The genetic diversity and certain disease assessments of wild tomato genetic resources and integration into breeding

Year 2025, Volume: 6 Issue: 3, 154 - 163, 31.12.2025

Hasan Can

https://doi.org/10.51753/flsrt.1711383

Abstract

Changing climate and pandemic-level disease affect tomato production as with all agricultural products. Moreover, the emergence of new diseases such as tomato brown rugose fruit virus has increased in recent years, and the cultivars are insufficient in production. To breed new cultivars that can respond to today's demands, the characteristics of genetic resources, including wild forms, need to be determined. In this context, the study attempted to screen some important tomato diseases, such as Tomato Spotted Wilt Virus (TSWV), Tomato yellow leaf curl virus (TYLCV), and root-knot nematode at the molecular level in tomato wild collections, and to reveal the genetic relationship between the wild forms available. For genetic diversity, 7 InDel and 8 SRAP markers (combination of 8 markers) and their combinations were included in the study, and a total of 60 polymorphic bands were scored from the given primer sets. The genetic relationship between wild forms was determined to be within 0.40 according to the simple matching similarity coefficient, and the result was also supported by principal coordinate analysis. The linked loci were amplified in wild forms and scored as resistant and susceptible using relevant primer sets. By evaluating all of these, the research indicated that the PI 128643 (Peru), PI 127830 (Peru), PI 212409 (Venezuela), PI 246586(Peru), PI 479211 (Colombia), and PI 487625 (Costa Rica) accessions possess considerable potential to enhance the breeding program.

