“Molecular mapping of flowering time
genes in chickpea (Cicer arietinum L.)”
Supervisors: Dr. Pooran Gaur, ICRISAT Dr. K. P. Viswanatha, UAS-Raichur
Mallikarjuna B.P. Ph.D. Scholar University of Agricultural Sciences, Raichur, Karnataka
Chickpea (Cicer arietinum L.)
A diploid (2n=2x=16), self-pollinated food legume with genome size of 740 Mbp
World’s second most important food legume, grown in 13 mha area, over 50 countries globally (FAOSTAT, 2015)
India - largest chickpea producing country having cultivated in 9.6 mha with total production of 8.8 m tonnes (FAOSTAT, 2015)
Major source of protein (22-28%), good source of Fe, Zn, β-carotene, dietary fiber
Mostly grown as a post-rainy season crop in the semi-arid tropics and a spring/summer crop in the Mediterranean and Temperate regions
2
Abiotic stress
Drought stress
Heat stress
Salinity stress
Low temperature stress
Biotic stress
Fusarium wilt (FW)
Ascochyta blight
dry root rot (DRR)
botrytis grey mold (BGM)
Pod borer
3
Constraints to chickpea production:
Breeding strategies: Developing early maturing varieties
• Escape end-of-season high/low temperature stress
• Can be cultivated in a short window of cropping season
• Enhance cropping intensity and crop diversification opportunities
Terminal drought/heat stress Moisture & high temperature stress that
occurs at pod filling & seed development stage with increasing severity towards the end-of-season
Major constraint to chickpea production in over 80% of global chickpea area
Importance of early maturing varieties
Number of days from sowing to appearance of first fully opened flower
Can be recorded with high precision and provides good indication of days to podding and maturity
Important component for adaption of chickpea to various environments
Influenced by many factors (temperature, photoperiod, altitude, latitude, genotype)
Four early flowering genes have been reported in chickpea
- efl-1 (in ICCV 2, ICCV 96029)
- elf-2 (in ICC 5810)
- efl-3 (in BGD 132) and
- efl-4 (in ICC 16641)
4
Flowering time
Objectives
I. Genetics of flowering time genes
II. Development of genetic linkage map
III. QTL mapping for flowering time genes
IV. Association of flowering time with maturity and yield related traits
Desi Kabuli
5
Objective 1
Genetics of flowering time genes
6
Materials and methods
Line Origin Early flowering gene reported
Reference
Female parents
ICCV 96029 Cross-bred efl-1 Kumar and Rheenen (2000)
ICC 5810 India ppd/efl-2 Or et al. (1999)
BGD 132 Cross-bred efl-3 Hegde (2010)
ICC 16641 Pakistan efl-4 Gaur et al. (2015)
Male parent
CDC Frontier Cross-bred (Canada)
- Warkentin et al. (2005)
Plant Material:
Experimental site: ICRISAT, Patancheru
All the four female lines were crossed to a common male parent (CDC Frontier) to develop F1s and the F1 seeds were selfed to develop F2 mapping populations
7
Sl. No.
Cross Population size
F2 F3
1 ICCV 96029 × CDC Frontier 190 164
2 ICC 5810 × CDC Frontier 190 174
3 BGD 132 × CDC Frontier 190 182
4 ICC 16641 × CDC Frontier 146 102
Post rainy season, 2013-14: Parental lines, F1s and F2 populations were evaluated for flowering time and yield related traits
Planting was done in 4m row at a wider spacing of 60 cm x 20 cm
Post rainy season, 2014-15: Parents and F3 progenies (20 plants in each progeny row of 2m length) were evaluated for flowering time
Evaluation for flowering time:
8
Desi Kabuli
Figure 1. General view of the experimental plot of evaluation of F2 populations for flowering time conducted during post-rainy season of 2013-14
Figure 2. Segregation for flowering time and maturity in the F2 population of the cross ICC 5810 × CDC Frontier
9
Early
Medium
Late
Table 1. Flowering time & maturity of parental lines
Sl.
No. Parents N
Flowering time Days to maturity
Mean ± SE Range Mean ± SE Range
1 ICCV 96029 20 26.85 ± 0.21 25-28 75.55 ± 0.30 75-81
2 ICC 5810 20 28.35 ± 0.15 28-30 77.25 ± 0.16 77-80
3 BGD 132 20 28.55 ± 0.11 28-29 78.95 ± 0.23 78-83
4 ICC 16641 20 29.00 ± 0.00 29-29 79.00 ± 0.00 79-79
5 CDC Frontier 20 66.90 ± 0.25 65-68 108.15 ± 0.59 104-112
Sl.
