Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.)

Bhunchoth, Anjana; Poncheewin, Wasin; Yongsuwan, Arweewut; Chiangta, Jirawan; Thunnom, Burin; Aesomnuk, Wanchana; Phironrit, Namthip; Phuangrat, Bencharong; Koohapitakthum, Ratree; Deeto, Rungnapa; Warin, Nuchnard; Wanchana, Samart; Arikit, Siwaret; Chatchawankanphanich, Orawan; Ruanjaichon, Vinitchan

doi:10.3390/plants14193036

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Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.)

by

Anjana Bhunchoth

^1,†,

Wasin Poncheewin

^1,†

,

Arweewut Yongsuwan

¹,

Jirawan Chiangta

¹,

Burin Thunnom

¹

,

Wanchana Aesomnuk

²,

Namthip Phironrit

¹,

Bencharong Phuangrat

¹,

Ratree Koohapitakthum

¹,

Rungnapa Deeto

¹,

Nuchnard Warin

¹,

Samart Wanchana

¹

,

Siwaret Arikit

^2,3

,

Orawan Chatchawankanphanich

¹

and

Vinitchan Ruanjaichon

^1,*

¹

National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand

²

Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140, Thailand

³

Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Plants 2025, 14(19), 3036; https://doi.org/10.3390/plants14193036

Submission received: 3 September 2025 / Revised: 24 September 2025 / Accepted: 26 September 2025 / Published: 1 October 2025

(This article belongs to the Section Plant Protection and Biotic Interactions)

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Abstract

Bacterial wilt, caused by Ralstonia solanacearum, is a major constraint to tomato production globally. To uncover resistance loci and develop efficient molecular tools for breeding, we conducted disease phenotyping over two growing seasons, which revealed consistent variation in resistance and moderate broad-sense heritability (H² = 0.22–0.28), suggesting a genetic basis. A genome-wide association study (GWAS) was performed on a diverse panel of 267 tomato accessions, evaluated against two R. solanacearum strains. A major resistance locus was identified on chromosome 12, with the strongest association observed at SNP S12_2992992, located within a gene encoding a leucine-rich repeat (LRR) receptor-like protein. Haplotype analysis indicated that the resistance-associated allele is relatively rare (~13.5%) in the population, underscoring its potential value in breeding programs. Functional validation in an F₂ population derived from a cross between the susceptible ‘Seedathip6’ and the resistant ‘Hawaii 7996’ confirmed that the TT genotype at S12_2992992 was significantly associated with enhanced resistance. A Kompetitive Allele Specific PCR (KASP) marker was developed for this SNP, facilitating cost-effective and high-throughput selection. Collectively, these findings establish S12_2992992 as a robust and functionally informative marker, offering a valuable tool for accelerating bacterial wilt resistance breeding in tomato through marker-assisted selection.

Keywords: tomatoes; bacterial wilt resistance; GWAS; SNP marker

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MDPI and ACS Style

Bhunchoth, A.; Poncheewin, W.; Yongsuwan, A.; Chiangta, J.; Thunnom, B.; Aesomnuk, W.; Phironrit, N.; Phuangrat, B.; Koohapitakthum, R.; Deeto, R.; et al. Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.). Plants 2025, 14, 3036. https://doi.org/10.3390/plants14193036

AMA Style

Bhunchoth A, Poncheewin W, Yongsuwan A, Chiangta J, Thunnom B, Aesomnuk W, Phironrit N, Phuangrat B, Koohapitakthum R, Deeto R, et al. Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.). Plants. 2025; 14(19):3036. https://doi.org/10.3390/plants14193036

Chicago/Turabian Style

Bhunchoth, Anjana, Wasin Poncheewin, Arweewut Yongsuwan, Jirawan Chiangta, Burin Thunnom, Wanchana Aesomnuk, Namthip Phironrit, Bencharong Phuangrat, Ratree Koohapitakthum, Rungnapa Deeto, and et al. 2025. "Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.)" Plants 14, no. 19: 3036. https://doi.org/10.3390/plants14193036

APA Style

Bhunchoth, A., Poncheewin, W., Yongsuwan, A., Chiangta, J., Thunnom, B., Aesomnuk, W., Phironrit, N., Phuangrat, B., Koohapitakthum, R., Deeto, R., Warin, N., Wanchana, S., Arikit, S., Chatchawankanphanich, O., & Ruanjaichon, V. (2025). Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.). Plants, 14(19), 3036. https://doi.org/10.3390/plants14193036

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Genome-Wide Association Analysis and Breeding-Oriented SNP Marker Development for Bacterial Wilt Resistance in Tomato (Solanum lycopersicum L.)

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