Evaluasi 18 primer SSR untuk pengembangan sidikjari DNA  tanaman karet  (Hevea brasiliensis Muell. Arg.) Evaluation of 18 SSR primers to develop DNA fingerprint of rubber tree  (Hevea brasiliensis Muell. Arg.)

Abstract Breeding program of rubber tree to produce elite clones is hampered by the length of selection cycles. On the other hand, attempts to increase production by extensification of the plantation area is also facing a problem from the availability of the rootstock, causing the occurence of fake clones without any information of their origin. Therefore, the availability of molecular markers to be used as DNA fingerprint of rubber tree clones is needed. This will help the breeder to shorten the length of selection program and to identify the purity of the clone. This research was aimed to evaluate 18 SSR primer pairs that had been published to identify 17 rubber clones. Pure genomic DNAs were isolated from 17 clones, followed by experiment to optimize annealing tempe-rature for each primer to obtain the best amplification product. Initially, the PCR product was run in both the agarose and polyacrylamide gels. However, the analysis of all PCR products were then conducted on SDS polyacrylamide gel, since this gel can separate DNA fragments with only a few bases differences. The results showed that 14 clones have been identified specifically using 11 primers. Four out of 18 primer pairs used could identify 12 rubber tree clones, which are PR 107, PR 261, SP 217, PB 330, PB 340, IRR 5, IRR 112, IRR 118, IRR 220, GT 1, BPM 101 and RRIM 712. Each clone can be distinguished from each other using only one primer pair. Identification of the other tree clones (PB 5/51, PB 260, and RRIC 110) has to be conducted by combining the several PCR products using different primer pairs. Although these results showed that SSR markers had high potential to be used as DNA fingerprint on rubber tree clones, the set of the primer pairs should be tested among other clones, as well as other SSR primers should be tested to identify the clones which could not be identified using the 18 primer pairs in this experiment.Abstrak Pemuliaan tanaman karet untuk menghasilkan klon-klon unggul baru menghadapi masalah lamanya siklus seleksi. Di sisi lain, upaya peningkatan produksi melalui pembukaan lahan baru, juga terkendala oleh ketersediaan bibit, yang memicu beredarnya bibit palsu, yang umumnya tidak jelas asal usulnya. Oleh karena itu, diperlukan ketersediaan marka yang dapat digunakan sebagai sidikjari DNA bagi klon-klon tanaman karet yang ada, sehingga dapat membantu mempercepat proses seleksi dan mengetahui kemurnian bibit. Penelitian ini bertujuan untuk mengevaluasi 18 primer SSR yang telah dipublikasikan untuk mengidentifikasi 17 klon karet. DNA yang murni diisolasi dari 17 klon, kemudian dilakukan optimasi suhu annealing untuk setiap jenis primer agar diperoleh hasil amplifikasi terbaik. Pada awal percobaan hasil PCR dicek pada gel agarosa dan gel poliakrilamida, namun analisis untuk seluruh hasil PCR dilakukan pada gel SDS poliakrilamid, karena gel ini secara nyata dapat memisahkan fragmen DNA yang hanya berbeda beberapa basa. Hasil percobaan menunjukkan bahwa 14 klon dapat diidentifikasi secara spesifik menggunakan 11 primer. Empat dari 18 pasang primer yang diuji dapat mengidentifikasi 12 klon yang dianalisis, yaitu PR 107, PR 261, SP 217, PB 330, PB 340,. IRR 5, IRR 112, IRR 118, IRR 220, GT 1, BPM 101 dan RRIM 712. Masing-maing klon tersebut dapat dibedakan dari klon lainnya hanya dengan menggunakan satu jenis primer. Sedangkan identifikasi tiga klon lainnya (PB 5/51, PB 260, dan RRIC110) harus dilakukan dengan menggabungkan hasil PCR menggunakan beberapa primer. Meskipun hasil percobaan ini menunjukkan bahwa marka SSR sangat berpotensi untuk digunakan sebagai sidikjari DNA klon-klon karet, namun primer yang sama perlu diuji untuk klon-klon lainnya. Demikian pula primer lain perlu diuji untuk mengidentifikasi klon-klon yang belum teridentifikasi menggunakan 18 primer dalam penelitian ini.

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Evaluasi 18 primer SSR untuk pengembangan sidikjari DNA tanaman karet (Hevea brasiliensis Muell. Arg.) Evaluation of 18 SSR primers to develop DNA fingerprint of rubber tree (Hevea brasiliensis Muell. Arg.)

