Drought is a major abiotic stress that affects chickpea productivity. Analysis of a chickpea biparental population identified a genomic region ("QTL-hotspot") linked to drought tolerance. Gene analysis of this region identified 13 candidate genes, including 3 transcription factors (TFs): DREB7, ERF110-like, and TFID-like. These TFs showed differential expression between drought-tolerant and sensitive chickpea genotypes. Predictive protein-protein interaction analysis identified potential interactors of the TFs, such as Ice1 and ABF2 for DREB7, and TAFs and EER4 for TFID-like. Yeast two-hybrid screening is being used to validate

1. Protein-protein interactions of transcription factors from the
drought QTL-hotspot linked to stress tolerance in chickpea
Abirami Ramalingam, Himabindu Kudapa, Spurthi N Nayak, Lekha Pazhamala, Deepa Jaganathan,
Sandeep Kale, L Krishnamurthy, Pooran M Gaur, Rajeev K Varshney*
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
*Address for correspondence: r.k.varshney@cgiar.org
Abstract
TFs Interactor Mode of
action
Evidence Confidence
Score
DREB7 ICE1 Activation,
Expression
Text mining 0.983
LT178 N/A Co-expression 0.958
ABF2 Binding Text mining 0.900
WRKY34 Expression Text mining 0.812
ERF
110-like
Amino acid Transporter N/A Text mining 0.921
Exonuclease N/A Text mining 0.921
Glycine rich protein N/A Text mining 0.919
LTP N/A Text mining 0.919
TFID-
like
TAF13 N/A Experiments and
Text Mining
0.999
EER4 N/A 0.999
TBP2 Binding 0.828
TBP1 Binding 0.828
PPI predicted for the TF (STRING v.9.05)
PPI predicted based on the high
similarity of Arabidopsis DREB1A with
chickpea DREB7, Arabidopsis AP2-
domain TF with chickpea ERF 110-like
and Arabidopsis TAF8 with chickpea
Inclusive Market-Oriented Development (IMOD) –
our approach to bringing prosperity in the drylands.
ICRISAT is a member of the CGIAR Consortium.
DREB7
AP2/ERF DNA binding
domain. Confidence:99.9%
TFID-like
Bromodomain associated
Confidence:99.2%
Differential expression of the TFs under drought
stress
ERF 110-like
AP2, GCC box DNA binding
domain. Confidence:99.9%
Predictive modelling of the TF functional domains
(Phyre 2, DeepView v4.1.0)
Gene enrichment and
expression analysis
identified 13 candidate
genes including 3 TFs
‘QTL-hotspot’
identified
from the biparental
population
(ICC 4958 × ICC
1882) for drought
tolerance related
traits
Identification of candidate genes from the ‘QTL-hotspot’
Analysis of predicted (STRING) functional partners with high
confidence score
JG 11 X ICC 4958
(high performing) (tolerant ; donor)
Three back crosses with JG 11
JG 11+ (BC3F3)
(tolerant, high performing)
 The 3 TFs DREB7, ERF-110-like and TFID -
like identified from chickpea ‘QTL-hotspot’ are
potential candidate genes that may have
suitable application in improving tolerance in
chickpea
 Further investigation is being carried out using
Y2H to confirm their physical interactions in
the yeast system
Summary
Drought is the most prominent abiotic stress that affects the productivity of chickpea. The signalling networks in response to
drought comprise several major components that include transcription factors (TFs). Drought related QTL analysis identified a
genomic region (QTL-hotspot) in the chickpea biparental population (ICC 4958 × ICC 1882) that comprise several genes. Gene enrichment and
expression analyses identified 13 genes which include genes of 3 TF such as : a dehydration responsive element binding protein (DREB7), ethylene
responsive factor like (ERF 110-like) and a transcription initiation factor like (TFID like). qRT-PCR data showed 2 to 6 fold differences between the
contrasting drought responsive chickpea genotypes for these TFs. To further understand their roles and the ability to interact with other components
in the stress signalling pathways, predictive protein-protein interaction (PPI) analysis was performed with STRING 9.1 using A. thaliana as a reference
model. Using query sequences with similarity to these TFs, several potential interactors were identified and the ones with the highest confident
scores were selected. DREB7 possibly interacts with Ice 1 (Inducer of CBF Expression1) and ABF2 (Abscisic acid responsive elements-binding factor
2). TFID-like showed predictive interaction with other transcription factors such as TAFs (TBP-Associated factors) and EER4 (Enhanced ethylene
response) while ERF 110-like showed predictive interactions with an LTP (Lipid transfer protein) and an amino acid transporter protein. Yeast two
hybrid screening has been initiated to validate protein interactions of these TFs. This study will enhance the identification of candidate genes linked
to drought tolerance for chickpea crop improvement.