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

Alibek Zatybekov; Yuliya Genievskaya; Shynar Anuarbek; Rajeev K Varshney; Rutwik Barmukh; Mukhtar Kudaibergenov; Yerlan Turuspekov; Saule Abugalieva

doi:10.1186/s12870-025-07749-3

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

Journal article

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Peer reviewed

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

Alibek Zatybekov, Yuliya Genievskaya, Shynar Anuarbek, Rajeev K Varshney, Rutwik Barmukh, Mukhtar Kudaibergenov, Yerlan Turuspekov and Saule Abugalieva

BMC plant biology, Vol.26, 42

2025

DOI: https://doi.org/10.1186/s12870-025-07749-3

PMID: 41331428

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Abstract

Chickpea

Yield components

GWAS

QTL mapping

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.

Details

Title: GWAS for QTLs associated with agronomic traits in Chickpea (Cicer arietinum L.) harvested in South-East Kazakhstan
Authors/Creators: Alibek Zatybekov - Institute of Plant Biology and Biotechnology
Yuliya Genievskaya - Institute of Plant Biology and Biotechnology
Shynar Anuarbek - Institute of Plant Biology and Biotechnology
Rajeev K Varshney - Murdoch University
Rutwik Barmukh - Murdoch University
Mukhtar Kudaibergenov - Kazakh Research Institute of Agriculture and Plant growing
Yerlan Turuspekov - Institute of Plant Biology and Biotechnology
Saule Abugalieva - Institute of Plant Biology and Biotechnology
Publication Details: BMC plant biology, Vol.26, 42
Publisher: Springer Nature
Grant note: AP19677444 / Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan
Identifiers: 991005836244207891
Murdoch Affiliation: Centre for Crop and Food Innovation; Food Futures Institute
Language: English
Resource Type: Journal article

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