No.
Cross N
Flowering time Days to maturity
Mean ± SE Range Mean ± SE Range
1 ICCV 96029 × CDC Frontier 20 61.20 ± 0.33 59-63 92.95 ± 0.46 90-95
2 ICC 5810 × CDC Frontier 20 54.15 ± 0.19 53-55 89.75 ± 0.76 84-95
3 BGD 132 × CDC Frontier 20 53.30 ± 0.31 51-55 94.50 ± 0.53 91-98
4 ICC 16641 × CDC Frontier 20 60.80 ± 0.39 59-64 94.65 ± 0.60 90-99
Table 2. Flowering time & maturity of F1s
Results: Post rainy season, 2013-14
10 N = Total no. of plants
Desi Kabuli
Figure 3. Frequency distribution of flowering time in F2 populations
11
Desi Kabuli
Sl.
No. Cross N
Observed Expected Ratio
tested χ2
P-value* Late Early Late Early
1 ICCV 96029 × CDC Frontier 190 138 52 142.5 47.5 3:1 0.57 0.5-0.3
2 ICC 5810 × CDC Frontier 190 108 82 106.8 83.1 9:7 0.03 0.9-0.8
3 BGD 132 × CDC Frontier 190 143 47 142.5 47.5 3:1 0.01 0.95-0.9
4 ICC 16641 × CDC Frontier 146 110 36 109.5 36.5 3:1 0.01 0.95-0.9
Table 3. Segregation of flowering time in F2 populations
*Null hypothesis of the test is that progeny segregate in the ratios tested. If the p-value (probability) is less
than or equal to 0.05, then reject the null hypothesis. Otherwise one fails to reject the null hypothesis.
12
ICCV 96029 × CDC Frontier
Figure 4. Segregation of flowering time in F3 progenies of different crosses
ICC 5810 × CDC Frontier
BGD 132 × CDC Frontier ICC 16641 × CDC Frontier
Early
Segregating Late
Late Segregating Early
Late Segregating Early Late Segregating Early
13
Desi Kabuli
Table 4. Segregation of flowering time in F3 progenies of four crosses
*Null hypothesis of the test is that progeny segregate in the ratios tested. If the p-value (probability) is less
than or equal to 0.05, then reject the null hypothesis. Otherwise one fails to reject the null hypothesis.
Sl.
No. Cross
Phenotypic
class
No. of
progeny
tested
Observed Expected Ratio
tested χ2
P-value* Segregating Non-
segregating Segregating
Non-
segregating
1
ICCV 96029 ×
CDC Frontier
Late 127 87 40 84.6 42.3 2:1 0.19 0.7-0.5
Early 37 0 37 0 37 0:1 0 1.0
2
ICC 5810 ×
CDC Frontier
Late 103 87 16 91.5 11.4 8:1 2.04 0.2-0.1
Early 71 44 27 40.5 30.4 4:3 0.67 0.5-0.3
3
BGD 132 ×
CDC Frontier
Late 138 94 44 92 46 2:1 0.13 0.8-0.7
Early 44 0 44 0 44 0:1 0 1.0
4
ICC 16641 ×
CDC Frontier
Late 77 54 23 51.3 25.6 2:1 0.41 0.7-0.5
Early 25 0 25 0 25 0:1 0 1.0
Post rainy season, 2014-15
14
Objective 2
Development of genetic linkage map
15
Marker No. Reference
KASPar SNPs 714 Hiremath et al. (2012); Jaganathan et al. (2013)
SSRs
CaM-series 146 Thudi et al. (2011)
Winter-series 135 Winter et al. (1999)
ICCM-series 124 Nayak et al. (2010)
H-series 57 Lichtenzveig et al. (2005)
NCPGR-series 10 Gaur et al. (2011); Sethy et al. (2006)
Total 472
Table 5. Markers used for parental polymorphism study
16
Sl. No.
