Identifikasi Molekuler dan Analisis Kekerabatan Aksesi Nenas Menggunakan Marka RAPD Menunjang Perakitan Varietas Unggul Baru

Sri Hadiati, Riry Prihatini, Ellina Mansyah

Abstract


(Molecular Identification and Relationships Among Several Pineapple Accessions Using RAPD Marker to Support the Assembling New Varieties)

Produksi dan produktivitas nenas dapat ditingkatkan antara lain melalui penggunaan varietas unggul. Dalam perakitan varietas, dibutuhkan informasi hubungan kekerabatan antartetuanya agar diperoleh efek heterosis yang tinggi melalui kegiatan identifikasi secara molekuler. Penelitian bertujuan (1) mengetahui tingkat polimorfisme primer yang digunakan,(2) mengidentifikasi fragmen DNA spesifik yang membedakan individu atau kelompok individu nenas, dan (3) mengetahui hubungan kekerabatan antarspesies dan aksesi nenas. Penelitian dilaksanakan mulai bulan Mei–Desember 2014 di Laboratorium Uji Mutu Benih dan Molekuler Balai Penelitian Tanaman Buah Tropika. Sampel yang digunakan sebanyak 19 aksesi dari empat spesies nenas (Ananas comosus, A. bracteatus, A. lucidus, dan A. nanus). Sebanyak 20 marka rapid amplified polymorphism DNA (RAPD) digunakan dalam analisis. Data diskor secara biner kemudian dianalisis menggunakan program NTSYSpc 2,1x. Hasil analisis menunjukkan bahwa polimorfisme 20 primer yang diuji berkisar 33–100% dengan rata-rata 87%. Primer dengan tingkat polimorfisme 100%, yaitu RAPD3, OPA13, OPAV3, OPC12, OPC16, dan OPY15. Kelompok Cayenne dicirikan oleh marka RAPD1 ukuran1.000 base-pair (bp) dan OPAV3 700 bp. Kelompok Queen dapat diidentifikasikan oleh marka RAPD3 ukuran 700 bp, kelompok Spanish dengan marka RAPD2 dan RAPD3 ukuran 1.500 bp. Analisis kluster menunjukkan bahwa 19 aksesi yang diuji terpisah menjadi enam kelompok pada koefisien kesamaan genetik 0,75, yaitu kelompok Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, dan A. nanus. Aksesi yang diuji mempunyai keragaman genetik yang luas dengan koefisien kesamaan genetik berkisar 0,41–0,85. Aksesi yang mempunyai kesamaan genetik tertinggi, yaitu antara N-73 dengan BB (0,85) dan terkecil, yaitu antara N-94 (A. nanus) dengan N-18 (Green Spanish) sebesar 0,41. Implikasi hasil penelitian adalah aksesi yang mempunyai kesamaan genetik tinggi salah satunya dapat dieliminasi untuk efisiensi dalam pengelolaan plasma nutfah, sedangkan aksesi-aksesi yang memiliki kesamaan genetik kecil, baik digunakan sebagai tetua persilangan agar diperoleh variabilitas genetik yang luas dan efek heterosis yang tinggi.

Keywords

Ananas spp.; Identifikasi; Karakterisasi; Kekerabatan genetik; Molekuler.

Abstract

Pineapple production and productivity can increased by the use of superior variety. Pertaining to variety assembling, the relationship information among parents are needed to gain heterosis effect through molecular identification activity. This research was aimed to (1) determine the level of polymorphism primers used, (2) identify specific DNA fragments which discrete individual or group of pineapple, and (3) reveal genetic relationship among pineapple species and accessions. The experiment was conducted on May to December 2014 in Seeds Quality Testing and Molecular Laboratory of Indonesian Tropical Fruit Research Institute. Nineteen accessions from four species (Ananas comosus, A. brachteatus, A. lucidus, and A. nanus) of pineapple were used as samples. Twenty rapid amplified polymorphism DNA (RAPD) markers were used on molecular analysis. The data were scored binary and then they were analyzed using NTSYSpc 2.1x computer software. The analysis showed that the 20 primers had 33–100%  polymorphic with 87% in average. Primers with 100% polymorphism level were RAPD3, OPA13, OPAV3, OPC12, OPC16, and OPY15. Cayenne group could be denoted with RAPD1 and OPAV3 markers by 1,000 base-pairs (bp) and 700 bp band, respectively. Meanwhile the Queen group can be identified by 700 bp band  RAPD3 marker. The Spanish group can be specified by1,500 bp band RAPD2 and RAPD3 markers. Based on cluster analysis the 19  accessions were separated  into six groups with 0.75 genetic similarity coefficient i.e., Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, and A. nanus. These accessions had a wide genetic diversity with 0.41 to (0.85) genetic similarity coefficients. The highest genetic similarity coefficient (0.85) was determined between N-73 and BB, whereas the lowest value down to 0.41 was indicated on N-94 (A. nanus) and N-18 (Green Spanish). The implications of this research are that one of two accessions that have high genetic similarities can be eliminated for efficiency in the management of germplasm. While accessions which  have little genetic similarity are both used as crosses parent in order to obtain wide genetic variability and high heterosis effects.


