Genetic diversity analysis of Indonesian soybean genotypes based on morphological characteristics and SSR markers

Tasma, I Made; Dyah, Rosliana Purwaning; Wibisono, Kunto; Rijzaani, Habib; Suhendar, Muhammad Ace

doi:10.15517/6xn1r608

Autores/as

I Made Tasma National Research and Innovation Agency (NRIA), Research Center for Food Crops. Bogor, Indonesia. Autor/a https://orcid.org/0000-0002-2366-3558
Rosliana Purwaning Dyah National Research and Innovation Agency (NRIA), Research Center for Food Crops. Bogor, Indonesia. Autor/a https://orcid.org/0009-0003-6725-7513
Kunto Wibisono National Research and Innovation Agency (NRIA), Directorate of Scientific Collection Management. Bogor, Indonesia. Autor/a https://orcid.org/0000-0002-7140-5537
Habib Rijzaani National Research and Innovation Agency (NRIA), Research Center for Food Crops. Bogor, Indonesia. Autor/a https://orcid.org/0000-0001-5981-1869
Muhamad Ace Suhendar National Research and Innovation Agency (NRIA), Research Center for Food Crops. Bogor, Indonesia. Autor/a https://orcid.org/0009-0001-0499-8600

DOI:

https://doi.org/10.15517/6xn1r608

Palabras clave:

antecedentes genéticos, distancia genética, marcadores genéticos, caracteres morfológicos

Resumen

Introducción. La soya es un cultivo importante debido a su alto contenido de proteína y aceite. Las variedades de semilla amarilla son preferidas para la elaboración de productos alimenticios. El análisis de la diversidad genética es un paso crucial para la selección de líneas parentales en programas de mejoramiento genético. Objetivo. Analizar la diversidad genética de genotipos de soya de Indonesia mediante características morfológicas y marcadores de repeticiones de secuencias simples (SSR). Materiales y métodos. La evaluación en campo se realizó en Bogor, Indonesia, de marzo a junio de 2023. Los datos morfológicos se analizaron mediante análisis de componentes principales (PCA) y análisis de coordenadas principales (PCoA). Posteriormente, los genotipos se analizaron utilizando 14 marcadores SSR. Resultados. El PCA reveló que PC1-PC4 explicaron el 72,63 % de la variación genética total. El análisis de marcadores SSR mostró características sobresalientes, como un alto número de alelos y valores elevados de PIC. Los genotipos se agruparon en dos clústeres con una clara distinción de genética. Cuatro pares de genotipos presentaron alta diversidad genética y rasgos morfológicos favorables relacionados con el rendimiento y sus componentes. Estos pares de genotipos representan posibles candidatos parentales para programas de mejoramiento genético de soya. Conclusiones. Las caracterizaciones morfológicas y mediante marcadores SSR diferenciaron claramente los genotipos de soya de Indonesia y permitieron identificar pares de genotipos con alta diversidad genética, adecuados como candidatos parentales para fines de mejoramiento. Ambos tipos de análisis de datos proporcionaron información complementaria, lo que permitió una evaluación más integral de la diversidad genética.

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Referencias

Abadi, F. R., Masithoh, R. E., Sutiarso, L., & Rahayoe, S. (2022). Effect of size reduction on yellow soybean seed characterization based on colorimetry. IOP Conference Series: Earth and Environmental Science, 1116(1), Article 012063. https://doi.org/10.1088/1755-1315/1116/1/012063

Asadi, Dewi, N., Nugroho, K., Terryana, R. T., Mastur, & Lestari, P. (2020). Evaluation of SSR and important agronomical characters of promising mutant lines of soybean. Biodiversitas, 21(1), 299–310. https://doi.org/10.13057/biodiv/d210137

Babu, B. K., Sood, S., Kumar, D., Joshi, A., Pattanayak, A., Kant, L., & Upadhyaya, H. D. (2018). Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.). 3 Biotech, 8(2), 95–114. https://doi.org/10.1007/s13205-018-1118-1

Cregan, P. B., Jarvik, T., Bush, A. L., Shoemaker, R. C., Lark, K. G., Kahler, A. L., Kaya, N., VanToai, T. T., Lohnes, D. G., Chung, J., & Specht, J. E. (1999). An integrated genetic linkage map of the soybean genome. Crop Science, 39(5), 1464–1490. https://doi.org/10.2135/cropsci1999.3951464x

Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15.