E-Journal Menara Perkebunan ◽

10.22302/iribb.jur.mp.v82i2.23 ◽

2016 ◽

Vol 82 (2) ◽

Author(s):

Asmini BUDIANI ◽

Sekar WOELAN ◽

Hayati MINARSIH ◽

. NUHAIMI-HARIS ◽

Riza Arief PUTRANTO

Keyword(s):

Molecular Markers ◽

Hevea Brasiliensis ◽

Rubber Tree ◽

The Other ◽

Dna Fingerprint ◽

Amplification Product ◽

Pcr Product ◽

Ssr Primers ◽

Pcr Products ◽

Genomic Dnas

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The control by ΔµH+ of the tonoplast-bound H+-translocating adenosine triphosphatase from rubber-tree (Hevea brasiliensis) latex

Biochemical Journal ◽

10.1042/bj2290459 ◽

1985 ◽

Vol 229 (2) ◽

pp. 459-467 ◽

Cited By ~ 6

Author(s):

B P Marin

Keyword(s):

Atpase Activity ◽

Equilibrium State ◽

Hevea Brasiliensis ◽

Adenosine Triphosphatase ◽

Atp Hydrolysis ◽

Rubber Tree ◽

The Other ◽

Proton Gradient ◽

Electrochemical Proton Gradient ◽

The Relationship

The relationship between tonoplast-bound ATPase activity and the magnitude of the electrochemical proton gradient has been investigated on tightly sealed vesicles prepared from rubber-tree (Hevea brasiliensis) latex. A variety of methods have been used to modify, either alone or together, the two components of the electrochemical proton gradient (delta mu H+). When the delta pH component was decreased either by titration with (NH4)2SO4 or by addition of protonophores or nigericin in the presence of K+, ATPase activity was stimulated. On the other hand, when the delta psi component was decreased either by addition of lipophilic cations or by addition of valinomycin in the presence of K+, ATPase activity decreased. It is concluded that activity of the tonoplast-bound ATPase is regulated by changes in the electrochemical proton gradient across the tonoplast, so that, once the maximum proton gradient is established across the tonoplast, any perturbation of the equilibrium state should result in the increased rate of ATP hydrolysis as the enzyme attempts to re-establish the initial gradient.

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Chloride-ion stimulation of the tonoplast H+-translocating ATPase from Hevea brasiliensis (rubber tree) latex. A dual mechanism

Biochemical Journal ◽

10.1042/bj2260085 ◽

1985 ◽

Vol 226 (1) ◽

pp. 85-94 ◽

Cited By ~ 4

Author(s):

B P Marin ◽

X Gidrol

Keyword(s):

Membrane Potential ◽

Atpase Activity ◽

Hevea Brasiliensis ◽

Rubber Tree ◽

Electrical Potential ◽

Chloride Ion ◽

The Other ◽

Potential Difference ◽

Dual Mechanism ◽

Stimulation Of

The effect of Cl- and other anions on the tonoplast H+-translocating ATPase (H+-ATPase) from Hevea brasiliensis (rubber tree) latex was investigated. Cl- and other anions stimulated the ATPase activity of tightly sealed vesicles prepared from Hevea tonoplast, with the following decreasing order of effectiveness: Cl- greater than Br- greater than SO4(2-) greater than NO3-. As indicated by the changes of the protonmotive potential difference, anion stimulation of tonoplast H+-ATPase was caused in part by the ability of these anions to dissipate the electrical potential. This interpretation assumes not a channelling of these anions against a membrane potential, negative-inside, but a modification of the permeability of these ions through the tonoplast membrane. In addition, Cl- and the other anions stimulated the ATPase activity solubilized from the tonoplast membrane. Consequently, the tonoplast H+-pumping ATPase can be considered as an anion-stimulated enzyme. These results are discussed in relation to various models described in the literature for the microsomal H+-ATPase systems claimed as tonoplast entities.

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Influence of fire on ambrosia beetles (Curculionidae, Scolytinae and Platypodinae) in rubber tree plantations (Hevea brasiliensis) in southern Brazil

10.1603/ice.2016.112050 ◽

2016 ◽

Author(s):

Gabriela Costa Pinheiro

Keyword(s):

Hevea Brasiliensis ◽

Rubber Tree ◽

Tree Plantations ◽

Southern Brazil ◽

Ambrosia Beetles

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Co- and post-translational processing of the hevein preproprotein of latex of the rubber tree (Hevea brasiliensis)

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)98499-1 ◽

1991 ◽

Vol 266 (24) ◽

pp. 15944-15948

Author(s):

H.I. Lee ◽

W.F. Broekaert ◽

N.V. Raikhel ◽

H. Lee

Keyword(s):

