Success story of MAS for

drought tolerance traits in

chickpea

Mahendar Thudi

On behalf of

Rajeev K. Varshney
ICRISAT, India
 Chickpea
(Cicer arietinum L.) GCP

 Third most important food

legume globally
 A winter crop in the semi-arid
tropics and a spring/summer crop
in the Mediterranean and
Temperate regions
 Self-pollinated
 Diploid, 2n= 16 chrmosomes
 Genome size= ~780 Mbp
 Global distribution
of chickpea area GCP
Grown on about 11 m ha across 51 countries

>6 m ha
0.5 to 1.0 m ha
150,000 to 210,000 ha
50,000 to 100,000 ha
10,000 to 40,000 ha
 Marginal environments in
Sub-Saharan Africa and Asia GCP

Kenya Ethiopia

Myanmar India
Climate change
GCP
 Genomics-assisted breeding:
Predicting the phenotype GCP
Genotype
Genetic Mapping EST Sequencing
Physical Mapping Genome Sequencing
Map-based Cloning

Gene(s)
Genetic Improved
Resources germplasm

Genetic Mapping Trait/QTL Transcriptomics

Proteomics
Association Mapping
Metabolomics
QTL Mapping
TILLING
Trait Correlations
EcoTILLING

Phenotype Trends Pl Science 2005;

Trends Biotech 2006
 Challenges in genomics-
assisted crop improvement GCP
 Narrow genetic base in the primary gene pool

 Very few molecular markers (SSR)

 Non-availability of appropriate germplasm such as

mapping populations

 Intraspecific genetic map with low marker density

 Non-availability of trait-associated markers in

breeding

 Issues of costs and expertise in molecular

breeding
 Genomics activities by
ICRISAT & partners
Genomic resources and genotyping platforms

Mapping populations
SSR genotyping DArT arrays GoldenGate SNP genotyping assay

Breeding lines
Genetic resources
Total RNA
Transcriptomic resources

Cultivars
Trait phenotyping
Sanger
sequencing Genetic map

Landraces
454/FLX
sequencing
QTL discovery Molecular breeding

Wild species
Superior lines for traits of interest
Illumina (Enhanced tolerance / resistance for abiotic stress and biotic stress)
sequencing
Genetic resources…
Germplasm sets

Core
collection

1956
300

3000

Composite
20,167 collection

Global / base
collection
Curr Opin Plant Biol 2010
 Identification of drought tolerant
germplasm in field conditions

RLD Over
 (cm cm-31500
) accessions
Moderate Severe
screened at ICRISAT
drought drought
YLD(2000/01)
for drought tolerance
HI YLD HI
0-15cm 0.344 0.354 0.442 0.404

 ICC4958,0.699
15-30cm the *most
0.672 * 0.718 ** 0.709 **
drought tolerant
genotype
30-45cm 0.406 0.544 0.779 ** 0.616 *

45-60cm 0.405 0.496 0.576 * 0.355


Total High root 0.613
biomass
* 0.681 * 0.659 * 0.565
responsible
 Mapping populations
Intra-specific mapping populations:
ICCV 283 × ICC 8261 - 289 RILs
ICCV 4958 × ICC 1882 - 268 RILs

Accession Root depth Root dry wt.

(cm) (g) 300
ICC 8261 123.3 1.25
ICCV 283 91.6 0.73

ICCV 4958 116.6 1.06

ICC 1882 83.9 0.71

and many other drought tolerance traits

Development of genomic resources…
 Development of
SSR markers
ICC 4958, ICC 1882 ICC 4958
JG 11, ICCV 2

EST/cDNA SSR enriched 10 X BAC 454/FLX

libraries library library libraries

Sanger Sanger Sanger sequencing 454/FLX

sequencing sequencing of of BAC-ends sequencing of
(ICRISAT/ SSR+ve clones (UC-Davis/ transcripts
JCVI) (ICRISAT) ICRISAT) (ICRISAT/JCVI)

Development and validation of

~2000 novel SSR markers BMC Genomics, 2009
(ICRISAT) Theor Appl Genet, 2010
PLoS ONE, 2011
 92 ICC67
96 ICC1431-1
72 ICC1069
96 ICC1496
98 ICC1882
98 ICC3986
98 ICC3696
86 ICC283P1-BP
56 ICC10673
86 ICC9644
52 ICC867
81 71 ICC4853
ICC3512

