Genetic Diversity of Commercial Japanese Pumpkins (Cucurbita maxima) in Thailand using SSR Markers
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Abstract
Genetic diversity is a fundamental component in plant breeding programs. Currently, studies on the genetic diversity of Japanese pumpkin (Cucurbita maxima) in Thailand using SSR (Simple Sequence Repeat) markers remain limited. Accordingly, this study aimed to evaluate the effectiveness of Simple Sequence Repeat (SSR) markers in assessing genetic diversity and population structure alongside fruit morphological characterization of 25 commercial Japanese pumpkin accessions. Cluster analysis was performed using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA). A total of 34 SSR markers generated 93 polymorphic bands out of 95 total bands (97.89%). The average Polymorphic Information Content (PIC) and Expected Heterozygosity (He) were 0.26 and 0.29, respectively. Notably, markers CMTp17, CMTmC43, and CMTm11 exhibited PIC and He values exceeding 0.5, indicating their high effectiveness in genetic differentiation. Genetic similarity coefficients ranged from 0.57 to 1.00, with an average of 0.78. Fruit trait-based clustering classified the accessions into three groups, primarily differentiated by skin color, fruit weight, and fruit shape. Based on SSR marker analysis, the accessions were categorized into three clusters and further resolved into four clades. Population structure analysis identified three genetic clusters, indicating admixture among accessions. Grouping based on SSR markers tended to be associated with fruit shape traits. These findings demonstrate that the commercial Japanese pumpkin accessions studied possess moderate genetic diversity. The informative SSR markers and genetic similarity coefficients identified in this study can be effectively utilized for cultivar classification and for selecting genetically distant parental lines to support the Japanese pumpkin breeding programs.
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King Mongkut's Agricultural Journal
References
Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 7(10), e08093. https://doi.org/10.1016/j.heliyon.2021.e08093.
Arbizu, C. I., Blas, R. H., & Ugás, R. (2022). Genetic Diversity and population structure assessed by SSR in a Peruvian germplasm collection of loche squash (Cucurbita moschata, Cucurbitaceae). Biology and Life Sciences Forum, 15(1), 6. https://doi.org/10.3390/IECD2022-12420.
Bulut, H., Öztürk, H., Donderalp, V., Korkut, R., & Dursun, A. (2022). Investigation of genetic diversity of squash (Cucurbita maxima Duchesne) genotypes collected from Erzincan in Turkey. Taiwania, 67(4), 469-478. https://doi.org/10.6165/tai.2022.67.469.
Chen, R., Shimono, A., Aono, M., Nakajima, N., Ohsawa, R., & Yoshioka, Y. (2020). Genetic diversity and population structure of feral rapeseed (Brassica napus L.) in Japan. PLoS ONE, 15(1), e0227990. https://doi.org/10.1371/journal.pone.0227990.
Chen, R., Takamura, K., Sugiyama, K., Kami, D., Shimomura, K., & Yoshioka, Y. (2021). Genetic diversity assessment of Cucurbita genetic resources in Japan by nuclear and organelle dna markers. The Horticulture Journal, 90(4), 382-392. https://doi.org/10.2503/hortj.UTD-292.
Coşkun, Ö. (2022). Determination of genetic diversity in some pumpkin genotypes using SSR marker technique. Erzincan University Journal of Science and Technology, 15(3), 942-952. https://doi.org/10.18185/erzifbed.1113553.
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x.
Ferriol, M., Picó, M. B., & Nuez, F. (2003). Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers. Genetic Resources and Crop Evolution, 50(3), 227-238.
Ferriol, M., Picó, B., & Nuez, F. (2004). Morphological and molecular diversity of a collection of Cucurbita maxima landraces. Journal of the American Society for Horticultural Science, 129(1), 60-69.
Gong, L., Stift, G., Kofler, R., Pachner, M., & Lelley, T. (2008). Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L. Theoretical and Applied Genetics, 117(1), 37-48. https://doi.org/10.1007/s00122-008-0750-2.
Hwang, S. K., & Kim, Y. M. (2000). A simple and reliable method for preparation of cross-contamination-free plant genomic DNA for PCR-based detection of transgenes. Journal of Biochemistry and Molecular Biology, 33(6), 537-540.
Jahnke, G., Smidla, J., & Poczai, P. (2022). MolMarker: A simple tool for DNA fingerprinting studies and polymorphic information content calculation. Diversity, 14(6), 497. https://doi.org/10.3390/d14060497.
Katengam, S. (2003). DNA markers in plant breeding. Journal of Ubon Ratchathani University, 5(2), 37-59. (in Thai).
