Molecular Biology Reports

, Volume 42, Issue 11, pp 1571–1580 | Cite as

Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height

  • Shefali Gupta
  • Tapan Kumar
  • Subodh Verma
  • Chellapilla Bharadwaj
  • Sabhyata Bhatia
Original Paper


Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight- 48 g and plant height- 53 cm) and BGD112 (100-seed weight- 15 g and plant height- 65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64 %) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24 % of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17 % of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.


Cicer arietinum EST-based markers Intra-specific linkage map QTLs Seed weight 



This work was supported by the National Institute of Plant Genome Research (NIPGR), New Delhi, India, Indian Agricultural Research Institute (IARI), New Delhi, India and Department of Biotechnology (DBT), Government of India under project number BT/01/08/NRC-PBI/01. The fellowships provided to SG by Council for Scientific and Industrial Research (CSIR), India and to SV by DBT, India is gratefully acknowledged.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Supplementary material 1 (XLS 96 kb)
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Supplementary material 2 (XLS 66 kb)
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Supplementary material 3 (XLS 49 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Shefali Gupta
    • 1
  • Tapan Kumar
    • 2
  • Subodh Verma
    • 1
  • Chellapilla Bharadwaj
    • 2
  • Sabhyata Bhatia
    • 1
  1. 1.National Institute of Plant Genome ResearchNew DelhiIndia
  2. 2.Indian Agricultural Research InstituteNew DelhiIndia

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