Keywords

Breeding , diseases , genetic resources , molecular markers , wild tomatoes

Project Number

yok

References

• Adithya, A., Indu Rani, C., Savitha, B. K., Murugan, M., Sudha, M. & Prabhu, M. (2025). Harnessing the crop wild relatives in genetic improvement of eggplant, potato and tomato. Genetic Resources and Crop Evolution, 72(3), 2613-2629. https://doi.org/10.1007/s10722-024-02165-2
• Ajayi, A. T., Gbadamosi, A. E., Osekita, O. S., Taiwo, B. H., Babawole, F. A., Adedeji, I., & Omisakin, T. F. (2022). Genotype × environment interaction and adaptation of cowpea genotypes across six planting seasons. Frontiers in Life Sciences and Related Technologies, 3(1), 7-15. https://doi.org/10.51753 /flsrt.1036051
• Al Shaye, N., Migdadi, H., Charbaji, A., Alsayegh, S., Daoud, S., Al-Anazi, W. & Alghamdi, S. (2018). Genetic variation among Saudi tomato (Solanum lycopersicum L.) landraces studied using SDS-PAGE and SRAP markers. Saudi Journal of Biological Sciences, 25(6), 1007-1015. https://doi.org/https://doi.org/10.1016/j.sjbs.2018.04.014
• Alzahib, R. H., Migdadi, H. M., Ghamdi, A. A. A., Alwahibi, M. S., Afzal, M., Elharty, E. H. & Alghamdi, S. S. (2021). Exploring genetic variability among and within hail tomato landraces based on sequence-related amplified polymorphism markers. Diversity, 13(3), 135. https://www.mdpi.com/1424-2818/13/3/135
• Anuradha, B., Saidaiah, P., Reddy, K. R., Harikishan, S., Geetha, A. & Hari, Y. (2025). Molecular Diversity Analysis in Tomato (Solanum lycopersicum L.) Using SSR Markers. Journal of Advances in Biology & Biotechnology, 28(5), 703-717. Brhane, H. & Hammenhag, C. (2024). Genetic diversity and population structure analysis of a diverse panel of pea (Pisum sativum) [Original Research]. Frontiers in Genetics, Volume 15 - 2024. https://doi.org/10.3389/fgene.2024.1396888
• Chawla, R., Sharma, H., Dadheech, A., Jattan, M., Devi, S., Kumar, P., Sachin & Singh, T. (2025). Genetic insights into diversity and population structure of ashwagandha (Withania somnifera (L.) Dunal) using EST-SSR, ISSR and SSR markers: Implications for enhancing agricultural and industrial value. Industrial Crops and Products, 224, 120242. https://doi.org/https://doi.org/10.1016/j.indcrop.2024.120242
• Chiffoleau, Y., Dourian, T., Enderli, G., Mattioni, D., Akermann, G., Loconto, A., Galli, F., Emese, G., Perényi, Z., Colombo, L., Massari, S. & Desclaux, D. (2024). Reversing the trend of agrobiodiversity decline by codeveloping food chains with consumers: A European survey for change. Sustainable Production and Consumption, 46, 343-354. https://doi.org/https://doi.org/10.1016/j.spc.2024.02.032
• Chitwood-Brown, J., Vallad, G. E., Lee, T. G. & Hutton, S. F. (2021). Breeding for resistance to fusarium wilt of tomato: A review. Genes, 12(11), 1673. https://www.mdpi.com/2073-4425/12/11/1673
• D’Agostino, N., Taranto, F., Camposeo, S., Mangini, G., Fanelli, V., Gadaleta, S., Miazzi, M. M., Pavan, S., di Rienzo, V., Sabetta, W., Lombardo, L., Zelasco, S., Perri, E., Lotti, C., Ciani, E. & Montemurro,
• C. (2018). GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars. Scientific Reports, 8(1), 15877. https://doi.org/10.1038/s41598-018-34207-y
• Devlet, A. (2021). Modern agriculture and challenges. Frontiers in Life Sciences and Related Technologies, 2(1), 21-29. https://doi.org/10.51753/flsrt.856349.
• Dianese, E. C., de Fonseca, M. E. N., Goldbach, R., Kormelink, R., Inoue-Nagata, A. K., Resende, R. O. & Boiteux, L. S. (2010). Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions. Molecular Breeding, 25(1), 133-142.
• Dong, P., Han, K., Siddique, M. I., Kwon, J.-K., Zhao, M., Wang, F. & Kang, B.-C. (2016). Gene-based markers for the tomato yellow leaf curl virus resistance gene Ty-3. Plant Breeding and Biotechnology, 4(1), 79-86.
• Doyle, J. J. & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin.
• Eisele, T. G., Constantino, L. V., Giacomin, R. M., Zeffa, D. M., Suzuki, C. H. & Gonçalves, L. S. (2022). Genotyping and phenotyping of grape tomato hybrids aiming at possible genitors for breeding program. Horticultura Brasileira, 40(4), 352-359.
• Emanuelli, F., Lorenzi, S., Grzeskowiak, L., Catalano, V., Stefanini, M., Troggio, M., Myles, S., Martinez-Zapater, J. M., Zyprian, E., Moreira, F. M. & Grando, M. S. (2013). Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biology, 13(1), 39. https://doi.org/10.1186/1471-2229-13-39
