Assessment of polymorphism using RAPD in the generalized hemiparasitic plant Helicanthes elasticus (Desv.)Danser collected from six different hosts

RAPD analysis was carried out to determine genetic diversity that occurred among the selected accessions of H.elasticus obtained from six different hosts. All together 10 random primers were used for the RAPD assay, of which primer S11 produced 12 amplified bands in which 10 are polymorphic. Primer S9 produced the least number of amplified fragments. 10 primers together resulted in 88 amplified fragments, of which 26 are found to be polymorphic. Considerable polymorphism was shown by 3 primers that can be represented in a descending order S11>S79>S10. Accessions of H.elasticus obtained from Anacardium occidentale and Citrus maxima produced more polymorphic bands with S11. The overall polymorphism obtained in the selected samples of this hemiparasite was 29.54 indicating that genetic similarity was more among these samples rather than genetic diversity.

PENETAPAN KERAGAMAN GENETIK NILAM (Pogostemon sp.) HASIL FUSI PROTOPLAS DENGAN TEKNIK RAPD

<p>Keragaman genetik dan kckerabatan tanaman nilam hasil fusi protoplas antara Nilam Jawa (Girilaya) dan Nilam Aceh (Sidikalang dan TT 75) dianalisis dengan menggunakan penanda RAPD. Bahan tanaman yang digunakan dalam penelitian ini adalah 9 genotipa yang tcrdiri dari 3 tetua dan 6 tanaman hibrida somatik (9 II 33, 9 II 21, 2 IV 8, 9 IV14, 9 II 7 dan 9 II 10). Primer yang digunakan dalam analisis tcrdiri atas 5 primer acak yaitu OPD 03, OPD 20, OPH 09, OPH 19 dan Abi 117.17. DNA dickstraksi dengan metode OROZCO-CASTJLLO et al. (1994) yang sudah dimodifikasi. Konsentrasi DNA ditetapkan dengan metode sambrook el al. (1989) dengan pcrbandingan kuantifikasi spektrofotometrik. Koefisien kemiripan dan kckerabatan antar genotipa dianalisis dengan menggunakan program NTsys ver. 1.80 dan UPGMA untuk menentukan sidik gerombol dan dendogram. Hasil analisis menunjukkan bahwa koefisien kemiipan dari amplifikasi DNA dengan 5 primer acak dari ke- 9 genotipa berkisar antara 0.48-1.0. Berdasarkan niatrik jarak genetik, kescmbilan genotipa tanaman yang diuji membentuk 2 kelompok besar yaitu kelompok I, tetua Girilaya (Nilam Jawa) dan kelompok II tcrdiri dari tetua Sidikalang dan TT 75 (Nilam Aceh) serta hibrida somatik. Kelompok II, tcrbagi menjadi dua sub kelompok yaitu sub kelompok I (9 II 33 dan 9 II 7) dan sub kelompok II yang tcrdii dari sub-sub kelompok II-I (9 II 21, S, TT 75) dan sub-sub kelompok II-II (2 IV 8, 9 IV 14, 9 II 10).</p><p>Kata kunci: Pogostemon sp., fusi protoplas, keragaman genetik, RAPD</p><p> </p><p><strong>ABSTRACTS </strong></p><p><strong>Assessment of genetic variability of patchoulli (Pogostemon sp.,) derived from protoplast fussion using RAPD </strong></p><p>Somatic hybrids of Pogostemon heyneaneus (cv. Girilaya) X P. cablin (cv. Sidikalang and TT 75) were tested for their genetic variability and relationship. The somatic hybrids tested were 9 II 33, 9 II 21, 2 IV 8, 9 IV14, 9 II 7 and 9 II 10. DNA of the plant materials used were extracted by using the modified method of orozcocastulo et al. (1994) and quantified spectrophotometrically according to SAMBROOK el al. (1989). Five random primers, OPD 03. OPD 20, OPH 09. OPH 19 and Abi 117.17, were applied to amplify the extracted DNA. The genetic relationship among the somatic hybrids were estimated by using the index of similarity to perform genctical matrix and dendogram. Index of similarity among genotypes were calculated by using NTsys ver. 1.80 program. Then, cluster analyses to perform dendogram were achieved based on similarity estimates by using the Unweighted Pair-Group Method Arithmetic Average (UPGMA). Results showed that index of similarities of the amplified DNA from 5 random primers ranged from 0.48 to 1.0. The somatic hybrids and their parental plants subjected to RAPD analyses were classified into 2 major groups, first, the parental group of Java patchouli and second, others parental plants, Aceh patchouli (Sidikalang and TT 75), and the somatic hybrids. The second group was then classified into 2 minor groups. First group consisted of somatic hybrids nos. 9 II 33 and 9 II 7, while the second were classified into 2 groups which consisted nos. 9 II 21, S, TT 75 and nos. 2 IV 8, 9 IV 14 and 9 II 10.</p><p>Key words : Pogostemon sp., protoplast fusion, genetic variability, RAPD</p>

Diversitatea moleculară a două ecotipuri de Datura inoxia provenite din vestul şi estul României

Molecular Diversity of two Ecotypes of Datura inoxia Originating from Western and Eastern Romania. To characterize genomic variation among genotypes, we have performed RAPD analysis using ten random primers. The results yielded 88 bands out of which 39 were polymorphic. The primers US1 and US7 showed 87.71% and 72.72% polymorphism respectively. The least polymorphism was shown by primer US9 (12.50%). The primer US15 did not produce any bands suggesting the absence of matching sequences in the genomic DNA. The dendrogram classified ecotypes into two clusters (A and B); cluster B possess three sub-clusters: B1 - Socodor 2; B2 - Flamura 1 and Flamura 2, and B3 - Flamura 3. Overall, the values of genetic similarity between ecotypes were low pointing out their particular origin and “evolution”.

