Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut

Sharma, V and Gangurde, S S and Nayak, S N and Gowda, A S and Sukanth, B S and Mahadevaiah, S S and Manohar, S S and Choudhary, R S and Anitha, T and Malavalli, S S and Srikanth, S N and Bajaj, P and Sharma, S and Varshney, R K and Latha, P and Janila, P and Bhat, R S and Pandey, M K (2023) Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut. Frontiers in Plant Science (TSI), 14. 01-21. ISSN 1664-462X

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Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%–38.6%, 10.6%–44.6%, and 10.1%–49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.

Item Type: Article
Divisions: Center of Excellence in Genomics and Systems Biology
Uncontrolled Keywords: heat stress - tolerance - molecular markers - QTL, genotyping by sequencing, candidate gene, peanut, genomic regions
Subjects: Mandate crops > Groundnut
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 02 Feb 2024 04:34
Last Modified: 02 Feb 2024 04:34
Official URL:
Projects: National Agricultural Science Fund, DBT-BioCARe
Funders: Indian Council of Agricultural Research, Department of Biotechnology, India, Bill & Melinda Gates Foundation (BMGF), USA
Acknowledgement: The authors thank the National Agricultural Science Fund (NASF) of the Indian Council of Agricultural Research (ICAR), India, for support in generating genotyping, and multi-location evaluation data as well as analysis for QTL and gene discovery. Authors also thank DBT-BioCARe (PR18251) of the Department of Biotechnology, India, for the support in generating additional phenotyping data and Bill & Melinda Gates Foundation (BMGF), USA, for the support in population development. VS acknowledges Chaudhary Charan Singh University (CCSU), Meerut, for collaborating with ICRISAT and for the opportunity given as a student to pursue this investigation at ICRISAT.
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