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Simple Sequence Repeat (SSR) profilingof cultivated Limau Madu (Citrus reticulata Blanco)in Malaysia

Published online by Cambridge University Press:  20 January 2012

Goh Pik Seah Elcy ,
Mansor Clyde Mahani ,
Yong-Jin Park  and
Normah Mohd Noor
Goh Pik Seah Elcy
Affiliation:
Sch. Biosci. Biotechnol., Fac. Sci. Technol., Univ. Kebangsaan Malaysia, 43600UKM Bangi, Selangor, Malaysia
Mansor Clyde Mahani
Affiliation:
Sch. Environ. Nat. Resour. Sci., Fac. Sci., Technol., Univ. Kebangsaan Malaysia, 43600UKM Bangi, Selangor, Malaysia
Yong-Jin Park
Affiliation:
Dep. Plant Resour., Coll. Ind. Sci., Kongju Ntl. Univ. Yesan, 340-702, Repub.Korea
Normah Mohd Noor*
Affiliation:
Sch. Biosci. Biotechnol., Fac. Sci. Technol., Univ. Kebangsaan Malaysia, 43600UKM Bangi, Selangor, Malaysia Inst. Syst. Biol. (INBIOSIS), Univ. Kebangsaan Malaysia, 43600UKM Bangi, Selangor, Malaysia. [email protected]
*
*Correspondence and reprints
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Abstract

Introduction. In Malaysia, Limau Madu (Citrusreticulata Blanco; Citrus suhuiensis Hort.ex Tanaka) is commercially cultivated for local consumption. Itis a loose-peel mandarin with fruits that are spherical in shapewith shiny green or greenish yellow peel. In Malaysia, Limau Maduis vegetatively propagated, thus it is presumed to exhibit minimalvariability. In our study, the genetic variability and genetic relatednessamong cultivated samples collected from different states in Malaysiawere assessed using Simple Sequence Repeat (SSR) primers. Materialsand methods. Thirty pairs of SSR primers derived from Citrusunshiu were screened and 22 SSR primer pairs were utilizedto assess genetic variability and relatedness among 118 cultivatedsamples. Results and discussion. The percentage of SSR transferabilityfrom C. unshiu to C. reticulata (LimauMadu) was 73.33%, which indicated that the primer sequences flankingsimple sequence repeats were conserved among these Citrus species.Most SSR loci revealed a large excess of heterozygotes. In our study,low allelic diversity was shown, with an average of 5.227 allelesper locus. Polymorphic information content (PIC) ranged from 0.048to 0.674. Based on UPGMA clustering analysis, four groups were identifiedfrom these citrus genotypes with a mean genetic distance of 0.170. Lowgenetic variability within species was probably due to vegetativepropagation or inability to detect differences among samples usingthese primers.

Keywords

MalaysiaCitrus reticulatagenetic resourcesgenetic variationgenetic markersmicrosatellitesMalaisieCitrus reticulataressource génétiquevariation génétiquemarqueur génétiquemicrosatelliteMalasiaCitrus reticulatarecursos genéticosvariación genéticamarcadores genéticosmicrosatélites
Type
Original article
Information
Fruits , Volume 67 , Issue 2 , March 2012 , pp. 67 - 76
Copyright
© 2012 Cirad/EDP Sciences