Development of 15 K DArT array

85 ICC10885
100 ICC7052
ICC6537
53 ICC2884
97 ICC8512

from 96 diverse genotyes

ICC8522
56
100 ICC6306 ICC1915
87
ICC14446
ICC14528
100 ICC6263
ICC6305
ICC5988
ICC5590
100 ICC5717
73
ICC5002
ICC5475

(A)
ICC14402
ICC506EB
ICC440
54 ANNIGIRI

Secondary gene pool

76 ICC7413
ICC5337
ICC13523
ICC93218 ICC17163 .14
ICC14916 IG72953-NM
IG72953-HCS
IG72937NM

Tertiary gene pool

.12
PI489777NM
54 ICCV95311
PI527930
PI510656
PI599044
PI489778
PI599092
PI599050
PI489777HCS
ICC17160
JG11-PMG .1
6695 JG11-NM PI599072
VIJAY .08

96 JG62 .06
60 ICC14614 ICCW38
ICCV2 .04 ILWC248
ICCW37
PB7
64 ICCV10NM .02
ICCV96029
66 ICC11255
ICCV94954 -.1ICC10673 ICC8512
ICC14446
ICC1915
ICC2884
ICC6306
ICC8522
ICC14528 -.05
ICC2679
ICC8200 .05 .1 .15 .2 .25 .3 .35 .4 .45 .5 .55 .6 .65 .7
61 ICC7052ICC3512
ICCV92311
ICC12379
ICC4853
ICCV92318
ICC10885JG72933
ICCC37
ICC17459
ICC12299
C104
ICCV93512
ICC3137-2
ICC15610 -.02
ANNIGIRIICC11944
ICC7413
ICC5988 WR315
ICC4958
ICC5475
ICC506EB VIJAY
ICCV04516 ICC8261P1-BP
ICC13523
ICC5002
ICC16796
ICC6013
ICC5717
ICC6305
ICC5590
ICC6263ICC506
ICC5337
ICC14614
ICC14402
ICCV95311
ICC6537
ICC4872
ICC440
ICC11255
ICC93218
ICCV96029 JG62
ICCV2
ICC6160
ICC14916
ICC8058
JG11-NM
ICCV04516
JG11-PMG
ICCV10NM
ICCV94954
ICC9644 PB7
58 ICC6013 ICC867
ICC3986
ICC3696
ICC1069
-.04
ICC4958 ICC283P1-BP
ICC67
ICC1431-1
ICC8058 -.06
97 ICC1882
ICC1496
70 ICC16796 -.08 ICCW69
ICC6160
ICC506 -.1
96 ICC12299
Cultivated
ILWC73
ICC11944 -.12
ICCC37

germplasm
100 WR315
50 ICC15610
97 ICC2679 ICC8200
(A) PCO analysis of 5,397 DArT markers
83
99 ICCV92318
ICCV92311
98 96
ICC17459
(B) Unweighted neighbour-joining dendrogram based on 901 DArT
87 53
80 ICCV93512
ICC12379
95 JG72933
83 ICC8261P1-BP
ICC4872 markers polymorphic for the set of 75 cultivated lines in the
red ellipse (1,000 bootstrap replicates)
C104
ICC3137-2

0 0.1
 Transcriptomic resources
NCBI JG 11 ICCV 2 ICC1882 ICC4958 PI 489777 ICC 506 ICCC 37

7,097 435,018 FLX/454 STRs

ESTs 20,162 ESTs

9,569 103,215 TUSs 22.1 15.6 26.3 23.1 58.1

TUSs (Ca TA) Million Million Million Million Million
Solexa Solexa Solexa Solexa Solexa
tags tags tags tags tags
105 DEGs Alignment to
the reference
2,974 DEGs 60 DEGs 121 DEGs
Hierarchical
clustering of genes MapMan
qRTPCR
analysis R>6
analysis
BMC Genomics 2009 Plant Biotech Jour 2011
 Development of
SNP markers
615 SNPs based on
legume COSs
768 SNPs GoldenGate assay
>50,000 SNPs based on
Illumina/Solexa 1G sequencing
742 CAPS markers
ICC 4958×ICC 1882
ICC 506×ICCC 37
ICC 4958×PI 489777
2,005 KASPar assays

