Phenotypic Evaluation and Genetic Profiling of Shallot Genotypes Adapted to Peatland of South Kalimantan Using Simple Sequence Repeat (SSR) Markers

Reflinur Reflinur, Tri Handayani, Iteu M. Hidayat, Ineu Sulastrini, Salamiah Salamiah, Lelya Pramudyani, Nurmalita Waluyo


The escalating demand of shallot has forced the increase of domestic production, including through extension of harvest area by utilization of arable land on peatland. This study was aimed to analyze genetic profile of shallot adapted in peatland areas using SSR markers. Twenty-one shallot genotypes were tested in the field and eighteen primers dispersed throughout the genome was applied to analyze genetic diversity of the peatland-adapted shallots. Phenotypic evaluation revealed that shallot yield potential ranged from 6.66 to 14.21 t/ha. Of these, seven shallot clones (11 NA, 1111 TA, 12 NA, 12 NC, 20 NA and 22 N) had good yield potential and comparable with those of five released shallot varieties. Nine out of 12 shallot clones were moderately resistant to Alternaria porii. Clustering analysis showed that shallot genotypes were clustered into two main groups, Clustered I and II which consisted of 13 and 8 genotypes, respectively. The closest genetic relatedness was observed between 8NC and 8NA (0.85), while the farthest ones was between 11NA and Kramat2 (0.51). This result implies that cross combination between 11NA and Kramat2 is valuable and suitable for breeding programs aimed at improving shallot potential yield in the future.


Allium cepa group Aggregatum; peatland; shallot; Simple Sequence Repeat (SSR)

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Araki, N., Masuzaki, S. I., Tsukazaki, H., Yaguchi, S., Wako, T., Tashiro, Y., … Shigyo, M. (2010). Development of microsatellite markers in cultivated and wild species of sections Cepa and Phyllodolon in Allium. Euphytica, 173(3), 321–328. crossref

Arifin, N. S., Ozaki, Y., & Okubo, H. (2000). Genetic diversity in Indonesian shallot (Allium cepa var. ascalonicum) and Allium x wakegi revealed by RAPD markers and origin of A. x wakegi identified by RFLP analyses of amplified chloroplast genes. Euphytica, 111(1), 23–31. crossref

Bachmann, K., Blattner, F., Fischer, D., Friesen, N., Fritsch, R., Klaas, M., … Pollner, S. (2001). Molecular markers in Allium: Range of application, reliability and taxonomic implications. Acta Horticulturae, 546, 159–163. crossref

Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314–331. Retrieved from website

Bredemeijer, G. M. M., Cooke, R. J., Ganal, M. W., Peeters, R., Isaac, P., Noordijk, Y., … Vosman, B. (2002). Construction and testing of a microsatellite database containing more than 500 tomato varieties. Theoretical and Applied Genetics, 105(6–7), 1019–1026. crossref

Cunha, C. P., Hoogerheide, E. S. S., Zucchi, M. I., Monteiro, M., & Pinheiro, J. B. (2012). New microsatellite markers for garlic, Allium sativum (Alliaceae). American Journal of Botany, 99(1), e17–e19. crossref

Doyle, J. J., & Doyle, J. L. (1990). A rapid total DNA preparation procedure for fresh plant tissue. Focus, 12, 13–15.

Directorate General of Horticulture. 2017. Horticultural Programs and Activities 2018. MUSRENBANGTAN. Jakarta. website (accessed on 21 June 2017.

Govindaraj, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015(431487), 1–14. crossref

Gramazio, P., Plesa, I. M., Truta, A. M., Sestras, A. F., Vilanova, S., Plazas, M., … Sestras, R. E. (2018). Highly informative SSR genotyping reveals large genetic diversity and limited differentiation in European larch (Larix decidua) populations from Romania. Turkish Journal of Agriculture and Forestry, 42, 165–175. Retrieved from pdf

Irianto, I., Yakup, Y., Harun, M. U., & Susilawati, S. (2017). Growth and yield characteristics of three shallot varieties affected by phosphate fertilizer dosages on ultisol. Russian Journal of Agricultural and Socio-Economic Sciences, 65(5).

Khar, A., Lawande, K. E., & Negi, K. S. (2011). Microsatellite marker based analysis of genetic diversity in short day tropical Indian onion and cross amplification in related Allium spp. Genetic Resources and Crop Evolution, 58(5), 741–752. crossref

Kim, H.-J., Lee, H.-R., Hyun, J. Y., Song, K. H., Kim, K.-H., Kim, J. E., … Harn, C. H. (2012). Marker development for onion genetic purity testing using SSR Finder. Korean Journal of Breeding Science, 44(4), 421. Retrieved from website

Liu, J., & Muse, S. V. (2005). PowerMarker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21(9), 2128–2129. crossref

Lombardi, M., Materne, M., Cogan, N. O. I., Rodda, M., Daetwyler, H. D., Slater, A. T., … Kaur, S. (2014). Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers. BMC Genetics, 15, 150. crossref

McCallum, J., Thomson, S., Pither-Joyce, M., Kenel, F., Clarke, A., & Havey, M. J. (2008). Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag–simple sequence repeat markers. Journal of the American Society for Horticultural Science, 133(6), 810-818.