Keywords


Ananas spp.; Identification; Characterization; Genetic relationship; Molecular

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References


Bairu, MW, Fennell, CW & van Staden, J 2006, ‘The effect of plant growth regulators on somaclonal variation in Cavendish banana (Musa AAA cv, Zelig)’, Scientia Horticulturae, vol. 108, no. 4, pp. 347–351.

Borojević, S & others 1990, Principles and methods of plant breeding, Elsevier, Amsterdam.

Brewbaker, JL & Gorrez, DD 1967, ‘Genetics of self-incompatibility in the Monocot genera, Ananas (pineapple) and Gasteria’, American Journal of Botany, pp. 611–616.

Carlier, J, Reis, A, Duval, M & Leitão, J 2004, ‘Genetic maps of RAPD, AFLP, and ISSR markers in Ananas bracteatus and A. comosus using the pseudo-testcross strategy’, Plant Breeding, vol. 123, no. 2, pp. 186–192.

Carvalho, VP, Ruas, CF, Ferreira, JM, Moreira, RMP & Ruas, PM 2004, ‘Genetic diversity among maize (Zea mays L,) landraces assessed by RAPD markers’, Genetics and Molecular Biology, vol. 27, no. 2, pp. 228–236.

Collins, J 1968, The pineapple, botany, cultivation, and utilization, Leonard Hill, London.

Doyle, J & Doyle, J 1987, ‘Isolation of plant DNA from fresh tissues’, Focus, no. 12, pp. 13–15.

Eeuwens, CJ, Lord, S, Donough, CR, Rao, V, Vallejo, G & Nelson, S 2002, ‘Effects of tissue culture conditions during embryoid multiplication on the incidence of``mantled’’flowering in clonally propagated oil palm’, Plant Cell, Tissue and Organ Culture, vol. 70, no. 3, pp. 311–323.

Feuser, S, Meler, K, Daquinta, M, Guerra, MP & Nodari, RO 2003, ‘Genotypic fidelity of micropropagated pineapple (Ananas comosus) plantlets assessed by isozyme and RAPD markers’, Plant Cell, Tissue and Organ Culture, vol. 72, no. 3, pp. 221–227.

Hadiati, S, Kuswandi, Ihsan, F & Ardiana, D 2015, ‘Karakterisasi morfologi dan pengelompokan beberapa aksesi jambu air berdasarkan RAPD’, in Prosiding Seminar Nasional Perhimpunan Hortikultura Indonesia, Pusat Kajian Hortikultura Tropika, Bogor, pp. 349 – 356.

Hadiati, S, Yulianti, S & Sukartini 2009, Pengelompokan dan jarak genetik plasma nutfah nenas berdasarkan karakter morfologi’, J, Hort., vol. 19, no. 3, pp. 264–274.

Ines, M, Magdalita, P, Vina, C, Cruz, F & Villegas, V 2009, ‘Randomly amplified polimorphic DNA (RAPD) analysis reveal genetic relationships among pineapple (A. comosus (L.) Merr) genotypes’, Philipinne Journal of Crop Science, vol. 34, no. 3, pp. 1–10.

Kato, CY, Nagai, C, Moore, PH, Zee, F, Kim, MS, Steiger, DL & Ming, R 2005, ‘Intra-specific DNA polymorphism in pineapple (Ananas comosus (L.) Merr,) assessed by AFLP markers’, Genetic Resources and Crop Evolution, vol. 51, no. 8, pp. 815–825.