153 SNPs from

allele specific
sequencing
 Comprehensive genetic mapGCP

LG8

LG2
LG1

Marker Loci: 1,291

Coverage: 845.56 cM LG7
LG3 LG4 LG5 LG6
 Cost-effective Homozygote

SNP assays GCP

Legume COSs Illumina/Solexa Allele specific Heterozygote

1G sequencing sequencing

Homozygote
KASPar assays designed
for 2,468 SNPs

2,005 KASPar assays validated KASPar assays

(625 CKAMs mapped)

ADT score
PIC value
calculation

ADT score >0.5 High PIC value

96-plex OPAs for

Veracode assays
BeadXpress system
for BeadXpress
 KASPars assays integrated
in transcript map GCP

Markers mapped : 1328

Map distance : 788.6cM
Hiremath et al. 2012 Average number of markers/LG : 166
Plant Biotech Jour Average inter-marker distance : 0.59cM
 Consensus genetic map
1 2 3 4 5 6 7 8

0.0 CaM0499
2.1 CaM1117
9.9 cpPb-677529
18.6 CaM1988 0.0 cpPb-682328
20.3 TR2 4.9 NCPGR189
21.2 NCPGR10 9.3 TR18
23.1 H3C06 9.8 H3A07
0.0 NCPGR184 0.0 CaM0236 24.7 CaM2031 0.0 NCPGR91 CaM0744 0.0 CISR42 0.0 NCPGR12 0.0 GA6
11.3
25.7 NCPGR268 12.4 NCPGR40 1.9 TA14
27.9 NCPGR255 14.3 TA42 3.5 STMS15
4.7 GA20 28.6 CaM1753 15.1 CaM0848
28.8 NCPGR278 15.9 CaM2098
7.5 CaM1855 7.0 CaM0772
29.2 NCPGR273 16.7 CaM2026
29.7 CaM1851 17.6 H2J09 9.8 TR35
30.1 CaM0204 17.9 CaM0639
CaM1765 13.0 cpPb-489187
30.6 12.6 Tp684964 18.1 TA5
CaM2181 14.5 NCPGR206
31.2 18.6 ICCM0202
14.9 GA16 17.8 TR40 14.6 TR24
31.3 CaM1835 18.7 H4H02
16.7 ICCM0009a ICCM0009b CaM0713 CaM1843 19.5 CaM1943
31.6 19.2 NCPGR233
CaM0157 20.3 CaM0500 17.9 NCPGR164
31.8 19.8 TAA137
CaM0326 20.8 TA153
31.9 20.9 NCPGR176
21.0 NCPGR144 CaM0003 21.2 TA120
32.1 21.1 TAA104
23.2 STMS21 21.7 TA103 TA34 22.0 CaM1402
32.3 21.3 NCPGR105
cpPb-677798 cpPb-171485 CaM0120 22.9 CaM0389
32.5 21.7 NCPGR81 24.7 TA118
25.0 cpPb-679323 cpPb-490962 CaM1024 23.9 TS105
32.8 22.6 CaM0169 26.1 TS45
cpPb-677038 cpPb-677672 NCPGR49 27.1 cpPb-680552 24.4 CaM1258
33.1 23.2 CaM0038 CaM2187
29.3 cpPb-489318 26.2 TR7 27.9
33.7 NCPGR100 24.0 TA11s
29.7 TA194 NCPGR173 30.0 STMS11 27.1 ICCeM051
34.1 24.8 NCPGR228
30.1 CISR2 GA119 27.9 CaM0421
32.2 TA103II 34.5 24.9 CaM1806
CaM1973 32.8 GA24 28.5 CaM1790 32.6 TA142
35.0 25.2 ICCM0123a
34.1 CaM1908 CaM0051 29.2 H3A052 CaM0636
35.9 35.3 TR11 25.5 CaM0964
H1F14 29.3 ICCM0242a 37.1 NCPGR138
36.1 25.6 CaM2158 36.7 TA76s
37.4 TA113 H3F08 30.1 CaM0677 37.7 TS23
38.0 TAA194 36.4 26.1 GA102
CaM1767 39.0 NCPGR21 30.5 CaM1826 39.4 CaM0800
39.6 CaM1907 36.8 26.4 CaM1517
ICCeM0018 ICCM0178 30.8 CaM0899 40.8 NCPGR223
cpPb-677690 cpPb-682106 41.1 CaM0142 37.3 33.5 CaM1389
41.5 TS17X 31.0 CaM1431 40.9 CaM1918