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References

Swingle W.T., Reece P.C., The botany of citrus and its wild relatives, in: Reuther W., Webber H.J., Batchelor L.D. (Eds.), The citrus industry, vol. 1, Univ. Calif. Press, Riverside, Calif., U.S.A., 1967.
Mabberley D.J., Mabberley’s plant-book: A portable dictionary of plants, 3rd ed., Camb. Univ. Press, Avon, U.K., 2008.
Roose M.L., Close T.J., Genomics of citrus, a major fruit crop of tropical and subtropical regions, in: Moore P.H., Ming R., (Eds.), Genomic of tropical crops plant, vol. 1, Springer Sci. + Bus. Media, N. Y., U.S.A., 2008.
Shokrollah, H., Abdullah, T.L., Sijam, K., Abdullah, S.N.A., Abdullah, N.A.P., Differential reaction of Citrus species in Malaysia to Huanglongbing (HLB) disease using grafting method, Am. J. Agri. Biol. Sci. 4 (2009) 32–38.CrossRefGoogle Scholar
Allen B.M., Malayan fruits: an introduction to the cultivated species, Donald Moore Press Ltd., Singap., 1967.
Makeen, M.A., Normah, M.N., Dussert, S., Clyde, M.M., The influence of desiccation and rehydration on the survival of polyembryonic seed of Citrus suhuiensis cv. Limau Madu, Sci. Hortic. 112 (2007) 376–381.CrossRefGoogle Scholar
Singh R., Rajam M.V., Citrus biotechnology achievements, limitations and future directions, Physiol. Mol. Biol. Plants (2009) 3–22.
Herrero, R., Asins, M.J., Carbonell, E.A., Navarro, L., Genetic diversity in the orange subfamily Aurantioideae. I. intraspecies and intragenus genetic variability, Theor. Appl. Genet. 92 (1996) 599–609.CrossRefGoogle ScholarPubMed
Ghanbari, A., Jelodar, N.B., Rahiman, H., Studying of genetic diversity in Satsuma (Citrus unshiu) mandarin utilizing microsatellite markers, Int. J. Agric. Res. 4 (2009) 88–86.Google Scholar
Hvarleva, T., Kapari-Isaia, T., Papayiannis, L., Atanassov, A., Hadjinicoli, A.Kyriakou, A., Characterization of citrus cultivars and clones in Cyprus through microsatellite and RAPD analysis, Biotechnol. Biotechnol. Eq. 22 (2008) 787–794.CrossRefGoogle Scholar
Koehler-Santos, P., Dornelles, A.L.C., De Freitas, L.B., Characterization of mandarin citrus germplasm from Southern Brazil by morphological and molecular analyses, Pesqui. Agropecu. Bras. (Brasilia) 38 (2003) 797–806.CrossRefGoogle Scholar
Campos, E.T., Espinosa, M.A.G., Warburton, M.L., Varela, A.S., Monter, A.V., Characterization of mandarin (Citrus spp.) using morphological and AFLP markers, Interciencia 30 (2005) 687–693.Google Scholar
Bull, L.N., Pabón-Peña, C.R., Freimer, N.B., Compound microsatellite repeats: practical and theoretical features, Genome Res. 9 (1999) 830–838.CrossRefGoogle ScholarPubMed
Barkley, N.A., Krueger, R.R., Federici, C.T., Roose, M.L., What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles, Plant Syst. Evol. 282 (2009) 71–86.CrossRefGoogle Scholar
Park, Y.J., Lee, J.K., Kim, N.S., Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops, Molecules 14 (2009) 4546–4569.CrossRefGoogle ScholarPubMed
Jatoi, S.A., Kikuchi, A., Yi, S.S., Naing, K.W., Yamanaka, S., Watanabe, J.A., Watanabe, K.N., Use of rice SSR markers as RAPD markers for genetic diversity analysis in Zingiberaceae, Breed. Sci. 56 (2006) 107–111.CrossRefGoogle Scholar
Brondani, R.P.V., Brondani, C., Tarchini, R., Gratta-Paglia, D., Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla, Theor. Appl. Genet. 97 (1998) 816–827.CrossRefGoogle Scholar
Oliveira, E.J., Pádua, J.G., Zucchi, M.I., Vencovsky, R., Vieira, M.L.C., Origin, evolution and genome distribution of microsatellites, Genet. Mol. Biol. 29 (2006) 294–307. CrossRefGoogle Scholar
Chen, C.X., Zhou, P., Choi, Y.A., Huang, S., Gmitter, Jr. F.G., Mining and characterizing microsatellites from citrus ESTs, Theor. Appl. Genet. 112 (2006) 1248–1257.CrossRefGoogle ScholarPubMed
