Terminal drought is one of major constraints that lead to considerable yield losses (~50%) in chickpea. By using linkage mapping approach on ICC 4958 × ICC 1882 population, a genomic region (~35cM) harbouring several QTLs for drought tolerance related traits was identified on linkage group 4 (LG04). 16 May 2014

1. Terminal drought is one of major constraints that lead to considerable yield losses (~50%) in chickpea. By using linkage
mapping approach on ICC 4958 × ICC 1882 population, a genomic region (~35cM) harbouring several QTLs for drought tolerance related
traits was identified on linkage group 4 (LG04). This region contained only four markers (TAA170, ICCM0249, STMS11 and GA24). In order
to increase marker density in this region, two approaches were adopted: (a) targeted mapping from the corresponding region from
published maps in chickpea, and (b) Medicago-Cicer synteny approach. In the former approach, a set of 43 SSR markers were chosen from
the corresponding region on the published genetic maps and genotyping data were generated for 19 polymorphic markers. In the later
approach, syntenic regions on Medicago chromosome 1 were identified by aligning the tentative orthologous (TOG) markers present in the
corresponding genomic region on the interspecific map (ICC 4958 × PI 489777). In summary, a set of 591 primer pairs were designed from
this syntenic region, of which 144 primers produced successful amplification in the intraspecific mapping population. A total of 75 SNPs
were identified between the parental genotypes through allele specific sequencing. Only 32 SNPs were found CAPS convertible and 3
markers were polymorphic between the parental lines. By combining these two approaches, three SSR marker loci and three DArT loci
were mapped in the QTL region for the intraspecific mapping population. At present, efforts are underway to saturate this region by using
RAD-sequencing approach on the mapping population.
Abstract
Towards fine mapping of drought tolerance related
QTL region in chickpea (Cicer arietinum L.)
Jaganathan D1, Thudi M1, Tuteja R2, Gaur PM1, Varshney RK1,3*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
2National University of Ireland (NUI), Galway, Ireland
3Generation Challenge Programme (GCP), c/o CIMMYT, Mexico DF, Mexico
*Corresponding author : r.k.varshney@cgiar.org
cpPb-49086723.5
Ca17738424.8
cpPb-32675826.2
STMS1127.0
TA4L-TA191R_291-28427.2
GA2427.4
GAA4727.7
LN5A28.2
P32_PisPR32_128.6
DSI29.3
CALTL29.5
M853_Mtmt_GEN_00853_01_129.6
cpPb-32544130.4
cpPb-32653730.5
CGMM00230.9
cpPb-32657631.9
ICCM029332.2
REP32.5
cpPb-323648
cpPb-68238240.2
cpPb-32793640.9
RL342.8
CGMM03643.3
LG9943.7
cpPb-48874344.3
cpPb-49059344.4
cpPb-172867
cpPb-679062
cpPb-678437
45.1
TA4L-TA199R-3_30046.1
cpPb-32796047.2
cpPb-32600847.5
ICCM000448.7
ICCM000348.8
ICCeM01349.5
GA249.9
ICCM002450.5
Ca1286316974739951.4
TA13052.5
TA3L-TS62R52.8
ICCM006353.5
ICCM024953.6
cpPb-32373853.9
TAA17054.6
CaM023256.7
cpPb-67829657.9
Thudi et al. 2011
QTL hot-spot on LG04
(ICC 4958 × ICC 1882)
1 2
Radhika et al. 2007 Millan et al. 2010
TA2x
TS54
TA146
TR35
TA72
UBC721
RGA8y
TR20s
H1A12
H4G11
UBC149z H4E09
NCPGR74
RGA8x
TA186
SSR6x
SSR6y
TS46
H1A10y
GA11
UBC335x
NCPGR58
H1G22
TS72
UBC844
UBC859y
H3A07
UBC335y
NCPGR98
UBC840
NCPGR27
TAA170
UBC886
UBC43x
UBC54
NCPGR93
UBC43y
UBC681
NCPGR45
NCPGR21
TR43
UBC149x
GA24
UBC809y
H3A04
UBC71y
NCPGR34
60
65
70
75
80
85
90
95
100
105
110
115
120
125
FCB
TA136
TA61
TR11
UBC181a
PsGEN3
ISSR8843
PR10_unten
UBC733b
OPX131408
TA4LTA191R291-284
OPAC12403
UBC402
OPA14-1
OPAC12450
GAA47
LN5A
STMS11
GA24
PsPR32
UBC884b
TA4L-TA199R-3_300
