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Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea

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Title Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea
 
Creator Sharma, Akash
Basu, Udita
Malik, Naveen
Daware, Anurag
Thakro, Virevol
Narnoliya, Laxmi
Bajaj, Deepak
Tripathi, Shailesh
Hegde, V. S.
Upadhyaya, Hari D.
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Chickpea
CNSNP
Drought
eQTL
GWAS
QTL
RIL
Transcription factor
Yield
 
Description Accepted date: 10 May 2019
Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment
in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified
431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on
a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly
web-database (http://www.cnsnpcicarbase.com). The CNSNP-based quantitative trait loci (QTL) and expression QTL
(eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression
landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred
lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought
stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a
histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs
and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3
gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitationquantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially
have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic
analysis in chickpea.
We are very much grateful to Mr. Sube Singh, lead
scientific officer, Grain Legumes Research Program/Genebank,
ICRISAT, Hyderabad, for assisting in collecting multi-environment field
phenotyping data of germplasm accessions and mapping population. The
timely support provided by all the scientific and technical staffs of NIPGR
and IARI, New Delhi and ICRISAT, Hyderabad, to conduct these research works are acknowledged. We are thankful to central instrumentation facility (CIF), plant growth facility (PGF), and DBT-eLibrary consortium (DeLCON) of NIPGR, New Delhi, for providing timely support
and access to e-resources for this research work. The financial support for this study is provided by a
research grant from the Department of Biotechnology (DBT),
Government of India. UB, AD, VT, and LN acknowledge the UGC
(University Grants Commission) and DBT, India for research fellowship
awards.
 
Date 2019-06-18T06:12:37Z
2019-06-18T06:12:37Z
2019
 
Type Article
 
Identifier Functional & Integrative Genomics, 19(6): 973-992
1438-7948
http://223.31.159.10:8080/jspui/handle/123456789/958
https://link.springer.com/article/10.1007%2Fs10142-019-00691-2
https://doi.org/10.1007/s10142-019-00691-2
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature Publishing AG