• Filiz, E., Uras, M. E., Ozturk, N., Gungor, H. & Ozyigit, I. I. (2024). Genetic diversity and phylogenetic analyses of Turkish sweet corn (Zea mays var. saccharata) varieties using ISSR markers and chloroplast trnL-F IGS region. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 52(2), 13551-13551.
• Fujii, S., Kubo, K.-i. & Takayama, S. (2016). Non-self-and self-recognition models in plant self-incompatibility. Nature Plants, 2(9), 1-9.
• Gill, U., Scott, J. W., Shekasteband, R., Ogundiwin, E., Schuit, C., Francis, D. M., Sim, S.-C., Smith, H. & Hutton, S. F. (2019). Ty-6, a major begomovirus resistance gene on chromosome 10, is effective against Tomato yellow leaf curl virus and Tomato mottle virus. Theoretical and Applied Genetics, 132(5), 1543-1554. https://doi.org/10.1007/s00122-019-03298-0
• Gonias, E. D., Ganopoulos, I., Mellidou, I., Bibi, A. C., Kalivas, A., Mylona, P. V., Osanthanunkul, M., Tsaftaris, A., Madesis, P. & Doulis, A. G. (2019). Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers. Genetic Resources and Crop Evolution, 66(6), 1295-1309. https://doi.org/10.1007/s10722-019-00786-6
• Hagenblad, J., Oliveira, H. R., Forsberg, N. E. G. & Leino, M. W. (2016). Geographical distribution of genetic diversity in Secale landrace and wild accessions. BMC Plant Biology, 16(1), 23. https://doi.org/10.1186 /s12870-016-0710-y
• Hoang, D. T., Vinh, L. S., Flouri, T., Stamatakis, A., von Haeseler, A. & Minh, B. Q. (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evolutionary Biology, 18(1), 11. https://doi.org/10.1186/s12862-018-1131-3
• Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin De La Société Vaudoise Des Sciences Naturelles, 44, 223-270.
• Jago, S., Elliott, K. F. V. A., Tovar, C., Soto Gomez, M., Starnes, T., Abebe, W., Alexander, C., Antonelli, A., Baldaszti, L., Cerullo, G., Cockel, C., Collison, D., Cowell, C., Delgado, R., Demissew, S., Devenish, A., Dhanjal-Adams, K., Diazgranados, M., Drucker, A. G., . . . Borrell, J. S. (2024). Adapting wild biodiversity conservation approaches to conserve agrobiodiversity. Nature Sustainability, 7(11), 1385-1394. https://doi.org/10.1038/s41893-024-01427-2
• Kabas, A., Fidan, H., Kucukaydin, H. & Atan, H. N. (2022). Screening of wild tomato species and interspecific hybrids for resistance/tolerance to Tomato brown rugose fruit virus (ToBRFV). Chilean Journal of Agricultural Research, 82(1), 189-196.
• Kaushal, A., Singh, A. & Jeena, A. S. (2017). Genetic diversity in tomato (Solanum lycopersicum L.) genotypes revealed by simple sequence repeats (SSR) markers. Journal of Applied and Natural Science, 9(2), 966.
• Kessous, I. M., Alves, R. J. V., da Silva, N. G. & Saporetti Junior, A. W. (2024). Plant community on a volcano mountaintop reveals unique high-altitude vegetation in southeastern Brazil. Journal of Mountain Science, 21(9), 3018-3030. https://doi.org/10.1007/s11629-024-8761-2
• Khoury, C. K., Brush, S., Costich, D. E., Curry, H. A., de Haan, S., Engels, J. M. M., Guarino, L., Hoban, S., Mercer, K. L., Miller, A. J., Nabhan, G. P., Perales, H. R., Richards, C., Riggins, C. & Thormann, I. (2022). Crop genetic erosion: understanding and responding to loss of crop diversity. New Phytologist, 233(1), 84-118. https://doi.org/https://doi.org/10.1111/nph.17733
• Kıymacı, G., Arı, B. Ç., Uncu, A. T., Uncu, A. Ö., Issı, N. & Türkmen, Ö. (2023). Determination of resistance levels of selected tomato genotypes to Meloidogyne incognita, Tomato yellow leaf curling virus (TYLCV) Verticillium wilt, Fusarium oxysporum radicis, Fusarium wilt, Tomato spotted wilt virus (TSWV). Selcuk Journal of Agriculture and Food Sciences, 37(1), 86-94.
• Kress, W. J., Erickson, D. L., Jones, F. A., Swenson, N. G., Perez, R., Sanjur, O. & Bermingham, E. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences, 106(44), 18621-18626. https://doi.org/doi:10.1073/pnas.0909820106
• Labate, J. A. & Robertson, L. D. (2012). Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles. BMC Plant Biology, 12(1), 133. https://doi.org/10.1186/1471-2229-12-133 Lange, W. H. & Bronson, L. (1981). Insect pests of tomatoes.