Cross
SNPs SSRs
Total No. of markers screened
No. of polymorphic markers
Total No. of markers screened
No. of polymorphic markers
1 ICCV 96029 × CDC Frontier
714 49 (6.9 %) 472 100 (21.4 %)
2 ICC 5810 × CDC Frontier
714 44 (6.2 %) 472 95 (20.1 %)
3 BGD 132 × CDC Frontier
714 36 (5 %) 472 90 (19 %)
4 ICC 16641 × CDC Frontier
714 29 (4 %) 472 93 (19.7 %)
Table 6. Parental polymorphism status
Results:
Polymorphic markers were genotyped on respective mapping population
Construction of Genetic linkage map: using JoinMap v. 4.0 software
17
Figure 5. Genetic linkage map of the cross ICCV 96029 × CDC Frontier
Desi Kabuli
CaM1451 0.0 TA8 0.8 TR43 1.2 ICCM0297 3.8 TR42 5.9
TR19 0.0 H4D08 4.3 TA59 4.9 TA96 5.1 H5A08 5.3 H6D11 6.0
TA110 13.9
CaM1122 0.0 TR13 1.7 H1B04 3.0 TR56 3.3 CaM0886; H3F09 3.5 CaM1515 3.6 H3C06 3.8 H3F08 4.8 ICCM0263a 6.1 NCPGR10 13.6
TA64 43.7
TS36 0.0 CaM1158 1.8 H1H15 2.4 CaM0507 2.6 H4G11 2.7 CaM2049 ; NCPGR7 2.9 ICCM0250 3.3
TAA170 18.9
GAA47 35.2 ICCM0192a 37.7
B/b 50.7
CaLG01 CaLG02 CaLG03 CaLG04
TA196 0.0
TR01 10.9
CaM1402 24.8 TR40 25.7 CaM0753 25.8 TA176 26.0 TA22 26.1 TA80 26.8 TR44 31.2
Sfl/sfl 40.0
GA34 54.8 NCPGR93 56.6
CaM0244 63.9
TA106 70.4
NCPGR19 0.0
H1C22 18.5 TA21 19.1 CaM0661 19.5 TAA58 19.7 TA180 19.9 CaM0111 20.2 TA78 20.3 ICCM0160 ; CaM0443 20.9 TA28 25.1 TS46 27.0
GA6 0.0
TA118 19.3 TS45 21.5
H1C092 44.4 TA144 45.2
CaLG06
CaLG07
CaLG08 TA71 0.0 TR18 TR29 1.7 TA11 2.3 TA116 2.9 CaM0805 3.1 TA05 3.3 CaM0038 3.4 CaM1228 4.1 TR59 5.5
CaLG05
Total No. of markers -77 Total Map length –262.25 cM
18
Figure 6. Genetic linkage map of the cross ICC 5810 × CDC Frontier
Desi Kabuli
TA122 0.0
TA30 ; H3D05 TR43
22.3
ICCM0297 27.8 TR42 28.3
GA16 0.0
TR19 20.9 TR14 28.6 H5A08 28.8 H6D11 H4D08 H4A04
28.9
TA96 29.0 TA59 29.2
TR56 TS5 0.0 TA34 0.6 TR13 0.7 H3F08 H3C06 0.9 H1F14 1.0 CaM0886 1.2 H3F09 2.1 CaM1020 3.4 CaM1358 4.5
TA142 27.6
TA64 40.9
TS72 0.0 TA132 6.1 ICCM0250 8.7 TS36 9.9 TS104 ; CaM2049 10.2 CaM0113 10.6 H4G11 10.8 CaM0507 11.4
TAA170 36.5
NCPGR21 49.4
GAA47 55.9
B/b 76.9
TR33 88.9
TA71 0.0 ICCM0243c 1.8 TA116 ; CaM0038 4.4 CaM0805 4.8 TA11 6.7
CaLG01 CaLG02 CaLG03 CaLG04
CaLG05
TA14 0.0
TR01 11.5
TR44 22.3 TA22 29.0 TR7 ; TA80 CaM1402 ; TA176 29.3
CaM0317 29.5
NCPGR93 60.7
CaM0244 70.4
TA106 76.3
TAA58 0.0 CaM0443 0.7 TA21 0.8 ICCM0160 ; TA78; CaM0661 ; TA180; H1C22
0.9
CaM0111 1.1 TA28 6.9 TS46 8.8
GA6 0.0
TA118 19.4
TS45 23.8
NCPGR89 45.8
TA144 56.6
CaLG06
CaLG07
CaLG08
Total No. of markers -76 Total Map length –335.74 cM
19
Figure 7. Genetic linkage map of the cross BGD 132 × CDC Frontier
TA122 0.0
H3D05 24.2