Hevea Brasiliensis ◽

Rubber Tree

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A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽

10.3390/plants10010004 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4

Author(s):

Oleg S. Alexandrov ◽

Olga V. Razumova ◽

Gennady I. Karlov

Keyword(s):

Polymerase Chain Reaction ◽

Molecular Markers ◽

Dna Markers ◽

5S Rdna ◽

Chain Reaction ◽

Closely Related Species ◽

Pcr Products ◽

Polymerase Chain ◽

Species Specific ◽

Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

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Ethrel® stimulant increases the activity of soluble invertase isoforms in rubber tree (Hevea brasiliensis) bark tissues

Australian Journal of Crop Science ◽

10.21475/ajcs.18.12.01.pne770 ◽

2018 ◽

Vol 12 (1) ◽

pp. 99-107

Author(s):

Débora Domiciano ◽

◽

Pollyanna Aparecida Carvalho ◽

Luiz Edson Mota de Oliveira ◽

Hilda Beatriz W. Cárdenaz ◽

...

Keyword(s):

Hevea Brasiliensis ◽

Rubber Tree

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Molecular characterization of some selected persimmon genotypes and cultivars by srap and ssr markers

Genetika ◽

10.2298/gensr1702693p ◽

2017 ◽

Vol 49 (2) ◽

pp. 693-704

Author(s):

Hasan Pinar ◽

Ercan Yildiz ◽

Mustafa Kaplankiran ◽

Celil Toplu ◽

Mustafa Unlu ◽

...

Keyword(s):

Ssr Markers ◽

Clonal Propagation ◽

Genetic Relationships ◽

The Other ◽

Diospyros Kaki ◽

Ssr Primers ◽

Similarity Ratio ◽

Polymorphic Bands ◽

Dna Primers

In this study, SRAP and SSR markers were employed to determine genetic relationships among 42 persimmon genotypes (Diospyros kaki Thunb) obtained from Hatay province and 3 persimmon cultivars, 2 of which belong to Diospyros kaki Thunb and one belongs to Diospyros oleifera Cheng. Genetic relationships were determined by using a total of 29 molecular DNA primers (SRAP and SSR). Of these primers, 21 SRAP primer combinations produced a total of 107 bands and 77.6% of them were polymorphic; 8 SSR primers produced 26 polymorphic bands with an average polymorphism ratio of 84.6%. The SRAP and SSR markers produced 4.6 bands as average and the number of bands produced per marker was calculated as 3.6. The lowest similarity was observed between MK-113 (Diospyros oleifera Cheng) and the other genotypes all belongs to Diospyros kaki Thunb (with similarity ratios of 0.41-0.69 for SRAP primers, between 0.25-0.67 for SSR primers). The genotypes/cultivars belongs to Diospyros kaki had similarity ratio between 0.98-1.00 according to SRAP and SSR markers. This synonym or similarity could be results of clonal propagation rather than autogamy.

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The relationship among freezing tolerance, vernalization requirement, Ppd alleles and winter hardiness in European wheat cultivars

The Journal of Agricultural Science ◽

10.1017/s0021859617000521 ◽

2017 ◽

Vol 155 (9) ◽

pp. 1353-1370 ◽

Cited By ~ 5

Author(s):

A. GORASH ◽

R. ARMONIENĖ ◽

Ž. LIATUKAS ◽

G. BRAZAUSKAS

Keyword(s):

Molecular Markers ◽

Western Europe ◽

Complex Trait ◽

Winter Hardiness ◽

Photoperiod Sensitivity ◽

The Other ◽

Wheat Cultivars ◽

Crucial Component ◽

Per Se ◽

The Relationship

SUMMARYWinter hardiness of wheat is a complex trait involving a system of structural, regulatory and developmental genes, which interact in a complex pathway. The objective of the present work was to study the relationship among the main traits determining the level of adaptation and the possibility for target manipulation of breeding material by using molecular markers and phenological parameters. Wheat cultivars from different ecoclimatic environments of Europe were included for analysis. Gene-specific assay showed that photoperiod sensitivity of the studied cultivars was determined by polymorphism in the Ppd-D1 allele. The study established the relationship among winter hardiness, LT50 (the temperature at which 50% of plants are killed), photoperiod sensitivity, vernalization duration and earliness per se genes in the environment of Lithuania. The cultivars from Northern and Western Europe exhibited stronger requirement for vernalization and photoperiod. Although the group of cultivars from the southern latitudes were characterized by earliness, they possessed a stronger level of LT50. The level of LT50 was found to be the most crucial component of winter hardiness, the other traits served as supplementary components.

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