cpPb-679216 cpPb-679915 43.6 H1H011 37.6 34.5 NCPGR254 42.5 NCPGR171
TA135 31.1 CaM0753 43.6 CaM1193
43.8 TA27 37.9 34.7 CaM1372 44.0 NCPGR141
44.6 TA122 TA6 31.8 CaM1530 44.8 NCPGR146
44.5 H1P092 38.2 42.3 NCPGR145
TS29 32.7 ICCM0242 46.7 NCPGR118
46.2 H1J04 38.3 46.7 TAA170 42.7 CaM1977
CaM1089 32.8 ICCM0104 CaM1567 49.0 NCPGR89
38.6 48.6 NCPGR127 43.0 CaM2029 49.8
49.1 TA206 CaM1568 33.2 H5A04 ICCeM0050 52.6 NCPGR209
39.6 51.5
50.4 ICCeM0040 50.8 CaM0293 CaM2095 33.4 NCPGR139 ICCM0197a 53.0 NCPGR264
40.3 52.4
53.1 TA59 CaM1232 34.6 NCPGR203 ICCeM0017 53.2 H3E052
40.5 NCPGR142 53.0
54.3 TA200 55.5 35.5 ICCeM0075 53.3 H5B04
40.9 CaM2102 55.8 TA180
CaM0861 57.3 ICCM0249 36.8 H1F21 53.7 CaM1399
55.9 NCPGR90 54.5 41.2 ICCeM0050 57.1 ICCM0160
CaM0043 58.5 TR8 37.1 H6F09 53.9 CaM1274
57.3 42.2 CaM1376 57.5 H1O12
TR19 58.8 CaM1214 38.4 H6G10 54.6 H1H14
57.6 42.7 STMS9 58.4 TA11 57.8 NCPGR99
62.4 ICCeM0058 39.6 H1L161 55.9 TA25
43.0 CaM2174 58.3 CaM0111
65.4 CaM1328 41.4 NCPGR87 57.1 TA127 TA3
62.7 CaM0393 43.5 TR13 58.8 CaM0598
65.8 NCPGR236 42.3 CaM0317 57.7 TR5
64.0 ICCM0297 44.2 TS58s 59.1 CaM2155
66.2 NCPGR30 44.5 H4H06 58.0 cpPb-677783
65.9 TA8 44.6 TS5 59.3 CaM0443
66.9 TA132 45.2 ICCeM0015 59.3 TS57
67.6 NCPGR136 45.0 CaM1905 59.7 CaM1942
67.5 NCPGR31 48.6 CaM1257 61.3 H3C11
68.8 NCPGR263 67.6 NCPGR193 45.5 NCPGR103 59.8 H1F24
68.7 CaM0923 50.0 NCPGR200 64.3 CaM2063
70.3 CaM0046 46.0 CaM0520 60.3 CaM2094
69.3 CaM2093 53.3 NCPGR123 65.1 TA159
70.4 CaM0015 CaM1702 46.1 CaM0998 60.6 CaM1469
69.5 CaM1077 54.0 STMS2 69.2 CaM0081
70.6 CaM0403 47.1 CaM0391 62.0 TA114
70.1 CaM0507 58.4 NCPGR93 TS24 71.5 CaM2189
71.0 TA203 47.5 CISR105 63.2 CaM0906
70.4 NCPGR27 61.7 NCPGR107
71.3 CaM1742 48.1 CaM0658 64.4 STMS25
75.7 NCPGR117 70.5 NCPGR7 64.7 NCPGR229
72.2 CaM0102 49.8 STMS10 65.1 STMS12
70.7 ICCM0069 72.3 NCPGR202
74.1 CaM0144 52.3 TAA169 66.6 CaM1687
70.9 ICCM0250 77.4 CaM1760
76.4 TA30s 68.2 cpPb-490100 67.5 CISR117
71.3 NCPGR245
77.0 H2A08 70.8 TR31 69.3 cpPb-490874
71.5 cpPb-322921 82.0 NCPGR4
79.7 TR43II 71.0 ICCM0199c
71.8 ICCM0068
82.7 TS71 73.0 H1P17
71.9 CaM0645
84.0 TR42 76.7 CaM1417
72.0 TA2
77.2 CaM2041
72.3 ICCeM0058
83.6 NCPGR19
72.9 CaM2074 89.3 TA106 84.1 NCPGR130
73.4 NCPGR231
88.0 TA44
74.0 H4G11
91.0 TA117
74.4 H1A19
75.0 cpPb-676868
95.6 TR55
75.6 CaM1684
77.5 TA146
81.2 NCPGR247
85.3 ICCM0065
86.4 CaM0924 102.7 H1I16
90.5 ICCM0257
97.7 TA89 105.3 GA26
107.2 TA30 101.2 CaM0615
102.0 CaM0821
102.4 CaM0856
102.5 CaM0845
105.1 GA137 112.5 ICCeM0035
112.0 cpPb-678284 cpPb-490776