ICCM0297 31.1 TR42 32.8
TR19 0.0 H4D08 ; TA96 H4A04 ; TA59 3.3
H5A08 3.5 H6D11 3.9 TA110 10.4
ICCM0263a 0.0 H3C06 2.5 TR56 3.9 CaM0886 4.1 H3F08 ; H1B04 H3F09 4.4
CaM1515 4.6 TR13 5.2 CaM1122 7.5 NCPGR10 14.6
TA142 28.2
TA64 41.7
NCPGR12 59.7
TA76 80.1
TS104 0.0 H4G11 ; CAM2049 0.6 CaM0507 0.9 TS36 ; CaM0113 1.1 H1H15 1.3
TAA170 26.9
ICCM0192a 45.2
TR29 0.0 TA71 2.6 H3A10 3.9 CaM0805 4.0 CaM1228 4.2 TR59 4.5 TA116 5.0 TA11 7.9
CaLG01
CaLG02
CaLG03 CaLG04
CaLG05
TA14 0.0
TA196 7.1
TR01 12.4
TR44 24.1 TR7 29.1 TR40 29.3 CaM1402 29.5 TA22 31.1
TA106 65.4
NCPGR19 0.0
H1C22 28.8 TAA58 ; CaM0111; TA21 ; CaM0443; TA78 ; H1N12; CaM0661
29.0
TS46 37.6
TA127 0.0 H1D24 3.4 GA6 4.4 TA144 4.5
TA118 31.8
CaLG06
CaLG07
CaLG08
Total No. of markers -68 Total Map length –311.10 cM
20
Figure 8. Genetic linkage map of the cross ICC 16641 × CDC Frontier
TA122 0.0
H3D05 32.3 TR43 34.1 TA8 34.6
ICCM0297 41.1
GA16 0.0
H5A08 ; H4A04 30.6 TA200 32.2
TA110 41.8
CaM1122 0.0 TS5 3.7 TR56 4.1 CaM1515 4.8 TR13 ; H3F08 5.0 H1F14 5.2 CaM0475 5.3 CaM0886 5.5 CaM1358 7.5 NCPGR10 15.5
TA142 22.9
TA64 34.6
TR32 58.7
TS72 0.0
TS36 11.4 CaM0507 ; H4G11 11.8 NCPGR7 ; CaM2049 12.4 ICCM0250 12.6 H1H15 12.9
TAA170 29.0
NCPGR21 39.7
GAA47 44.5 ICCM0192a 46.8
TR33 74.8
TA71 0.0 TA05 4.2 CaM1228 4.5 TA116 5.6 CaM0805 5.8 TA179 6.1 CaM0038 6.6 TA11 7.7 TR18 10.7
CaLG01 CaLG02 CaLG03
CaLG04
CaLG05
TA14 0.0
TR44 17.4
TA22 26.1 CaM1402 26.3 TA176 27.9
NCPGR93 56.6 CaM0244 60.2
TA106 65.6
CaLG06
NCPGR19 0.0
ICCM0160 33.2 CaM0661 ; CaM0443 33.7 TAA58 ; H1C22 34.0 TA78 35.4
TS46 46.3
CaLG07
GA6 0.0
ICCM0130a 5.7
TA118 18.5 TS45 19.8
H1D24 46.3
CaLG08
Total No. of markers -67 Total Map length –385.13 cM
21
Table 9. Features of Consensus map based on four mapping populations
Linkage group
No. of
markers
common
among four
crosses
Consensus map
No. of markers mapped
Map distance (cM)
Inter marker distance (cM)
CaLG01 1 8 32.04 4.01
CaLG02 1 11 36.91 3.36
CaLG03 5 22 61.65 2.80
CaLG04 5 18 82.23 4.57
CaLG05 4 13 6.94 0.53
CaLG06 4 17 73.41 4.32
CaLG07 6 13 33.87 2.61
CaLG08 2 9 37.39 4.15
Total 28 111 364.44 3.28
22
Figure 9. Consensus map based on four mapping populations
TR42 0.0 ICCM0297 1.3 CaM1451 4.8 TA8 5.7 TR43 6.3 TA30 6.8 H3D05 7.4
TA122 32.0
GA16 0.0
TR19 23.4 TA200 27.0 H4D08 28.6 H5A08 28.7 H4A04 ; TA96 TA59 28.9
TR14 29.3 H6D11 29.4 TA110 36.9
TA142 0.0 CaM1122 9.9 CaM1020 11.3 H3C06 12.7 TS5 13.1 TR56 13.2 H1B04 13.5 H3F09 13.6 CaM1515 13.7 CaM0886 13.9 H1F14 ; CaM0475 14.1 TA34 H3F08 14.2 TR13 14.8 CaM1358 16.9 ICCM0263a 17.1 NCPGR10 23.5 TA64 24.2
NCPGR12 41.3
TR32 46.8
TA76 61.7
