Publications of NIPGR Scientists

Permanent URI for this communityhttps://ndkr-library.nipgr.ac.in/handle/123456789/1

Browse

Author: search.filters.author.Bajaj, DeepakSubject: search.filters.subject.Transcription factor

Search Results

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea
    (Springer Nature Publishing AG, 2019) 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.
    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.
  • Thumbnail Image
    Item
    Identifying transcription factor genes associated with yield traits in chickpea
    (Springer, 2017) Shimray, Philanim Wungmarong; Bajaj, Deepak; Srivastava, Rishi; Daware, Anurag; Upadhyaya, Hari D.; Kumar, Rajendra; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.
    Identification of potential transcription factor (TF) gene-derived natural SNP allelic variants regulating pod and seed yield component traits by large-scale mining and genotyping of SNPs in natural germplasm accessions coupled with high-resolution association mapping is vital for understanding the complex genetic architecture of quantitative yield traits in chickpea. In these perspectives, the current study employed a genome-wide GBS (genotyping-by-sequencing) and targeted gene amplicon resequencing-based simultaneous SNP discovery and genotyping assays, which discovered 1611 novel SNPs from 736 TF genes physically mapped on eight chromosomes and unanchored scaffolds of kabuli chickpea genome. These SNPs were structurally and functionally annotated in diverse synonymous and non-synonymous coding as well as non-coding regulatory and intronic sequence components of chickpea TF genes. A high-resolution genetic association analysis was performed by correlating the genotyping information of 1611 TF gene-based SNPs with multi-location/years field phenotyping data of six major pod and seed yield traits evaluated in a constituted association panel (326 desi and kabuli germplasm accessions) of chickpea. This essentially identified 27 TF gene-derived SNPs exhibiting significant association with six major yield traits, namely days to 50% flowering (DF), plant height (PH), branch number (BN), pod number (PN), seed number (SN) and seed weight (SW) in chickpea. These trait-associated SNPs individually and in combination explained 10–23% and 32% phenotypic variation respectively for the studied yield component traits. Interestingly, novel non-synonymous coding SNP allelic variants in five potential candidate TF genes encoding SBP (squamosal promoter binding protein), SNF2 (sucrose non-fermenting 2), GRAS [Gibberellic acid insensitive (GAI)-Repressor of GAI (RGA)-SCARECROW (SCR)], bZIP (basic leucine zipper) and LOB (lateral organ boundaries)-domain proteins associated strongly with DF, PH, BN, PN, SN and SW traits respectively were found most promising in chickpea. The functionally relevant molecular signatures (TFs and natural SNP alleles) delineated by us have potential to accelerate marker-assisted genetic enhancement by developing high pod and seed yielding cultivars of chickpea.