A chickpea MAGIC population to dissect the genetics of complex traits

Akinlade, O J and Robinson, H and Kang, Y and Thudi, M and Samineni, S and Gaur, P M and Smith, M R and Voss-Fels, K P and Costilla, R and Varshney, R K and Dinglasan, E and Hickey, L T (2025) A chickpea MAGIC population to dissect the genetics of complex traits. The Plant Genome (TSI), 18 (3). pp. 1-17. ISSN 1940-3372

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Abstract

Multiparent populations are now widespread in crop genetic studies as they capture more genetic diversity and offer high statistical power for detecting quantitative trait loci (QTLs). To confirm the suitability of using a recently developed chickpea (Cicer arietinum L.) multi-parent advanced generation intercross (MAGIC) population for genetic studies, we characterized the diversity of the eight founder lines and explored the linkage disequilibrium decay, marker coverage, segregation distortion, allelic variation, and structure of the population. The MAGIC population was genotyped using whole-genome sequencing; following marker curation, a total of 4255 high-quality polymorphic single nucleotide polymorphism markers were used for genomic analyses. To demonstrate the effectiveness of the MAGIC population to dissect the genetics of key agronomic traits (days to 50% flowering and plant height), we employed both a genome-wide mapping approach using fixed and random model circulating probability unification and a haplotype-based mapping using the local genomic estimated breeding value approach. Our analyses confirmed the role of genomic regions previously reported in the literature and identified several new QTLs for days to 50% flowering and plant height. We also showed the potential for trait improvement through stacking the top 10 haploblocks to develop early flowering chickpea and selection of desirable haplotypes on chromosome 4 to improve plant height. Our results demonstrate the chickpea MAGIC population is a valuable resource for researchers and pre-breeders to study the genetic architecture of complex traits and allelic variation to accelerate crop improvement in chickpea.

Item Type:	Article
Divisions:	Global Research Program - Accelerated Crop Improvement
CRP:	UNSPECIFIED
Uncontrolled Keywords:	genetics, chickpea, accelerate crop improvement, genetic architecture, gronomic traits
Subjects:	Mandate crops > Chickpea Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	17 Mar 2026 05:12
Last Modified:	17 Mar 2026 05:12
URI:	http://oar.icrisat.org/id/eprint/13548
Official URL:	https://acsess.onlinelibrary.wiley.com/doi/full/10...
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We are grateful for the development of the MAGIC population by the researchers at International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). Open access publishing facilitated by The University of Queensland, as part of the Wiley - The University of Queensland agreement via the Council of Australian University Librarians.
Links:	Google Scholar

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