• Li, J., Sun, Q., Yu, N., Zhu, J., Zou, X., Qi, Z., Ghani, M. A. & Chen, L. (2014). The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium. BMC plant biology, 14(1), 296. https://doi.org/10.1186/s12870-014-0296-1
• Li, P., Zhan, X., Que, Q., Qu, W., Liu, M., Ouyang, K., Li, J., Deng, X., Zhang, J., Liao, B., Pian, R. & Chen, X. (2015). Genetic diversity and population structure of toona ciliata roem. based on sequence-related amplified polymorphism (SRAP) markers. Forests, 6(4), 1094-1106. https://www.mdpi.com/1999-4907/6/4/1094
• Li, W., Li, Y., Liang, Y., Ni, L., Huang, H., Wei, Y., Wang, M., Zhang, L. & Zhao, L. (2023). Generating Novel Tomato Germplasm Using the Ancestral Wild Relative of Solanum pimpinellifolium. Horticulturae, 9(1), 34. https://www.mdpi.com/2311-7524/9/1/34
• Losa, A., Sala, T., Toppino, L., Fricano, A., Rossi, G., Gipli, V. & Landoni, M. (2025). Genetic diversity and distinctiveness of common beans (Phaseolus vulgaris L.) between landraces and formal cultivars supporting ex situ conservation policy: The Borlotti case study in northern Italy. Agronomy, 15(4), 786. https://www.mdpi.com/2073-4395/15/4/786
• Lyzenga, W. J., Pozniak, C. J. & Kagale, S. (2021). Advanced domestication: harnessing the precision of gene editing in crop breeding. Plant Biotechnology Journal, 19(4), 660-670.
• Maluf, W. R., Maciel, G. M., Gomes, L. A. A., Cardoso, M. d. G., Gonçalves, L. D., da Silva, E. C. & Knapp, M. (2010). Broad‐spectrum arthropod resistance in hybrids between high‐and low‐acylsugar tomato lines. Crop Science, 50(2), 439-450.
• McGovern, R. J. (2015). Management of tomato diseases caused by Fusarium oxysporum. Crop Protection, 73, 78-92. https://doi.org/https://doi.org/10.1016/j.cropro.2015.02.021
• Moreels, P., Bigot, S., Defalque, C., Correa, F., Martinez, J.-P., Lutts, S. & Quinet, M. (2023). Intra- and inter-specific reproductive barriers in the tomato clade [Review]. Frontiers in Plant Science, Volume 14 - 2023. https://doi.org/10.3389/fpls.2023.1326689
• Mortazavi, P., Ali, A., Tatar, M., Ölmez, F., Altaf, M. T., Nadeem, M. A., Dasgan, H. Y., Ikiz, B., Temtek, T., Bilgin, Ö. F., Mücahitoğlu, A., Bayram, M., Alsaleh, A. & Baloch, F. S. (2025). Molecular screening of diverse Tomato germplasm for root-knot nematode resistance using the Mi23 marker. Physiological and Molecular Plant Pathology, 136, 102607. https://doi.org/https://doi.org/10.1016/j.pmpp.2025.102607
• Mutlu, N., Demirelli, A., Ilbi, H. & Ikten, C. (2015). Development of co-dominant SCAR markers linked to resistant gene against the Fusarium oxysporum f. sp. radicis-lycopersici. Theoretical and Applied Genetics, 128(9), 1791-1798. https://doi.org/10.1007/s00122-015-2547-4
• Nakazato, T., Franklin, R. A., Kirk, B. C. & Housworth, E. A. (2012). Population structure, demographic history, and evolutionary patterns of a green-fruited tomato, Solanum peruvianum (Solanaceae), revealed by spatial genetics analyses. American Journal of Botany, 99(7), 1207-1216. https://doi.org/https://doi.org/10.3732/ajb.1100210
• Ofori, E., Yeboah, S., Nunoo, J., Quartey, E., Torgby-Tetteh, W., Gasu, E. & Ewusie, E. (2014). Preliminary studies of insect diversity and abundance on twelve accessions of tomato, Solanum lycopersicon L. grown in a coastal savannah agro ecological zone. Journal of Agricultural Science, 6(8), 72.
• Okumus, A., & Dagidir, S. (2021). Assessment of genetic diversity on tomato (Lycopersicon esculentum Mill.) landraces using SSR molecular markers in Turkey. Frontiers in Life Sciences and Related Technologies, 2(2), 51-59. https://doi.org/10.51753/flsrt.957055
• Ozyigit, I. I., Dogan, I., Tabanli, F., Mart, D., Yorgancilar, O., Turkeri, M., Atmaca, E. & Yorgancilar, A. (2024). Investigation of resistance using STMS markers against Ascochyta blight in the chickpea varieties. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 52(1), 13502-13502.
• Rai, N., Tiwari, S., Kumar, R., Singh, M. & Bharadwaj, D. (2011). Genetic resources of Solanaceous vegetables in India. National symposium on vegetable biodiversity. Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, MP April, (pp. 4-5).
• Ramírez-Ojeda, G., Peralta, I. E., Rodríguez-Guzmán, E., Sahagún-Castellanos, J., Chávez-Servia, J. L., Medina-Hinostroza, T. C., Rijalba-Vela, J. R., Vásquez-Núñez, L. P. & Rodríguez-Pérez, J. E. (2021). Edaphoclimatic Descriptors of Wild Tomato Species (Solanum Sect. Lycopersicon) and Closely Related Species (Solanum Sect. Juglandifolia and Sect. Lycopersicoides) in South America [Original Research]. Frontiers in Genetics, Volume 12 - 2021. https://doi.org/10.3389/fgene.2021.748979