Dyah, R. P., Wibisono, K., Terryana, R. T., Nugroho, K., Utari, R., Suparjo, S., Umar, Lestari, P., & Tasma, I. M. (2024). Diversity analysis of 53 soybean accessions introduced from China based on morphological characteristics and SSR markers. Current Applied Science and Technology, 24(3), Article e0259116. https://doi.org/10.55003/cast.2024.259116

Fattah, A., Idaryani, Herniwati, Yasin, M., Suriani, S., Salim, Nappu, M. B., Mulia, S., Hannan, M. F. I., Wulanningtyas, H. S., Saenong, S., Dewayani, W., Suriany, Winanda, E., Manwan, S. W., Asaad, M., Warda, Nurjanani, Nurhafsah, … Ella, A. (2024). Performance and morphology of several soybean varieties and responses to pests and diseases in South Sulawesi. Heliyon, 10(5), Article e25507. https://doi.org/10.1016/j.heliyon.2024.e25507

Gebregziabher, B. S., Zhang, S. R., Azam, M., Qi, J., Agyenim-Boateng, K. G., Feng, Y., Liu, Y., Li, J., Li, B., & Sun, J. (2023). Natural variations and geographical distributions of seed carotenoids and chlorophylls in 1 167 Chinese soybean accessions. Journal of Integrative Agriculture, 22(9), 2632–2647. https://doi.org/10.1016/j.jia.2022.10.011

Greenacre, M., Groenen, P. J. F., Hastie, T., Iodice d’Enza, A., Markos, A., & Tuzhilina, E. (2022). Principal component analysis. Nature Reviews Methods Primers, 2(1), Article 100. https://doi.org/10.1038/s43586-022-00184-w

Guler, B. A., & Imamoglu, E. (2023). Molecular marker technologies in food plant genetic diversity studies: an overview. Foods and Raw Materials, 11(2), 282–292. https://doi.org/10.21603/2308-4057-2023-2-575

Kumar, S., & Pandey, G. (2020). Biofortification of pulses and legumes to enhance nutrition. Heliyon, 6(3), Article e03682. https://doi.org/10.1016/j.heliyon.2020.e03682

Kumawat, G., Singh, G., Gireesh, C., Shivakumar, M., Arya, M., Agarwal, D. K., & Husain, S. M. (2015). Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India. Physiology and Molecular Biology of Plants, 21, 101–107. https://doi.org/10.1007/s12298-014-0266-y

Lazer, I. J., & Horvath-Lazar, E. (2010). GelAnalyzer 2010a [Software]. GelAnalyzer. http://www.gelanalyzer.com/index.html

Li, Y., & Qi, B. (2022). Phytochemicals in soybeans: bioactivity and health benefits. CRC Press. https://doi.org/10.1201/9781003030294

Liu, K., & Muse, S. V. (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics, 21(9), 2128–2129. https://doi.org/10.1093/bioinformatics/bti282

Malek, M. A., Rafii, M. Y., Afroz, S. S. M., Nath, U. K., & Mondal, M. M. A. (2014). Morphological characterization and assessment of genetic variability, character association, and divergence in soybean mutants. The Scientific World Journal, 2014(1), Article 968796. https://doi.org/10.1155/2014/968796

Meena, V. K., Shekhawat, H. V. S., Chand, S., Choudhary, K., Sharma, J. K., & Lekha, L. (2023). Advances in molecular marker technology and their significance in plant improvement strategies. In M. A. El-Esawi (Ed.), Recent trends in plant breeding and genetic improvement (pp. 1–29). IntechOpen. https://doi.org/10.5772/intechopen.1002773

Nugroho, K., Kosmiatin, M., Husni, A., Tasma, I. M., & Lestari, P. (2020). Identification of soybean (Glycine max [L.] Merr.) mutants and improved varieties having diverse drought tolerance character using SSR marker. IOP Conference Series: Earth and Environmental Science, 482, Article 012014. https://doi.org/10.1088/1755-1315/482/1/012014

Nugroho, K., Terryana, R. T., Manzila, I., Priyatno, T. P., & Lestari, P. (2019). The use of molecular markers to analyze the genetic diversity of Indonesian pepper (Capsicum spp.) varieties based on anthracnose resistance. Makara Journal of Science, 23(3), 137–147. https://doi.org/10.7454/mss.v23i3.11261

Nurdianawati, S., Wicaksana, N., & Anas, A. (2016). Analisis kesesuaian marka SSR (simple sequence repeats) untuk identifikasi keragaman genetik pada kacang bambara asal Jawa Barat. Agrikultura, 27(2), 120–123.