Markers mapped : 352

119.9 CaM0399

124.1 ICCeM0033

Map distance : 771.3cM

127.9 cpPb-677304 cpPb-676765
128.0 cpPb-679660

Average number of markers/LG : 44

Average inter-marker distance 156.0 NCPGR249
: 2.3cM
Trait phenotyping…
 Semi-automated precise
high- throughput phenotyping

Crane for lifting root cylinders for Phenotyping of mapping populations

moisture under water stress for root traits in two years
determinations
Drought tolerance phenotyping
in field conditions- rainfed
Drought tolerance phenotyping
in field conditions- irrigated
Phenotyping in Sub-Saharan Africa
(Kenya, Ethiopia, Tanzania)
 Assembling of phenotyping data
for drought tolerance
ICC 4958 × ICC 1882 ICC 283 × ICC 8261 Reference set
Trait Reps Year Location Reps Year Location Reps. Year Location
.
Root traits 3 2005, Patancheru 3 2006, Patancheru 3 2007, Patancheru
2007 2008 2008,
2009
Yield and HI 1 2005, Patancheru 1 2005, Patancheru 2 2008, EIAR
related traits 2006, 2006, 2009 Eger Uni
2007 2007 IIPR
Yield and HI 2 2008 Patancheru 2 2010 Patancheru - - -
related traits Nandyal Nandyal,
rainfed and Sehore Durgapura
irrigated
conditions 2009 Patancheru
Nandyal,
Durgapura,
Hiryeur
Transpiration 2 2008 Patancheru 2 2010 Patancheru 3 2008 Patancheru
efficiency Nandyal Nandyal, 2009 Patancheru
(δ13C) in Sehore Durgapura
rainfed and
irrigated 2009 Patancheru
conditions Nandyal,
Durgapura,
Hiryeur
Association mapping
 Genotyping data for
association analysis GCP

Marker type Marker data Markers used

available for association
studies
SSR 36 36
DArT 1157 1072
SNP 651 651
Gene based SNPs 113 113
Total 1957 1872
 Phenotyping data
GCP
Root traits Morphological traits Yield and yield component
traits
Traits Seasons Traits Seasons Traits Seasons
Root length (cm) 3 Plant height (cm) 14 Pods/plant 2
Root length density Plant width (cm) 7 100 seed weight 10
-3
(cm cm )
3 2
Root volume (cm ) 3 Plant stand 7 Yield (g/m ) 3
Root dry weight (g) 3 Apical primary branch 7 Yield (Kg/ha) 10

Rooting depth (cm) 3 Apical secondary 7 Yield per plant 7

branch
Root surface area 3 Basal primay branch 7 Production 7

R-T ratio(%) 3 Basal secondary 7 Biomass 6

branch
Shoot dry weight 3 Teritiary branches 7 Biomass/plant 1
Stem dry weight 3 Phenological traits Harvest index 6
Leaf dry weight 3 Days to flowering 13 Total dry matter 1
2
weight (g/m )
13
Projected area 2 Days to maturity 9 C 2
Average diameter 2 Seeds per pod 7 SPAD 2
Seeds/plant 1
 Genetic structure
of reference set GCP

