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

Wang, R and Gangola, M P and Irvine, C and Gaur, P M and Baga, M and Chibbar, R N (2019) Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration. Theoretical and Applied Genetics (TSI), 132 (4). pp. 1263-1281. ISSN 0040-5752

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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. Abstract 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.

Item Type: Article
Divisions: Research Program : Asia
Uncontrolled Keywords: chickpea, crop yield, seed, seed composition, recombinant inbred lines, RILs
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Others > Seed Systems
Depositing User: Mr Ramesh K
Date Deposited: 09 Sep 2019 10:46
Last Modified: 09 Sep 2019 10:46
Official URL:
Acknowledgement: 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.
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