to map QTLs for resistance to
European corn borer, Mediterranean corn borer, Asian corn borer, maize
weevil, Fall army worm and sugarcane borer.
Therefore, the results of the present study are novel as it constitutes a
major step toward identification of genomic regions associated with shoot
fly resistance.
Major components accounting for resistance are dead heart and leaf injury.
Putative QTL associated with various component traits were detected on
chromosome 1, 2, 4, 6 and 9
Co-localization of QTL for different traits may result from either tight
linkage of several genes or the pleiotropic effect of a gene.
QTL interval Xtxp65-Xtxp30 of sorghum chromosome 10 was found to be
syntenic to regions of chromosome 9.
Lines possessing superior resistance to shoot fly were also identified and
are being used as germplasm source for breeding shoot fly resistance.
Fine mapping of QTL is in progress.
Conclusions

27. THANKS