• Seah, S., Williamson, V. M., Garcia, B. E., Mejia, L., Salus, M. S., Martin, C. T. & Maxwell, D. P. (2007). Evaluation of a co-dominant SCAR marker for detection of the Mi-1 locus for resistance to root-knot nematode in tomato germplasm. Tomato Genetic Cooperative Report, 57, 37-40.
• Shanmugam, S. P., Murugan, M., Shanthi, M., Elaiyabharathi, T., Angappan, K., Karthikeyan, G., Arulkumar, G., Manjari, P., Ravishankar, M., Sotelo-Cardona, P., Oliva, R. & Srinivasan, R. (2024). Evaluation of Integrated pest and disease management combinations against major insect pests and diseases of tomato in Tamil Nadu, India. Horticulturae, 10(7), 766. https://www.mdpi.com/2311-7524/10/7/766
• Shen, Y., Wu, C., Cheng, J., Li, Y., Lin, Z. & Cao, J. (2025). Genetic diversity and population structure of 305 tobacco accessions revealed by simple sequence repeats (SSRs) and newly developed insertion-deletion (Indels) polymorphisms. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-025-02471-3
• Sinesio, F., Cammareri, M., Cottet, V., Fontanet, L., Jost, M., Moneta, E., Palombieri, S., Peparaio, M., Romero del Castillo, R. & Saggia Civitelli, E. (2021). Sensory traits and consumer’s perceived quality of traditional and modern fresh market tomato varieties: A study in three European countries. Foods, 10(11), 2521.
• Singh, V. K., Singh, A. K. & Kumar, A. (2017). Disease management of tomato through PGPB: current trends and future perspective. 3 Biotech, 7(4), 255. https://doi.org/10.1007/s13205-017-0896-1
• Sohrab, S. S., Bhattacharya, P. S., Rana, D., Kamal, M. A. & Pande, M. K. (2015). Development of interspecific Solanum lycopersicum and screening for Tospovirus resistance. Saudi Journal of Biological Sciences, 22(6), 730-738. https://doi.org/10.1016/j.sjbs.2014.11.009
• Sun, Y., Yang, H. & Li, J. (2022). Transcriptome Analysis Reveals the Response Mechanism of Frl-Mediated Resistance to Fusarium oxysporum f. sp. radicis-lycopersici (FORL) Infection in Tomato. International Journal of Molecular Sciences, 23(13), 7078. https://www.mdpi.com/1422-0067/23/13/7078
• Suprun, I. I., Stepanov, I. V., Vahdati, K., Tokmakov, S. V., Balapanov, I. M., Al-Nakib, E. A., Khokhlov, S. Y. & Sokolova, V. V. (2024). Analysis of genetic diversity in three Eastern European walnut germplasm collections. Scientia Horticulturae, 334, 113275. https://doi.org/https://doi.org/10.1016/j.scienta.2024.113275
• Suzuki, R. & Shimodaira, H. (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics, 22(12), 1540-1542.
• Wang, Y., Li, Y.-D., Wang, S., Tihelka, E., Engel, M. S. & Cai, C. (2025). Modeling compositional heterogeneity resolves deep phylogeny of flowering plants. Plant Diversity, 47(1), 13-20. https://doi.org/https://doi.org/10.1016/j.pld.2024.07.007
• Warsadiharja, S. M., Amarillis, S., Heo, J., Park, S., Kang, H.-y., Kim, Y. J., Lee, J., Cha, K. I., Lee, E. S., Jang, J. I., Joh, A. r., Kim, K., Lee, Y. K., Hong, J. C. & Park, S. J. (2025). Genetic mapping of tomato mutants using InDel markers between S. pimpinellifolium and two S. lycopersicum cultivars. Plant Biotechnology Reports. https://doi.org/10.1007/s11816-025-01010-x
• Xie, Q., Liu, B., Wang, X., Wu, H., Du, J. & Liu, Z. (2025). Assessment of genetic diversity and population structure of common walnut (Juglans regia) germplasm with simple sequence repeat (SSR) markers. Genetic Resources and Crop Evolution, 72(2), 2265-2276. https://doi.org/10.1007/s10722-024-02096-y
• Yang, J., Wang, Y., Shen, H. & Yang, W. (2014). In silico identification and experimental validation of insertion–deletion polymorphisms in tomato genome. DNA Research, 21(4), 429-438. https://doi.org/10.1093/dnares/dsu008
• Zatybekov, A., Genievskaya, Y., Fang, C., Abugalieva, S. & Turuspekov, Y. (2025). Uncovering the genetic landscape of soybean accessions from Kazakhstan in comparison with global germplasm using whole genome resequencing. BMC Genomics, 26(1), 802. https://doi.org/10.1186/s12864-025-12024-8
• Zhou, R., Wu, Z., Cao, X. & Jiang, F. (2015). Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers. Genetics and Molecular Research, 14(4), 13868-13879.