GWAS for QTLs associated with agronomic traits in Chickpea (Cicer arietinum L.) harvested in South-East Kazakhstan

Zatybekov A. Genievskaya Y. Anuarbek S. Varshney R.K. Barmukh R. Kudaibergenov M. Turuspekov Y. Abugalieva S.
December 2026 BioMed Central Ltd

BMC Plant Biology
2026 #26 Issue 1

Background: Chickpea (Cicer arietinum L.) is vital for global food security; however, its productivity is limited by genotype-environment interactions and restricted genetic diversity. This study dissected the genetic architecture of six agronomic traits in chickpea using genome-wide association studies (GWAS) to identify stable quantitative trait loci (QTLs). Results: Phenotypic analysis of 238 chickpea accessions across three growing seasons revealed significant variation in plant height (PH), height to lowest pod (HLP), number of lateral branches (NLB), number of seeds per plant (NSP), thousand-seed weight (TSW), and yield per plant (YP). Broad-sense heritability (h²) ranged from 0.15 (NSP) to 0.88 (TSW). GWAS identified 40 stable QTLs, including major-effect loci on chromosomes 2 (Q_YP_2.1, R² = 0.45) and 4 (Q_TSW_4.1, R² = 0.22). Candidate genes linked to polyamine biosynthesis (LOC101508792) and carbohydrate metabolism (LOC101492955) were implicated. Conclusions: The study highlights the potential of marker-assisted selection for enhancing chickpea resilience and productivity, particularly in drought-prone regions such as Kazakhstan.

Chickpea , GWAS , QTL mapping , Yield components

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Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty, 050040, Kazakhstan
State Agricultural Biotechnology Centre, Murdoch University, Murdoch, 6150, Australia
Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, 040909, Kazakhstan

Laboratory of Molecular Genetics
State Agricultural Biotechnology Centre
Kazakh Research Institute of Agriculture and Plant Growing

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