Group III
Group I

Group II

Neighbour joining tree constructed

based on 1157 DArT loci data

Group I Group II
Group III

Three subpopulations based on STRUCTURE analysis, diversity analysis

 Genetic diversity
GCP

Neighbour joining tree constructed Neighbour joining tree constructed

based on allelic data of 36 SSR loci based on 791 SNP loci data on reference
on reference set set

NO SPECIFIC GROUPING OF THE REFERENCE SET GENOTYPES

INDICATE THAT THE SET IS MOST SUITABLE FOR
ASSOCIATION ANALYSIS
 Marker trait associations
identified GCP
Trait Number of p- value Phenotypic
markers variation (%)
associated
Root traits
-4 -6
Shoot dry weight 4 5.61 × 10 - 1.76 × 10 4.6 - 12.2
-4 -4
Root volume 4 7.34 × 10 - 3.4 × 10 4.7 - 9.9
-4
Root length density 1 7.1 × 10 4.2
-4 -4
Root diameter 2 8.12 × 10 - 7.93 × 10 4.1
-4 -4
Root dry weight 4 7.4 × 10 - 3.38 × 10 4.8 -6.5
-4 -4
Root surface area 4 8.92 × 10 - 1.65 × 10 4.7 - 17.3
-4
Rooting depth 1 3.89 × 10 4.8
-4
Projected area 1 1.32 × 10 5.7
-4
R-T ratio 1 3.17 × 10 4.8
Morphological traits
-4 -5
Plant stand 11 8.74 × 10 - 8.69 × 10 6.7 - 13.4
-4 -4
Plant height 18 8.76 × 10 - 4.72 × 10 4.4 - 16.2
-4 -4
Plant width 3 8.52 × 10 - 6.63 × 10 6.2 - 11.3
-4 -4
Apical primary branch 7 4.74 × 10 - 3.21 × 10 6.2 - 7
-4 -4
Apical secondary branch 7 7.77 × 10 - 2.09 × 10 7.3 -12.8
-4 -5
Basal primary branch 8 6.34 × 10 - 2.23 × 10 6.2 - 9.8
-4 -5
Basal secondary branch 2 1.84 × 10 - 7.44 × 10 5.7 - 22.4
-4 -4
Teritiary branches 4 9.82 × 10 - 2.08 × 10 5.6 - 7.3
× -4 × -4
Trait Number of markers p- value Phenotypic
associated variation (%)
Phenological and yield related traits
-4 -5
Days to flowering 9 9.78 × 10 - 2.36 × 10 4.4 -24.5 GCP
-4 -5
Days to maturity 9 7.19 × 10 - 3.93 × 10 4.5 - 22.6
-4 -4
Flowering days 4 9.42 × 10 - 4.37 × 10 5.9 - 6.7
-4 -9
Seeds per pod 28 9.99 × 10 - 2.13 × 10 4.1 -19.5
-4 -4
Pods per plant 11 9.92 × 10 - 2.66 × 10 4.3 - 10.9
2 -4 -6
Pods per m 6 6.32 × 10 - 1.60 × 10 4.7 - 17.9
2 -4 -9
Seeds number per m 13 9.66 × 10 - 5.03 × 10 4.3 -18.4
-4
Per day seed 1 6.77 × 10 13.6
Per day shoot 1 6.97 × 10-4 6.1
-4 -12
100-seed weight 30 9.62 × 10 - 1.15 × 10 2.3 - 38.5
-4 -5
Biomass 3 4.05 × 10 - 2.79 × 10 5.2 - 7
-4 -5
Harvest index 8 7.33 × 10 - 8.44 × 10 4.5 -7.5
-4 -4
Yield 14 9.94 × 10 - 1.04 × 10 2.8 - 14.7
-4 -5
Total shoot biomass 4 9.68 × 10 - 3.31 × 10 5.5 - 14.3
-4 -4
Production 7 8.31 × 10 - 1.32 × 10 5.7 - 10.9
Transpiration efficiency related traits
-4 -6
Delta Carbon 14 6.99 × 10 - 8.05 × 10 4.5 -17.2
-4 -5
Specific leaf area 3 8.57 × 10 - 5.17 × 10 4.6 - 22.8
-4 -5
SPAD 2 1.32 × 10 - 1.32 × 10 5.3 - 7.4
-4 -5
Total dry matter weight 6 8.74 × 10 - 1.50 × 10 4.7 -13.1
QTLs and molecular breeding…
 “Hotspot” harbouring several
QTLs for drought tolerance
RLD_06
RLD_08
RDW_06
RDW_08
RT DEPTH_06
RT DEPTH_08
SDW_06
SDW_08
RT VOL_06
RT VOL_08
RSA_06
RSA_08
RL_06
RL_08
STEM DW_06
209 LDW_06
ICCM0249

