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

Vinay Sharma; Sunil S Gangurde; Spurthi N Nayak; Anjan S Gowda; B S Sukanth; Supriya S Mahadevaiah; Surendra S Manohar; Rakeshkumar S Choudhary; T Anitha; Sachin S Malavalli; S N Srikanth; Prasad Bajaj; Shailendra Sharma; Rajeev K Varshney; Putta Latha; Pasupuleti Janila; Ramesh S Bhat; Manish K Pandey

doi:10.3389/fpls.2023.1182867

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

Front Plant Sci. 2023 May 23:14:1182867. doi: 10.3389/fpls.2023.1182867. eCollection 2023.

Authors

Vinay Sharma^{1

2}, Sunil S Gangurde¹, Spurthi N Nayak³, Anjan S Gowda³, B S Sukanth³, Supriya S Mahadevaiah³, Surendra S Manohar¹, Rakeshkumar S Choudhary³, T Anitha⁴, Sachin S Malavalli³, S N Srikanth³, Prasad Bajaj¹, Shailendra Sharma², Rajeev K Varshney¹, Putta Latha⁴, Pasupuleti Janila¹, Ramesh S Bhat³, Manish K Pandey¹

Affiliations

¹ Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India.
² Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India.
³ Department of Biotechnology, University of Agricultural Sciences, Dharwad, India.
⁴ Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India.

Abstract

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.

Keywords: heat stress — tolerance — molecular markers — QTL; candidate gene; genomic regions; genotyping by sequencing; peanut.

Grants and funding

The authors are thankful to the National Agricultural Science Fund (NASF) of the Indian Council of Agricultural Research (ICAR), India, and partial support from DBT-BioCARe (PR18251) of the Department of Biotechnology, India, and Bill & Melinda Gates Foundation (BMGF), USA, for financial assistance.