Novelli, V.M., Cristofani, M., Souza, A., Machado, M.A., Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck), Genet. Mol. Biol. 29 (2006) 90–96.CrossRefGoogle Scholar
Dixit, A., Chung, J.W., Zhao, W.G., Lee, G.A., Lee, D.H., Ma, K.H., Lee, M.C., Gwag, J.G., Kim, C.H., Park, Y.J., Development of new microsatellite markers for molecular diversity analysis of Citrus species, J. Hortic. Sci. Biotechnol. 85 (2010) 521–527.CrossRefGoogle Scholar
Doyle, J., Doyle, L., Isolation of plant DNA from fresh tissue, Focus 12 (1990) 13–15.Google Scholar
Puchooa, D., A simple, rapid and efficient method for the extraction of genomic DNA from lychee (Litchi chinensis Sonn.), Afr. J. Biotechnol. 3 (2004) 253–255.Google Scholar
Schuelke, M., An economic method for the fluorescent labelling of PCR fragments, Nat. Biotechnol. 18 (2002) 233–234.CrossRefGoogle Scholar
Peakall, R., Smouse, P.E., GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research, Mol. Ecol. Notes 6 (2006) 288–295.CrossRefGoogle Scholar
Liu, K., Muse, S.V., PowerMarker: an integrated analysis environment for genetic marker analysis, Bioinformatics 21 (2005) 2128–2129.CrossRefGoogle ScholarPubMed
Waits, L.P., Luikart, G., Taberlet, P., Estimating the probability of identity among genotypes in natural populations: cautions and guidelines, Mol. Ecol. 10 (2001) 249–256.CrossRefGoogle ScholarPubMed
Valière, N., GIMLET: a computer program for analyzing genetic individual identification data, Mol. Ecol. Notes 2 (2003) 377–379.Google Scholar
Nei, M., Tajima, F., Tateno, Y., Accuracy of estimated phylogenetic trees from molecular data, J. Mol. Evol. 19 (1983) 153–170. CrossRefGoogle ScholarPubMed
Tamura, K., Dudley, J., Nei, M., Kumar, S., MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol. 24 (2007)1596–1599.CrossRefGoogle ScholarPubMed
Kovach W.L., MVSP-A Multi Variante Statistical Package for Windows, ver. 3.1., Kovach Comput. Serv., Pentraeth, Wales, U.K., 1999.
Golein, B., Talaine, A., Zamani, Z., Moradi, B., Development and characterization of new microsatellite loci from lemon (Citrus limon), Int. J. Agri. Biol. 8 (2006) 172–174.Google Scholar
Barkley, N.A., Roose, M.L., Krueger, R.R., Federici, C.T., Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs), Theor. Appl. Genet. 112 (2006) 1519–1531.CrossRefGoogle Scholar
Cristofani-Yaly M., Novelli V.M., Bastianel M., Machado M.A., Transferability and level of heterozygosity of microsatellite markers in Citrus species, Plant. Mol. Biol. Rep. (2010) 1–6.
Luro, F.L., Constantino, G., Terol, J., Argout, X., Allario , T., Wincker, P., Talon, M., Ollitrault, P., Morillon, R., Transferability of the EST-SSRs developed on Nules Clementine (Citrus Clementine Hort. ex Tan.) to other Citrus species and their effectiveness for genetic mapping, BMC Genomics 9 (2008) 287. CrossRefGoogle ScholarPubMed
Bayer, R.J., Mabberley, D.J., Morton, C., Miller, C.H., Sharma, I.K., Pfeil, B.E., Rich, S., Hitchock, R., Sykes, S., A molecular phylogeny of the orange subfamily (Rutaceae: Aurantioideae) using nine cpDNA sequence, Am. J. Bot. 96 (2009) 668–685.CrossRefGoogle Scholar
Federici, C.T., Fang, D.Q., Scora, R.W., Roose, M.L., Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis, Theor. Appl. Genet. 96 (1998) 812–822.CrossRefGoogle Scholar
Sonnante, G., Pignone, D., Hammer, K., The domestication of artichoke and cardoon: from Roman Times to the Genomic Age, Ann. Bot. 100 (2007) 1095–1100.CrossRefGoogle ScholarPubMed
Liu, Y., Liu, D.C., Wu, B., Sun, Z.H., Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers, Chin. J. Agr. Biotechnol. 3 (2006) 119–126.Google Scholar
Shaaban, E.A., Abd-EL-Aal, S.K.H., Zaied, N.S., Rizkalla, A.A., Assessment of genetic variability on some orange accessions using RAPD-DNA markers, Res. J. Agric. Biol. Sci. 2 (2006) 564–570.Google Scholar