TAA170

STMS11
CaM0856

GA24

CAM1903
TAA170
NC142

TA130
ICCM0249
R-T RATIO_06

LG5: ICC 4958 x ICC 1882 LG5: ICC 283 x ICC 8261
 Molecular breeding for
enhancing drought tolerance
Crosses: 3 Cultivars x 2 Donors for root traits
(JG11, KAK2, ICC 92318) ↓ (ICC 4958, ICC 8261)
BC1: Cultivar x F1
↓ JG 11
BC1F1
D BC2: Cultivar x BC1F1 JG 11 x ICC 4958
↓
O BC2F1
N Subjected to foreground and background selection

E BC3: Cultivar x BC2F1

As in BC2
↓
BC3F1
Selected heterozygous plants for QTL-linked markers JG11
and over 90% genome of the recurrent parent
↓ ICC 4958
BC3F2
Select homozygous plants for QTL-linked markers Heterozygous
↓ for both alleles
BC3F3
Seed multiplication Homozygous
↓ for B alleles
Multilocation evaluation BC3F4 lines Homozygous
for A allele
Phenotyping of MABC
products in ROS
 Enhanced root length MABC
ICC 4958 products from ICC 4958

BC3F3 progenies
JG11
 Evaluation of MABC
products (BC3F3)
1.7
Donor line Elite line MABC lines
Root dry weight (g cylinder-1)

1.5

1.3

1.1

0.9

0.7

0.5

Mean of
ICC 4958

ICC 1882

JG 11

F2-P173

F2-P242

F2-P187

F2-P150

F2-P105

BC3F3s
090013-
090013-

090013-

090013-

090013-
ICCX-

ICCX-

ICCX-

ICCX-

ICCX-
(2010)

0.50
Donor line Elite line MABC lines
0.45
0.40
RLD (cm cm-3)

0.35
0.30
0.25
0.20
(2010)

Mean of
4958

BC3F3s
F2-P105

F2-P187

F2-P216

F2-P242

F2-P173
JG 11

090013-
090013-

090013-

090013-

090013-
ICC

1882

ICCX-

ICCX-

ICCX-

ICCX-

ICCX-
ICC

Vertical bars denote standard error of differences. The means were significantly different at 0.001 level
and were based on 8 replicated cylinders with 2 plants in each cylinder)
 Evaluation of BC3F4 lines
in field conditions

Evaluated under water-stressed and unstressed conditions at

multi-locations (3 locations in India and 3 locations in Africa)
during 2011/12
Evaluation of BC3F4 for
grain yield (Nandyal)
 MABC by NARS
partners
NARS partner Cross Generation

EIAR, Ethiopia Ejere × ICC 4958 BC2F1

EU, Kenya ICCV 97105 × ICC 4958 BC4F1

ICCV 95423 × ICC 4958 BC3F3

IIPR, India DCP92-3 × ICC 4958 BC1F1

KWR108 × ICC 4958 BC2F1

IARI, India Pusa 362 × ICC 4958 BC1F1

 For MAGIC populations
GCP
Eight well performing elite chickpea lines (TLI & TLII)
Parental line Remarks

ICC 4958 Drought tolerant genotype found promising in Ethiopia,

Kenya and India; drought tolerant parent of two mapping
populations
ICCV 10 Widely adapted drought tolerant cultivar found
promising in India and Kenya
JAKI 9218 Farmer-preferred cultivar in central and southern India
JG 11 Farmer-preferred cultivar in southern India and also
performing well in Kenya
JG 130 Farmer-preferred cultivars from central India
JG 16 Farmer-preferred cultivar in northern and central India
ICCV 97105 Farmer-preferred elite line identified in Kenya and
Tanzania
ICCV 00108 Farmer-preferred elite line identified in Tanzania
 Current status of MAGIC
populations GCP
8 parents: A) ICC 4958, B) JAKI 9218, C) JG 130, D) ICCV 00108,
E) ICCV 97105, F) ICCV 10, G) JG 11, H) JG 16
28 2-ways
Oct 09 – Feb 10
Field