OPAF161025
MmGEN12
OPM02950
EAAMCTT08
TA3L-TS62R
TA130
R11899
GA2
OPQ05293
CS44a
OPAF16985
Enp2
EAAMCTA13
ISSR8401
UBC721b
UBC836b
TA186
EAAMCTT01
ECAMCAC03 TS54
TA2
TA146
0
5
10
15
20
25
30
35
40
45
50
55
Targeted marker development
 A total of 43 markers that are flanking ICCM0249, TAA170, STMS11 and GA24
were selected from published genetic maps (Thudi et al. 2011; Millan et al. 2010;
Nayak et al. 2010; Kottapalli et al. 2009; Radhika et al. 2007)
Synteny based marker development
Additional markers in QTL region
Summary
Acknowledgements
TA640.0
CaM061519.3
CaM084520.5
CaM085620.7
CaM065823.6
NCPGR17125.8
CaM082126.6
NCPGR14127.8
CaM198830.9
ICCM0199c34.9
H1H1336.3
CaM210338.5
ICCM0197a38.6
H1N1240.2
CaM115841.7
H1D2442.3
ICCM006543.2
ICCM016043.7
H2I0145.2
CaM183546.0
CaM130646.1
CaM0410 TR847.1
CaM1903 TAA5849.0
TA7250.0
TA13550.4
STMS2850.9
ICCeM001851.2
ICCeM005951.5
TA7851.7
ICCeM005852.0
CaM132853.8
CISR11754.6
cpPb-682025 cpPb-49040654.8
ICCeM005055.2
TA13255.7
cpPb-32292155.9
cpPb-67686856.5
STMS956.8
CaM168457.4
NCPGR3058.0
CaM043458.5
STMS1458.6
CaM115758.9
NCPGR3159.4
CaM092359.8
TS1959.9
CaM064560.3
CaM107760.5
CaM2093 CaM1026
CaM092460.9
CaM011361.1
CaM050761.3
NCPGR2762.2
NCPGR762.5
ICCM006962.6
ICCM006862.7
ICCM025063.0
H1B1763.3
NCPGR24563.8
TR2064.5
NCPGR23165.2
H1A1965.7
H4G1165.9
TA1866.7
NCPGR23667.1
CaM090668.2
H1A1272.0
CaM204973.6
TA4676.9
ICCM024978.8
ICCM025783.8
NCPGR12788.1
TAA17094.2
NCPGR2197.3
cpPb-680552102.8
cpPb-490776 cpPb-678284105.4
GA24108.2
STMS11111.2
CaM0446123.4
Tp684964131.7
NCPGR91148.3
 A total of six new markers (three SSR markers and three DArT loci) are
mapped in the QTL region
Markers highlighted in red are
additional markers added in the
present study and markers in blue are
previously reported markers in the
QTL region
 A total of 19 polymorphic SSR markers, 3 CAPS, 5 EST-SSR
markers and 14 previously unmapped DArT loci were used for
integration into genetic map
 Targeted and synteny based approaches resulted in addition of
six new markers (ICCM0257, NCPGR21, NCPGR127,
cpPb-680552, cpPb-490776 and cpPb-678284) in the QTL region
 SNPs identified from RAD sequencing will be used for
increasing the markers density
Financial support from Generation Challenge program (GCP),
Australia-India Strategic Research Fund (AISRF) and technical
assistance from Neetu Singh, Katta Sushmita, Preethi Dauthal are
greatly appreciated
Alignined against Medicago
Priority region 1 Priority region 2
TOG markers with in 5cM upstram and down stream of
QTL markers on Thudi et al. 2011 is Priority region 1 and
within 10cM is Priority region 2
RAD sequencing for SNP marker development
Restriction site associated DNA (RAD) sequencing is one of the
quick approaches for discovery of large scale SNP markers
The parental genotypes of mapping population (ICC 4958 and ICC
1882), 208 recombinant inbred lines (RILs), JG 11 and 33 near
isogenic lines (NILs) were used for RAD sequencing
On an average 654 SNPs were identified among RILs and 191
SNPs were identified among NILs
Multiple sequence alignment of sequences generated through
allele-specific sequencing for identification of SNPs among
ICC 4958, ICC 1882, ICC 283, ICC 8261 and PI 489777
LG04 of chickpea is syntenic to chromosome 1 of Medicago truncatula
(Nayak et al. 2010; Milan et al. 2010)
QTL hot-spot on LG04
(ICC 4958 × ICC 1882)
80 Tentative orthologous gene
(TOG) based markers selected
(Hiremath et al. 2012)
702 genes identified from Mt1
(19.5 Mb to 23.5 Mb)
591 CISR
primer pairs designed
341 CISR markers Sequenced
75 SNPs identified and 32
converted to CAPS
3 CAPS polymorphic
0