TS72 0.0 TA132 6.7 TS36 9.9 TS104 10.3 CaM0113 10.6 CaM0507 10.8 H4G11 11.0 CaM2049 11.3 NCPGR7 11.5 H1H15 11.6 ICCM0250 12.0 CaM1158 12.7
TAA170 31.7
NCPGR21 43.9
GAA47 49.7 ICCM0192a 51.9
B/b 71.6
TR33 82.2
TA71 0.0 ICCM0243c 1.1 TR59 2.0 H3A10 2.5 CaM1228 2.8 TA05 3.2 CaM0805 3.4 TA116 3.7 CaM0038 4.2 TA179 4.4 TA11 5.6 TR29 6.5 TR18 6.9
CaLG01 CaLG02 CaLG03 CaLG04
CaLG05 TA14 0.0
TA196 4.5 TR01 12.2 Sfl/sfl 16.2 TR44 23.6 TR40 29.5 CaM1402 29.9 TR7 30.0 TA80 30.2 CaM0317 30.3 CaM0753 30.4 TA176 30.6 TA22 31.0
GA34 58.3 NCPGR93 60.4
CaM0244 67.4
TA106 73.4
CaLG06
NCPGR19 0.0
H1C22 24.8 TAA58 25.0 TA21 25.2 CaM0661 25.3 H1N12 25.4 TA78 25.5 CaM0111 25.6 TA180 25.7 CaM0443 25.8 ICCM0160 26.1 TA28 31.3 TS46 33.9
CaLG07
TA118 0.0 TS45 2.7
ICCM0130 15.5
GA6 21.7 TA127 24.5 H1D24 25.9 TA144 28.7 H1C092 29.2
NCPGR89 37.4
CaLG08
Total No. of markers -111 Total Map length –364.44 cM
23
Objective 3
QTL mapping for flowering time genes
24
The linkage map data and phenotyping data was used for
QTL analysis by using QTL-ICiMapping (ICIM) software
version 4.0 (Wang et al. 2014).
Results:
Table 8. QTLs identified for flowering time in four chickpea crosses
25
Sl.
No Cross QTL CaLG Position
(cM) LOD
PVE
(%)
Additive
effect
Flanking markers Closest
marker Left
marker
Right
marker
1
ICCV 96029 ×
CDC Frontier
Qefl1-1 03 0.0 3.55 7.07 -4.44 CaM1122 TR13 CaM1122
Qefl1-2 04 36.0 5.95 12.34 -5.42 GAA47 ICCM0192a GAA47
2
ICC 5810 ×
CDC Frontier
Qefl2-1 01 15.0 12.77 20.13 -3.26 TA122 TA30 TA30
Qefl2-2 03 21.0 16.82 25.19 -6.65 CaM1358 TA142 TA142
Qefl2-3 04 55.0 9.10 10.44 -4.40 NCPGR21 GAA47 GAA47
Qefl2-4 08 15.0 17.68 25.57 -7.03 GA6 TA118 TA118
3 BGD 132 ×
CDC Frontier
Qefl3-1 03 5.0 5.17 4.28 -1.23 CaM1515 TR13 TR13
Qefl3-2 03 31.0 4.21 3.99 -3.36 TA142 TA64 TA142
Qefl3-3 08 2.0 44.83 65.35 -13.0 TA127 H1D24 H1D24
4 ICC 16641 ×
CDC Frontier Qefl4-1 06 9.0 55.60 88.19 -16.75 TA14 TR44 TR44
Figure 10. QTLs for flowering time in the cross ICCV 96029 × CDC Frontier
CaLG04
0
5
10
15
20
25
30
35
40
45
50
“Qefl1-2”
LOD=5.95
PVE=12.34 %
CaLG03
0
5
10
15
20
25
30
35
40
45
“Qefl1-1”
LOD=3.55
PVE=7.07 %
26
B/b
Figure 11. QTLs for flowering time in the cross ICC 5810 × CDC Frontier CaLG01
“Qefl2-1”
LOD=12.77
PVE=20.13 %
0
5
10
15
20
25
30
LOD Score
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
“Qefl2-3”
LOD=9.10
PVE=10.44 %
CaLG04
“Qefl2-4”
LOD=17.67
PVE=25.57 %
0
5
10
15
20
25
30
35
40
45
50
55
LOD Score CaLG08
0
5
10
15
20
25
30
35
40
“Qefl2-2”
LOD=16.82
PVE=25.19 %
CaLG03
B/b
27
Figure 12. Major QTL for flowering time in the cross BGD 132 × CDC Frontier
CaLG08
Figure 13 (a) Mapping of major flowering time gene “efl-3” on CaLG08
