Theoretical and Applied Genetics

, Volume 132, Issue 4, pp 1263–1281 | Cite as

Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration

  • Runfeng Wang
  • Manu P. Gangola
  • Craig Irvine
  • Pooran M. Gaur
  • Monica Båga
  • Ravindra N. ChibbarEmail author
Original Article


Key message

Major QTL on LG 1 and 3 control seed filling and seed coat development, thereby affecting seed shape, size, color, composition and weight, key determinants of crop yield and quality.


A chickpea (Cicer arietinum L.) population consisting of 189 recombinant inbred lines (RILs) derived from a cross between medium-protein ICC 995 and high-protein ICC 5912 genotypes of the desi market class was analyzed for seed properties. Seed from the parental lines and RILs was produced in four different environments for determination of seed shape (SS), 100-seed weight (100-SW), protein (PRO) and starch (STA) concentration. Polymorphic genetic markers for the population were identified by Genotyping by Sequencing and assembled into a 522.5 cM genetic map. Phenotype data from the different growth environments were analyzed by QTL mapping done by single and multi-environment analyses and in addition, single marker association mapping. The analyses identified in total 11 QTL, of which the most significant (P < 0.05) loci were located on LG 1 (q-1.1), LG 2 (q-2.1), LG 3 (q-3.2, q-3.3), LG 4 (q-4.2), and LG 5 (q-5.1). STA was mostly affected by q-1.1, which explained 19.0% of the phenotypic variance for the trait. The largest QTL effects were demonstrated by q-3.2 that explained 52.5% of the phenotypic variances for 100-SW, 44.3% for PRO, and 14.6% for SS. This locus was also highly associated with flower color (COL; 95.2% explained) and showed q-3.2 alleles from the ICC 5912 parent conferred the blue flower color and production of small, round seeds with relatively high protein concentration. Genes affecting seed filling at q-1.1 and seed coat development at q-3.2, respectively, were considered to underlie differences in seed composition and morphology in the RIL population.



This work was financially supported by Canada Research Chairs Program, Natural Sciences and Engineering Research Council, and Agriculture and Agri-Food Canada Internationalization program. The core research grant of International Crops Research Institute for Semi-Arid Tropics (ICRISAT, Patancheru, India) is acknowledged for the development of the chickpea RIL population and field trial at ICRISAT. RW is a grateful recipient of the China Scholarship Council fellowship for Ph.D. We are very grateful to Mr. John Bennet (Biggar Saskatchewan) and Mr. Jeff Sopatyk (Aberdeen, Saskatchewan) who provided land for the field trials.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Supplementary material

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Plant SciencesUniversity of SaskatchewanSaskatoonCanada
  2. 2.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, HyderabadIndia

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