Kaźmińska, K., Sobieszek, K., Targońska-Karasek, M., Korzeniewska, A., Niemirowicz-Szczytt, K., & Bartoszewski, G. (2016). Genetic diversity analysis of winter squash (Cucurbita maxima Duchesne) accessions using SSR markers. In Proceedings of Cucurbitaceae 2016: the XIth Eucarpia Meeting on Cucurbit Genetics & Breeding, July 24–28, 2016, pp. 210-213. Sigma.
Kaźmińska, K., Sobieszek, K., Targońska-Karasek, M., Korzeniewska, A., Niemirowicz-Szczytt, K., & Bartoszewski, G. (2017). Genetic diversity assessment of a winter squash and pumpkin (Cucurbita maxima Duchesne) germplasm collection based on genomic Cucurbita-conserved SSR markers. Scientia Horticulturae, 219(1), 37-44. https://doi.org/10.1016/j.scienta.2017.02.035.
Kong, Q., Chen, J., Liu, Y., Ma, Y., Liu, P., Wu, S., Huang, Y., & Bie, Z. (2014). Genetic diversity of Cucurbita rootstock germplasm as assessed using simple sequence repeat markers. Scientia Horticulturae, 175(1), 150-155. https://doi.org/10.1016/j.scienta.2014.06.009.
Kurnianingsih, R., Mastuti, R., Nikmatullah, A., & Arumingtyas, E. (2025). Morphological characterization of the banana indigenous cultivar ‘Haji’(Musa x paradisiaca) for germplasm development in Indonesia. SABRAO Journal of Breeding and Genetics, 57(2), 668-682. http://doi.org/10.54910/sabrao2025.57.2.24.
Lee, C. Y., Wang, J. F., Chang, C. H., & Tung, C. W. (2023). Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits. Plant Genome, 16(4), e20393. https://doi.org/10.1002/tpg2.20393.
Li, Y. L., & Liu, J. X. (2018). StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources, 18(1), 176-177. https://doi.org/10.1111/1755-0998.12719.
Liu, C., Ge, Y., Wang, D. J., Li, X., Yang, X. X., Cui, C. S., & Qu, S. P. (2013). Morphological and molecular diversity in a germplasm collection of seed pumpkin. Scientia Horticulturae, 154(1), 8-16. https://doi.org/10.1016/j.scienta.2013.02.015.
Ngorian, S., Kansup, J., Chanroj, V., Amawan, S., & Wongtiem, P. (2022). Genetic diversity and DNA fingerprint of cassava (Manihot esculenta Crantz.) using SSR markers. Thai Agricultural Research Journal, 40(3), 251-264. (in Thai). https://doi.org/10.14456/thaidoa-agres.2022.21.
Nyabera, L. A., Nzuki, I. W., Runo, S. M., & Amwayi, P. W. (2021). Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers. Molecular Biology Reports, 48(3), 2253-2260.
Paris, H. S. (2016). Genetic Resources of Pumpkins and Squash, Cucurbita spp. Springer.
Pavlícek, A., Hrdá, S., & Flegr, J. (1999). Free-Tree--freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Application in the RAPD analysis of genus Frenkelia. Folia Biologica, 45(3), 97-99.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959. https://doi.org/10.1093/genetics/155.2.945.
Rambaut, A. (2018). FigTree–Tree Figure Drawing Tool Version v.1.4.4. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh. Retrieved from: https://tree.bio.ed.ac.uk/software/figtree/
Reddy, U. K., Natarajan, P., Abburi, V. L., Tomason, Y., Levi, A., & Nimmakayala, P. (2022). What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima. Frontiers in Genetics, 13(1), 1005158. https://doi.org/10.3389/fgene.2022.1005158.
Sara, J., Janphen, K., Samat, J., Jaroenkit, T., Lithanatudom, S., Lanumteang, K., & Pongjaroenkit, S. (2024). Assessment of genetic diversity of guava (Psidium guajava L.) using SSR marker for application in guava breeding program. Khon Kaen Agriculture Journal, 52(1), 52-74. (in Thai).
Theanjumpol, P., Chitworakool, S., & Muenmanee, N. (2021). Quality changes of Japanese pumpkin during harvesting. Postharvest Newsletter, 20(3), 1-6. (in Thai).
Zhao, D., Wen, L., Bi, H., Zhu, Z., Liu, J., Zhang, J., Shi, Q., You, H., Dong, D., & Liu, Q. (2017). Genetic diversity of Cucurbita maxima assessed using morphological characteristics and random-amplified polymorphic DNA markers in China. Acta Agriculturae Scandinavica, Section B - Soil & Plant Science, 67(2), 155-163. https://doi.org/10.1080/09064710.2016.1236981.