based on F3 segregating data of the cross BGD 132 × CDC Frontier (b)
Identification of major QTL for flowering time “Qefl3-3” on CaLG08
(a) (b)
efl-3
GA6 TA144 H1D24
TA127
TA118
CaLG08
0
5
10
15
20
25
30
TA127 H1D24
GA6 TA144
TA118
0 5 10 15 20 25 30 35 40
LOD Score
“Qefl3-3”
LOD=44.83
PVE=65.35 %
28
Figure 13. Major QTL for flowering time in the cross ICC 16641 × CDC Frontier
TA14
efl-4
TR44
TA22 CaM1402 TA176
NCPGR93
CaM0244
TA106
CaLG06
Figure 14 (a) Mapping of major flowering time gene “efl-4” on CaLG06 based on F3
segregating data in the cross ICC 16641 × CDC Frontier (b) Identification of major QTL
for flowering time “Qefl4-1” on CaLG06
(a) (b)
0
5
10
15
20
25
30
35
40
45
50
55
TA14
TR44
CaLG06
CaM1402 TA176
NCPGR93
CaM0244
TA106
TA22
0 5 10 15 20 25 30 35 40 45 50 55
LOD Score
“Qefl4-1”
LOD=55.6
PVE=88.19 %
60
65
(b)
29
Figure 14. Genomic regions identified for flowering time genes
TR42 0.0 ICCM0297 1.3 CaM1451 4.8 TA8 5.7 TR43 6.3 TA30 6.8 H3D05 7.4
TA122 32.0
GA16 0.0
TR19 23.4 TA200 27.0 H4D08 28.6 H5A08 28.7 H4A04 ; TA96 TA59 28.9
TR14 29.3 H6D11 29.4 TA110 36.9
TA142 0.0 CaM1122 9.9 CaM1020 11.3 H3C06 12.7 TS5 13.1 TR56 13.2 H1B04 13.5 H3F09 13.6 CaM1515 13.7 CaM0886 13.9 H1F14 ; CaM0475 14.1 TA34 H3F08 14.2 TR13 14.8 CaM1358 16.9 ICCM0263a 17.1 NCPGR10 23.5 TA64 24.2
NCPGR12 41.3
TR32 46.8
TA76 61.7
TS72 0.0 TA132 6.7 TS36 9.9 TS104 10.3 CaM0113 10.6 CaM0507 10.8 H4G11 11.0 CaM2049 11.3 NCPGR7 11.5 H1H15 11.6 ICCM0250 12.0 CaM1158 12.7
TAA170 31.7
NCPGR21 43.9
GAA47 49.7 ICCM0192a 51.9
B/b 71.6
TR33 82.2
TA71 0.0 ICCM0243c 1.1 TR59 2.0 H3A10 2.5 CaM1228 2.8 TA05 3.2 CaM0805 3.4 TA116 3.7 CaM0038 4.2 TA179 4.4 TA11 5.6 TR29 6.5 TR18 6.9
CaLG01 CaLG02 CaLG03 CaLG04
CaLG05 TA14 0.0
TA196 4.5 TR01 12.2 Sfl/sfl 16.2 TR44 23.6 TR40 29.5 CaM1402 29.9 TR7 30.0 TA80 30.2 CaM0317 30.3 CaM0753 30.4 TA176 30.6 TA22 31.0
GA34 58.3 NCPGR93 60.4
CaM0244 67.4
TA106 73.4
CaLG06
NCPGR19 0.0
H1C22 24.8 TAA58 25.0 TA21 25.2 CaM0661 25.3 H1N12 25.4 TA78 25.5 CaM0111 25.6 TA180 25.7 CaM0443 25.8 ICCM0160 26.1 TA28 31.3 TS46 33.9
CaLG07
TA118 0.0 TS45 2.7
ICCM0130 15.5
GA6 21.7 TA127 24.5 H1D24 25.9 TA144 28.7 H1C092 29.2
NCPGR89 37.4
CaLG08
efl1
efl4
efl3 efl-1
efl-3
efl-4
Identification of candidate genes in flowering time QTL regions
Primer sequences (of flanking markers) were blasted (BLASTN) against the CDC Frontier genome (Varshney et al. 2013)
For each primer pair, the best hit was selected based on the E-value and percent identity
Gene ontology was carried out by the BLAST of these genes against the SWISS-PROT and TrEMBL database.