14 4-ways
Jun 10- Sep 10
Green house

7 8-ways
Oct 10-Feb 11
Field

F1s raised and selfed in green house Mar 11- Jun 11

F2s raised and selfed in green house Jun 11- Sep 11

SSD method
1200 F3 progenies raised in field Oct 11- Feb 12
SSD method
1200 F4 progenies raised in field Feb 12- May 12
SSD method
SNP genotyping 1200 F5 progenies will be raised in field Jun 12- Sep 12
SSD method
1200 F6 progenies will be raised in field Oct 12- Feb 13
 Integration of genomics in
breeding: challenges GCP

Curr Opin Plant Biol 2010

 Take home message…
GCP
 Genomic tools can be used to harness the
potential of genetic resources
 NGS and HTP genotyping technologies has
accelerated resource development very rapidly
 Large scale and precise phenotyping, though
not trivial, but possible; field phenotyping
necessary
 Molecular breeding activities have been
initiated in chickpea for drought tolerance!!
 Adoption of genomic technologies by NARS
partners in Africa and Asia- critical
 Acknowledgements
GCP

 ICRISAT, Patancheru, India: Pooran Gaur,

Hari Upadhyaya, L Krishnamurthy, Junichi Kashiwagi,
Vincent Vadez, Mahendar Thudi, Spurthi Nayak,
Siva Kumar, Hima Bindu, Pavana Hiremath
 UC-Davis, USA: Doug Cook
 NCGR, USA: Greg May
 JCVI, USA: Chris Town
 NRCPB, New Delhi, India: R Srinivasan
 NIPGR, New Delhi, India: Sabhyata Bhatia
 Uni Frankfurt, Germany: Peter Winter, Guenter Kahl
 Egerton University, Kenya: Paul Kimurto, Serah
 EIAR, Addis Abba, Ethiopia: Million Eshete
 LZARDI, Debre Zeit, Tanzania: Robert Kileo
 UAS-Bangalore, India: S Sheshashayee
 IIPR-Kanpur, India: SK Chaturvedi, Aditya Garg
 ICRISAT, Nairobi, Kenya: N Gangarao, S Silim
 VI International Conference on Legume Genetics and
Genomics (VI ICLGG)
Hyderabad Marriott Hotel & Convention Center, Hyderabad, India
GCP
October 2-7, 2012 Featured Speakers:
David Bertioli, Catholic Uni, Brazil
Doug Cook, UC-Davis, USA
Martin Crespi, ISV-CNRS, France
Conference Topics: Jeff Doyle, Cornell Uni, USA
Peter Gresshoff, Queensland Uni, Australia
• Next generation genomics Valérie Geffroy, Paris Uni-Sud, France
CLL Gowda, ICRISAT, India
• Nutrition Georgina Hernández, UNAM, Mexico
• Development T J Higgins, CSIRO, Australia
Sachiko Isobe, KDRI, Japan
• Evolution and Diversity Scott Jackson, Purdue Uni, USA
Eva Kondorosi, IPG-Szeged, Hungary
• Symbiosis Günter Kahl, FrankfurtUni, Germany
Suk-Ha Lee, Seoul National Uni, Korea
• Abiotic Stress Da Luo, Sun Yat Sen Uni, China
• Pathogenesis and disease Greg May, NCGR, USA
Henry Nguyen, Missouri Uni, USA
resistance N Nadarajan, IIPR, India
• Translational genomics Giles Oldroyd, JIC, UK
Karam Singh, CSIRO/UWA, Australia
• Genomics-assisted breeding Richard Thompson, INRA-Dijon, France
Ana Torres, IFAPA, Spain
• Harnessing germplasm resources Michael Udvardi, Noble Foundation, USA
Carroll Vance, Minnesotta Uni, USA
Bert Vandenberg, Saskatchewan Uni, Canada
… and many more !

www.icrisat.org/gt-bt/VI-ICLGG/Homepage.htm
ICLGG2012@gmail.com; r.k.varshney@cgiar.org