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Functional & Integrative Genomics

, Volume 17, Issue 6, pp 711–723 | Cite as

Genetic dissection of plant growth habit in chickpea

  • Hari D. Upadhyaya
  • Deepak Bajaj
  • Rishi Srivastava
  • Anurag Daware
  • Udita Basu
  • Shailesh Tripathi
  • Chellapilla Bharadwaj
  • Akhilesh K. Tyagi
  • Swarup K. ParidaEmail author
Original Article

Abstract

A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima’s D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.

Keywords

Chickpea GWAS Plant growth habit QTL SNP 

Notes

Acknowledgments

The authors gratefully acknowledge the financial support for this study provided by a research grant from the Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14).

Supplementary material

10142_2017_566_MOESM1_ESM.pdf (298 kb)
Figure S1 (PDF 298 kb)
10142_2017_566_MOESM2_ESM.pdf (35 kb)
Table S1 (PDF 35 kb)
10142_2017_566_MOESM3_ESM.pdf (181 kb)
Table S2 (PDF 180 kb)
10142_2017_566_MOESM4_ESM.pdf (1.8 mb)
Table S3 (PDF 1880 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Hari D. Upadhyaya
    • 1
  • Deepak Bajaj
    • 2
  • Rishi Srivastava
    • 2
  • Anurag Daware
    • 2
  • Udita Basu
    • 2
  • Shailesh Tripathi
    • 3
  • Chellapilla Bharadwaj
    • 3
  • Akhilesh K. Tyagi
    • 2
    • 4
  • Swarup K. Parida
    • 2
    Email author
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  2. 2.National Institute of Plant Genome Research (NIPGR)New DelhiIndia
  3. 3.Division of GeneticsIndian Agricultural Research Institute (IARI)New DelhiIndia
  4. 4.Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia

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