Dissecting the genomic regions, candidate genes and pathways using multi-locus genome-wide association study for stem rot disease resistance in groundnut

Authors: VEERENDRAKUMAR, H - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SUDINI, HARI KISHAN - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; KIRANMAYEE, BANGARU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; DEVIKA, TALWAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GANGURDE, SUNIL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VASANTHI, R - Acharya Ng Ranga Agricultural University (ANGRAU); KUMAR, A.R. NIRMAL - Acharya Ng Ranga Agricultural University (ANGRAU); BERA, SANDIP - Icar – Indian Institute Of Agricultural Biotechnology (IIAB); Guo, Baozhu; LIAO, BOSHOU - Chinese Academy Of Agricultural Sciences; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/30/2025
Publication Date: 8/12/2025
Citation: Veerendrakumar, H.V., Sudini, H., Kiranmayee, B., Devika, T., Gangurde, S.S., Vasanthi, R.P., Kumar, A., Bera, S.K., Guo, B., Liao, B., Varshney, R.K., Pandey, M.K. 2025. Dissecting the genomic regions, candidate genes and pathways using multi-locus genome-wide association study for stem rot disease resistance in groundnut. BMC Plant Biology. 18:e70089. https://doi.org/10.1002/tpg2.70089.
DOI: https://doi.org/10.1002/tpg2.70089

Interpretive Summary: Peanut is one of the important oilseed crops and a useful food legume globally. But peanut production is facing many challenges like various biotic and abiotic stresses. Biotic stress is a major cause of yield loss, particularly caused by soil borne diseases like stem rot caused by Sclerotium rolfsii. The only reliable method for the management of this disease is host-plant resistance. Therefore, it is essential to identify sources of resistance and to apply the resistance in breeding programs for development of resistant cultivars. In this study, we explored the genetic basis of variation for stem rot resistance in peanut diverse germplasm collection using ICRISAT minicore of 184 accessions. This collection was screened for three years in diseased field and genotyped using peanut 58K SNP Array. This study described the identified genomic regions and potential candidate genes responsible for stem rot resistance. This study also suggested that the resistance for this disease is only present in the Virginia type (both bunch and runners) peanut. Further applications in breeding needs to be tested.

Technical Abstract: Stem rot disease, caused by Sclerotium rolfsii, is a soil borne disease found in all groundnut production areas. Host resistance is one important strategy in managing this disease. In this study we evaluated the ICRISAT minicore collection of 184 germplasm accessions for three years in the field and used the ‘Axiom_Arachis’ Array with 58K SNPs to genotype the collection. We identified 13 associated genomic regions on eight chromosomes with the LOD score ranging from 4.5 to 12.4 and the R2-value ranging from 6.9% to 58%. A total of 145 Candidate genes were identified. GO enrichment has indicated that the significant association of the candidate genes with GO terms and divided them into biological process, molecular function, cellular components. The pathway was elucidated using enzyme IDs and KEGG IDs of genes, delineating the intricate dynamics of plant-pathogen interactions. This analysis revealed the biochemical compounds synthesized by the plant to boost its immune response and promote cellular homeostasis, thereby facilitating the maintenance of its overall health. If the plant fails to save the cell it signals the hypersensitive response through the identified genes it leads to Apoptosis. All the MTAs identified in this study are validated and confirmed their association with stem rot resistance.