The resulted genes were assigned with Uniprot ID and the functions for these genes were retrieved from Uniprot KB database (http://www.uniprot.org/).
31
http://www.uniprot.org/http://www.uniprot.org/http://www.uniprot.org/http://www.uniprot.org/http://www.uniprot.org/http://www.uniprot.org/http://www.uniprot.org/
Results: The results of BLAST search indicated two relatively narrow regions on
Ca4 (0.7 Mb region between the markers GAA47-ICCM192a) and Ca08 (region of about 3.5 Mb within the markers GA6-TA118).
Gene ontology analysis by the blast of these genes against the SWISS-PROT and TrEMBL database resulted in 30 flowering related genes (06 genes on CaLG04 and 24 genes on Ca LG08 region) assigned with Uniprot ID.
Ca Genes Function Reference
4 ELF6, JMJ11 Acts as Repressor of the photoperiodic flowering pathway
Noh et al. (2004)
4 TEM1 Acts as Transcritptional repressor of flowering time in long day plants
Castillejo and Pelaz (2008)
8 SUVR5 , SET6 Regulators of flower timing in Arabidopsis Krichevsky et al. (2007)
8 HOS1 Controls flowering time in response to ambient temperatures
Lee et al. (2012)
8 VRN2 Plays a central role in vernalization Gendall et al. (2001)
8 AP2 Early floral meristem identity and transition into floral meristem
Drews et al. (1991)
Table 9. Important flowering related genes
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Objective 4
Association of flowering time with maturity and yield related traits
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Cross Days to pod initiation
Days to maturity
Plant height
Biomass Pods per plant
Seeds per plant
Yield per plant
100 Seed weight
Harvest index
ICCV 96029 × CDC Frontier
0.988** 0.882** 0.507** 0.264** -0.032 -0.047 0.055 0.281** -0.431**
ICC 5810 × CDC Frontier
0.987** 0.888** 0.189** 0.181* -0.088 -0.126 -0.01 0.309** -0.442**
BGD 132 × CDC Frontier
0.992** 0.934** 0.453** 0.331** 0.133 0.093 0.135 0.237** -0.486**
ICC 16641 × CDC Frontier
0.997** 0.950** 0.471** 0.280** -0.052 -0.088 -0.087 -0.059 -0.616**
Results:
Table 10: Association of flowering time with maturity and yield related traits
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Conclusions:
Major gene inheritance for flowering time
- Selection in F2 and subsequent generations is effective
Four genetic maps & consensus map developed
- Can be used to develop high density genetic map
Ten QTLs (7 major & 3 minor) identified for flowering time
- Major genes/QTLs can be transferred to any desired genetic background through simple crossing
- Genomic regions can be fine mapped to identify candidate genes for flowering time
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Acknowledgements
Chickpea Breeding Unit, ICRISAT Dr. Pooran Gaur (Co-Chairperson) Dr. S Srinivasan
Dr. S Shoban
Advisory committee Dr. KP Viswanatha (Chairman) Dr. R Lokesh Dr. BS Janagoudar Dr. Ayyanagouda Patil
Centre of Excellence in Genomics, ICRISAT Dr. Rajeev Varshney, Director (RPGL) Dr. Mahendar Thudi
Department of Genetics & Plant Breeding, UAS-Raichur, Karnataka CGIAR Research Programme (CRP) on Grain Legumes Learning System Unit, ICRISAT Library and information services, ICRISAT Housing and food services, ICRISAT
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Thank you
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