Microsatellite polymorphism for molecular characterization of pomelo (Citrus maxima) accessions from Indonesia
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Abstract. Susandarini R, Subandiyah S, Daryono BS, Rugayah. 2020. Microsatellite polymorphism for molecular characterization of pomelo (Citrus maxima) accessions from Indonesia. Biodiversitas 21: 2390-2395. Citrus maxima (Burm.) Merr. (pomelo) as a minor fruit crop deserve attention on its phenotypic and genotypic variability to avoid the risk of extinction. Previous study showed that pomelo from Indonesia has high morphological variability, and thus it is interesting to explore its genotypic variability using molecular markers. Microsatellite is a molecular marker widely used in Citrus taxonomy studies. This study aimed at revealing microsatellite polymorphism and its potential application in cultivar characterization of C .maxima. Eighty accessions of C. maxima consisting of registered cultivars and landraces from Indonesia were used in this study. Analysis of microsatellite sequences from genomic DNA amplified using DY296883 primer showed that C. maxima microsatellite has high polymorphism in the form of repeat length variation of (GA)n, ranging from (GA)7 to (GA)19. This study proved the existence of high genotypic variability in C. maxima, and confirmed the role of microsatellite as a useful molecular marker for uncovering variability at intraspecific level. Observation of the microsatellite polymorphisms indicated that variability of (GA)n can be used to distinguish some pomelo cultivars.
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References
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Victoria FC, da Maia LC, de Oliveira AC. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11:15. https://doi.org/10.1186/1471-2229-11-15
Zhao Y, Williams R, Prakash CS, He G. 2013. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biol. 12: 237. https://doi.org/10.1186/1471-2229-12-237
Arora RK. 2000. In Situ Conservation of Biological Diversities in Citrus. GCGN Meeting, 7-8 December 2000.
Barkley NA, Roose ML, Krueger RR, Federici CT. 2006. Assessing genetic diversity and population structure in citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor. Appl. Genet. 112: 1519-1531. DOI 10.1007/s00122-006-0255-9
Cordeiro GM, Pan YB, Henry RJ. 2003. Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci. 165: 181-189. DOI 10.1016/S0168-9452(03)00157-2
Cristofani-Yaly M, Novelli VM, Bastianel M, Machado MA. 2011. Transferability and level of heterozygosity of microsatellite markers in Citrus species. Plant. Mol. Biol. Rep. 19: 418-423. DOI 10.1007/s11105-010-0241-x
Ellegren H. 2004. Microsatellites: simple sequences with complex evolution. Nature Reviews – Genetics 5: 435-445. DOI 10.1038/nrg1348
Golein B, Koltunow AM, Talaie A, Zamani Z, Ebadi, A. 2005. Isolation and characterization of microsatellites loci in the lemon (Citrus limon). Mol. Ecol. Notes 5: 253–255. https://doi.org/10.1111/j.1471-8286.2005.00896.x
Ijaz S. 2011. Microsatellite markers: An important fingerprinting tool for characterization of crop plants. Afr. J. Biotechnol. 10 (40): 7723-7726. DOI 10.5897/AJBx10.021
Kumar P, Gupta VK, Misra AK, Modi DR, Pandey BK. 2009. Potential of Molecular Markers in Plant Biotechnology. Plant Omics Journal 2 (4):141-162.
Lee EJ, Jin GN, Lee KL, Han MS, Lee YH, Yang MS. 2011. Exploiting expressed sequence tag databases for the development and characterization of gene-derived simple sequence repeat markers in the opium poppy (Papaver somniferum L.) for forensic applications. J. Forensic Sci. 56 (5): 1131-1135. DOI 10.1111/j.1556-4029.2011.01810.x
Li C, Zhou A, Sang T. 2006. Rice domestication by reducing shattering. Science 311:1936-1939. DOI 10.1126/science.1123604
Luro FL, Constantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitraut P, Morillon R. 2008. Transferability of the EST-SSRs developed on Nules Clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287. DOI 10.1186/1471-2164-9-287
Mondini L, Noorani A, Pagnotta MA. 2009. Assessing plant genetic diversity by molecular tools. Diversity 1: 19-35. DOI 10.3390/d1010019
Niyomdham C. 1992. Citrus maxima (Burm.) Merr. In: Coronel, R.E. & Verheij, E.W.M. (Eds.): Plant Resources of South-East Asia. No.2: Edible Fruits and Nuts. Prosea Foundation, Bogor, Indonesia. pp. 128-131.
Novelli VM, Cristofani-Yaly M, Soza AA, Machado MA. 2006. Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis (L.) Osbeck). Genet. Mol. Biol. 29 (1): 90-96. https://doi.org/10.1590/S1415-47572006000100018
Palmieri DA, Novelli VM, Bastianel M, Cristofani-Yaly M, Astúa-Monge G, Carlos EF, de Oliveira AC, Machado, MA. 2007. Frequency and distribution of microsatellites from ESTs of citrus. Genet. Mol. Biol. 30 (3): 100 9-1018. https://doi.org/10.1590/S1415-47572007000500029
Park YJ, Lee JK, Kim NS. 2009. Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14: 4546-4569. DOI 10.3390/molecules14114546
Pickersgill B. 2009. Domestication of plants revisited – Darwin to the present day. Bot. J. Linn. Soc. 161: 203–212. https://doi.org/10.1111/j.1095-8339.2009.01007.x
Powell W, Machray GC, Provan J. 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1 (7): 215-222. https://doi.org/10.1016/1360-1385(96)86898-1
Qing-Qin C, Hai-Jun M, Xiao-Peng W, Hua-Lin Y, Xiu-Xin D. 2007. Genetic diversity of male sterile and low fertility germplasm of Citrus revealed using SSR markers. Chin. J. Agric. Biotechnol. 4 (2): 99-104. https://doi.org/10.1017/S1479236207001453
Ruiz C, Breto MP, Asins MJ. 2000. A quick methodology to identify sexual seedlings in citrus breeding programs using SSR markers. Euphytica 112: 89-94. https://doi.org/10.1023/A:1003992719598
Sonah H, Deshmukh RK, Singh VP, Gupta DK, Singh NK, Sharma TR. 2011. Genomic resources in horticultural crops: status, utility and challenges. Biotechnol. Adv. 29: 199-209. https://doi.org/10.1016/j.biotechadv.2010.11.002
Sthapit BR, Rao VR, Sthapit S. 2012. Tropical Fruit Tree Species and Climate Change. Bioversity International, New Delhi, India.
Susandarini R, Subandiyah S, Rugayah, Daryono BS, Nugroho LH. 2013. Assessment of Taxonomic Affinity of Indonesian Pummelo (Citrus maxima (Burm.) Merr.) Based on Morphological Characters. Am. J. Agric. Biol. Sci.8 (3): 182-190. DOI 10.3844/ajabssp.2013.182.190
Victoria FC, da Maia LC, de Oliveira AC. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11:15. https://doi.org/10.1186/1471-2229-11-15
Zhao Y, Williams R, Prakash CS, He G. 2013. Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biol. 12: 237. https://doi.org/10.1186/1471-2229-12-237
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