Pasaribu, A., Putri, L. A. P., & Suryanto. (2017). First analysis of molecular varians in palm oil (Elaeis guineensis Jacq.) used five primer of SSR (simple sequence repeats). Jurnal Online Pertanian Tropik, 4(1), 47–56.

Rani, R., Raza, G., Tung, M. H., Rizwan, M., Ashfaq, H., Shimelis, H., Razzaq, M. K., & Arif, M. (2023). Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers. PLoS One, 18(5), Article e0286099. https://doi.org/10.1371/journal.pone.0286099

Rohlf, F. J. (2000). NTSYS-pc: numerical taxonomy and multivariate analysis system (Version 2.2). Applied Biostatistics Inc.

Shrestha, P., Pandey, M. P., Dhakal, K. H., Ghimire, S. K., Thapa, S. B., & Kandel, B. P. (2023). Morphological characterization and evaluation of soybean genotypes under rainfed ecosystem of Nepal. Journal of Agriculture and Food Research, 11, Article 100526. https://doi.org/10.1016/j.jafr.2023.100526

Singh, P. K., Shrestha, J., & Kushwaha, U. K. S. (2020). Multivariate analysis of soybean genotypes. Journal of Agriculture and Natural Resources, 3(1), 69–76. https://doi.org/10.3126/janr.v3i1.27092

Tasma, I. M., Dyah, R. P., Terryana, R. T., Satyawan, D., Nugroho, K., & Asadi, A. (2024). DNA fingerprinting analysis of edamame advanced lines based on SSR markers. AIP Conference Proceedings, 2957(1), Article 080005. https://doi.org/10.1063/5.0184004

Tasma, I. M., Lorenzen, L. L., Green, D. E., & Shoemaker, R. C. (2001). Mapping genetic loci for flowering time, maturity, and photoperiod insensitivity in soybean. Molecular Breeding, 8, 25–35. https://doi.org/10.1023/A:1011998116037

Tasma, I. M., & Shoemaker, R. C. (2003). Mapping flowering time gene homologs in soybean and their association with maturity (E) loci. Crop Science, 43(1), 319–328. https://doi.org/10.2135/cropsci2003.3190

Tasma, I. M., Yani, N. M. G., Purwaningdyah, R., Satyawan, D., Nugroho, K., Lestari, P., Trijatmiko, K. R., & Mastur, M. (2018). Genetic diversity analysis and F2 population development for breeding of long juvenile trait in soybean. Jurnal AgroBiogen, 14(1), 11–22.

Terryana, R. T., Nugroho, K., Rijzaani, H., & Lestari, P. (2018). Karakterisasi keragaman genetik 27 genotipe cabai berdasarkan marka SSR (simple sequence repeats). Berita Biologi, 17(2), 183–194.

Union for the Protection of New Varieties of Plants. (1998). Guidelines for the conduct of tests for distinctness, homogeneity and stability (soybean).

United States Department of Agriculture. (2006). Mapped soybean SSR loci. https://sgil.ba.ars.usda.gov/cregan/soymap3.mht

Upadhyay, P., Shrivastava, M. K., Amrate, P. K., Sharma, S., Thakur, S., & Anand, K. J. (2022). Assessing genetic diversity of exotic lines of soybean based on D2 and principal component analysis. The Pharma Innovation Journal, 11(5), 89–93.

Wibisono, K., Dyah, R. P., Utari, R., Rijzaani, H., Hakim, L., Suhendar, A., Purwanto, O. D., Satyawan, D., Lestari, P., & Tasma, I. M. (2025). Genetic diversity and DNA barcoding construction of tropical soybean advanced lines based on SSR markers. Indonesian Journal of Agricultural Sciences, 30(2), 293−304. https://doi.org/10.18343/jipi.30.2.293

Zatybekov, A., Yermagambetova, M., Genievskaya, Y., Didorenko, S., & Abugalieva, S. (2023). Genetic diversity analysis of soybean collection using simple sequence repeat markers. Plants, 12(19), Article 3445. https://doi.org/10.3390/plants12193445