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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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Abstract

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 immunoprecipitation-quantitative 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.

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Acknowledgments

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.

Funding

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.

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  1. Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

    Akash Sharma, Udita Basu, Naveen Malik, Anurag Daware, Virevol Thakro, Laxmi Narnoliya, Deepak Bajaj, Akhilesh K. Tyagi & Swarup K. Parida

  2. Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India

    Shailesh Tripathi & V. S. Hegde

  3. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India

    Hari D. Upadhyaya

  4. Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India

    Akhilesh K. Tyagi

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  1. Akash Sharma
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Sharma, A., Basu, U., Malik, N. et al. Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Funct Integr Genomics 19, 973–992 (2019). https://doi.org/10.1007/s10142-019-00691-2

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