Plant Molecular Biology Reporter

, Volume 35, Issue 5, pp 562–574 | Cite as

Identifying Transcription Factor Genes Associated with Yield Traits in Chickpea

  • Philanim Wungmarong Shimray
  • Deepak Bajaj
  • Rishi Srivastava
  • Anurag Daware
  • Hari D. Upadhyaya
  • Rajendra Kumar
  • Chellapilla Bharadwaj
  • Akhilesh K. Tyagi
  • Swarup K. ParidaEmail author
Original Paper


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.


Association mapping Chickpea Desi Kabuli SNP Transcription factor 



The authors gratefully acknowledge the financial support by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India.

Supplementary material

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Figure S1

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High-resolution image (TIFF 4635 kb)
11105_2017_1044_MOESM2_ESM.pdf (227 kb)
Table S1 (PDF 226 kb)


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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Philanim Wungmarong Shimray
    • 1
  • Deepak Bajaj
    • 2
  • Rishi Srivastava
    • 2
  • Anurag Daware
    • 2
  • Hari D. Upadhyaya
    • 3
  • Rajendra Kumar
    • 4
  • Chellapilla Bharadwaj
    • 1
  • Akhilesh K. Tyagi
    • 2
    • 5
  • Swarup K. Parida
    • 2
    Email author
  1. 1.Division of Genetics, Indian Agricultural Research Institute (IARI)New DelhiIndia
  2. 2.National Institute of Plant Genome Research (NIPGR)New DelhiIndia
  3. 3.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  4. 4.U.P. Council of Agricultural ResearchLucknowIndia
  5. 5.Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia

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