Mansyah, E 2012, ‘Struktur genetik manggis (Garcinia mangostana L,) berbasis marka morfologi dan molekuler’, Disertasi, Program Pascasarjana, Institut Pertanian Bogor, Bogor.

Masoud, S & Hamta, A 2008, ‘Cytogenetic analysis of somaclonal variation in regenerated plants of berseem clover (Trifolium alexandrium L,)’, Caryologia, vol. 61, no. 4, pp. 392–396.

Nandariyah, Soemartono & Taryono 2004, ‘Keragaman kultivar salak (Salacca zalacca)’, Agrosains, vol. 6, no. 2, pp. 75 – 79.

Pusat Data dan Informasi Pertanian 2016, Jakarta (ID): Kementerian Pertanian, Pusat Data dan Sistem Informasi Pertanian.

Popluechai, S, Onto, S & Eungwanichayapant, PD 2007, ‘Relationships between some Thai cultivars of pineapple (Ananas comosus) revealed by RAPD analysis’, Songklanakarin Journal of Science & Technology, vol. 29, no. 6.

Py, C, Lacoeuilhe, J & Teisson, C 1987, The pineapple, cultivation and uses, GP Maisonneuve & Larose, Paris.

Rohlf, J 2000, Numerical taxonomy and multivariate analisys system, version 2,1, Exceter softwer, New York.

Roostika, I, Khumaida, N & Ardie, SW 2015, ‘RAPD analysis to detect somaclonal variation of pineapple in vitro cultures during micropropagation’, BIOTROPIA-The Southeast Asian Journal of Tropical Biology, vol. 22, no. 2, pp. 109–119.

Ruas, CF, Ruas, PM & Cabral, JRS 2001, ‘Assessment of genetic relatedness of the genera Ananas and Pseudananas confirmed by RAPD markers’, Euphytica, vol. 119, no. 3, pp. 245–252.

Ruas, PM, Ruas, CF, Fairbanks, DJ, Andersen, WR & Cabral, JS 1995, ‘Genetic relationship among four varieties of pineapple, Ananas comosus, revealed by random amplified polymorphic DNA (RAPD) analysis’, Revista Brasileira de Genética, vol. 18, p. 413.

Rugayah 2006, ‘Eksplorasi, koleksi, karakterisasi, evaluasi, konservasi, dan pemanfaatan sumber daya genetik’, in Prosiding workshop penguatan sistem pengelolaan sumber daya genetik hortikultura lingkup Puslitbang Hortikultura, Puslitbang Hortikultura, Jakarta, pp. 10–18.

Santos, MDM, Buso, GCS & Torres, AC 2008, ‘Evaluation of genetic variability in micropropagated propagules of ornamental pineapple [Ananas comosus var. bracteatus (Lindley) Coppens and Leal] using RAPD markers’, Genetics and Molecular Research, vol. 7, no. 4, pp. 1097–1105.

Soneji, JR, Rao, PS & Mhatre, M 2002, ‘Suitability of RAPD for analyzing spined and spineless variant regenerants of pineapple (Ananas comosus L., Merr.)’, Plant Molecular Biology Reporter, vol. 20, no. 3, p. 307.

Sripaoraya, S, Blackhall, NW, Marchant, R, Power, JB, Lowe, KC & Davey, MR 2001, ‘Relationships in pineapple by random amplified polymorphic DNA (RAPD) analysis’, Plant Breeding, vol. 120, no. 3, pp. 265–267.

Sriyadi, B, Setiamihardja, R, Baihaki, A & Astika, W 2002, ‘Hubungan kekerabatan genetik antar tanaman the f1 dari persilangan TRI 2024 X PS 1 berdasarkan penanda RAPD’, Zuriat, vol. 13, no. 1.

Tatineni, V, Cantrell, RG & Davis, DD 1996, ‘Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPDs’, Crop Science, vol. 36, no. 1, pp. 186–192.

Williams, JGK, Kubelik, AR, Livak, KJ, Rafalski, JA & Tingey, S V 1990, ‘DNA polymorphisms amplified by arbitrary primers are useful as genetic markers’, Nucleic acids research, vol. 18, no. 22, pp. 6531–6535.




DOI: http://dx.doi.org/10.21082/jhort.v28n1.2018.p1-12

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