Mason, A. S. (2015). SSR genotyping. In Methods in molecular biology (Methods and protocols) (pp. 77–89). New York: Humana Press. crossref

Masuzaki, S., Araki, N., Yamauchi, N., Yamane, N., Wako, T., Kojima, A., & Shigyo, M. (2006). Chromosomal locations of microsatellites in onion. HortScience, 41(2), 315–318. Retrieved from website

Nanda, S., Chand, S. K., Mandal, P., Tripathy, P., & Joshi, R. K. (2016). Identification of novel source of resistance and differential response of Allium genotypes to purple blotch pathogen, Alternaria porri (Ellis) Ciferri. Plant Pathology Journal, 32(6), 519–527. crossref

Nei, M., & Li, W. H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America, 76(10), 5269–5273. Retrieved from pdf

Noor, M. (2012). Lahan gambut: Pengembangan, konservasi, dan perubahan Iklim (2nd ed.). Yogyakarta, ID: Gadjah Mada University Press.

Phumichai, C., Phumichai, T., & Wongkaew, A. (2015). Novel chloroplast microsatellite (cpSSR) markers for genetic diversity assessment of cultivated and wild Hevea rubber. Plant Molecular Biology Reporter, 33(5), 1486–1498. crossref

Purbiati, T., Umar, A., & Supriyanto, A. (2010). Pengkajian adaptasi varietas-varietas bawang merah pada lahan gambut di Kalimantan Barat. In I. M. S. Utama, A. D. Susila, R. Purwanto, N. S. Antara, N. K. Putra, & K. B. Sussrusa (Eds.), Prosiding Seminar Hortikultura Indonesia (pp. 1–8). Retrieved from pdf

Rahayu, R., Mujiyo, M., & Arini, R. U. (2018). Land suitability evaluation of shallot (Allium ascalonicum L.) at production centres in Losari District, Brebes. Journal of Degraded and Mining Lands Management, 6(1), 1505-1511.

Rohlf, F. J. (2002). Geometric morphometrics and phylogeny. In N. MacLeod & P. L. Forey (Eds.), Morphology, Shape and Phylogeny (pp. 175–193). Boca Raton: CRC Press. crossref

Sharma, S. R. (1986). Effect of fungicidal sprays on purple blotch and bulb yield of onion. Indian Phytopathology, 39, 78-82.

Singh, S. R., Ahmed, N., Lal, S., Ganie, S. A., Amin, M., Jan, N., & Amin, A. (2013). Determination of genetic diversity in onion (Allium cepa L.) by multivariate analysis under long day conditions. African Journal of Agricultural Research, 8(45), 5599–5606. Retrieved from website

Singh, S. K., Singh, R. S., Maurya, D. M., & Verma, O. P. (1987). Genetic divergence among lowland rice cultivars. The Indian Journal of Genetics and Plant Breeding, 47(1), 11-14. Retrieved from website

Song, Y. S., Suwabe, K., Wako, T., Ohara, T., Nunome, T., & Kojima, A. (2004). Development of microsatellite markers in bunching onion (Allium fistulosum L.). Breeding Science, 54(4), 361–365. crossref

Subagyo, H. (2002). Penyebaran dan potensi tanah gambut di Indonesia untuk pengembangan pertanian. In CCFPI (Climate change, forests and peatlands in Indonesia): Sebaran gambut di Indonesia (pp. 197-227). Seri Prosiding 02. Bogor, ID: Wetlands International Indonesia; Programme dan Wildlife Habitat Canada.

Tsukazaki, H., Fukuoka, H., Song, Y.-S., Yamashita, K., Wako, T., & Kojima, A. (2006). Considerable heterogeneity in commercial F1 varieties of bunching onion (Allium fistulosum) and proposal of breeding scheme for conferring variety traceability using SSR Markers. Breeding Science, 56, 321–326. crossref

Tsukazaki, H., Honjo, M., Yamashita, K., Ohara, T., Kojima, A., Ohsawa, R., & Wako, T. (2010). Classification and identification of bunching onion (Allium fistulosum) varieties based on SSR markers. Breeding Science, 60(2), 139–152. crossref

Tsukazaki, H., Yamashita, K. I., Yaguchi, S., Masuzaki, S., Fukuoka, H., Yonemaru, J., … Wako, T. (2008). Construction of SSR-based chromosome map in bunching onion (Allium fistulosum). Theoretical and Applied Genetics, 117, 1213. crossref

Usatov, A. V., Klimenko, A. I., Azarin, K. V., Gorbachenko, O. F., Markin, N. V., Tikhobaeva, V. E., … Getmantseva, L. (2014). The relationship between heterosis and genetic distances based on SSR markers in Helianthus annuus. American Journal of Agricultural and Biological Sciences, 9(3), 270–276. crossref

Vajire, D., Thakare, K., Solunke, R., Panche, A., & Tiwari, A. (2017). The possibilities of the prediction of heterosis in elite lines of onion based on the assessment of genetic diversity. EC Microbiology, 10(5), 211–219. Retrieved from pdf

Weir, B. S. (1996). Genetic data analysis II: Methods for discrete population genetic data. Sunderland MA: Sinauer Associates. crossref

Weising, K., Atkinson, R. G., & Gardner, R. C. (1995). Genomic fingerprinting by microsatellite-primed PCR: A critical evaluation. PCR Methods and Applications, 4, 249–255. crossref

Widaningsih, N. A., Purwanto, E., Nandariyah, & Reflinur. (2014). The use of DNA microsatellite markers for genetic diversity identification of soybean (Glycine max (L.) Meriil.) as a supplementary method in reference collections management. Indonesian Journal of Biotechnology, 19(2), 136–145. crossref


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