Use of RAPD Markers Technique to Evaluate Genetic Variation in Two Types of Local Ducks

This study was carried out to assess the genetic variation between two local Iraqi (white and grey) ducks by RAPD-PCR technique using five random primers. The total number of bands that shown by the primers (APO-08, APOF-O9, APO-10, APO-16, APO-18) was 63, 53, 79, 81, 68 for local white ducks, while it was 62, 61, 66, 69, 58 for the local gray ducks respectively. Additionally, all primers showed 59 common bands. OPA-08 primer showed the highest number of common bands (22) while APF-09 primer resulted the lowest number of common bands (4 bands). The overall number of specific bands in local white ducks were higher than those of local grey ducks (285 and 257 bands, respectively). The average of similarity ratio between local ducks was (35.76) while individually, APO-08 primer showed the highest similarity ratio (70.4%) comparing with the lowest similarity percentage (14.04%) that represented by OPF-09 primer.

Diversitas Genetik Populasi Tumbuhan Andaliman (Zanthoxylum acanthopodium DC.) Sumatera Utara Berbasis Molekuler

Andaliman adalah tumbuhan yang khas dijumpai di Sumatera Utara dan hanya dikenal untuk masakan Batak serta tumbuh secara liar. Saat ini dikhawatirkan akan menjadi punah karena mengalami penurunan jumlah individu (tidak ada upaya membudidayakan). Diversitas genetik suatu tumbuhan sangat penting karena akan mempengaruhi eksistensinya di alam dan diperlukan untuk program pemuliaan tanaman. Tujuan penelitian ini untuk mengklarifikasi keragaman genetik populasi andaliman Sumatera Utara. Sebanyak 30 aksesi andaliman dari berbagai ketinggian yang digunakan berasal dari 3 populasi yaitu dari Kabupaten Dairi, Tanah Karo dan Simalungun. Analisis molekuler RAPD dilakukan dengan menggunakan 10 primer acak. Kesepuluh primer tersebut menghasilkan 50 pola pita DNA, dengan tingkat polimorfisme mencapai 90 %. Selanjutnya koefisien keragaman genetik dan dendogram filogenetik diperoleh menggunakan software Darwin 6.0 dan GenAlEx 6.502. Hasil ini menunjukkan bahwa 30 aksesi andaliman tersebut dikelompokkan menjadi tiga kelompok. Dalam setiap kelompok terdapat aksesi andaliman yang berasal dari tiga kabupaten tersebut dan dari ketinggian yang berbeda, artinya setiap aksesi andaliman tidak mengelompok berdasarkan daerah dan ketinggian tempatnya. Hasil penelitian ini menunjukkan bahwa 30 aksesi dari tiga lokasi menunjukkan keragaman genetik yang tinggi. Andaliman is a typical plant found in North Sumatra and is known for Batak cuisine and grows wildly. At present, it is feared that it will become extinct due to a decline in the number of individuals (there is no effort to cultivate). The genetic diversity of a plant is very important because it will affect its existence in nature and is needed for plant breeding programs. This study aims to clarify the genetic diversity of the North Sumatra andaliman population. A total of 30 andaliman accessions from various heights used came from 3 populations, such as from Dairi District, Tanah Karo, and Simalungun. RAPD molecular analysis was carried out using 10 random primers. The ten primary produce 50 DNA banding patterns, with a level of polymorphism reaching 90%. Furthermore, the genetic diversity coefficient and phylogenetic dendogram were obtained using software of Darwin 6.0 and GenAlEx 6.502. These results indicate that 30 andaliman accessions are grouped into three groups. In each group there are Andaliman accessions originating from the three districts and from different heights, meaning that each of Andaliman's accessions does not group based on the area and height of the place. The results of this study indicate that 30 accessions from three locations showed high genetic diversity.

Targeted reduction of highly abundant transcripts with pseudo-random primers

Transcriptome studies based on quantitative sequencing estimate gene expression levels by measuring the abundance of target RNAs in libraries of sequence reads. The sequencing cost is proportional to the total number of sequenced reads. Therefore, in order to cover rare RNAs, considerable quantities of abundant and identical reads have to be sequenced. This major limitation can be lifted by strategies used to deplete the library from some of the most abundant sequences. However, these strategies involve either an extra handling of the input RNA sample, or the use of a large number of reverse-transcription primers (termed "not-so-random primers"), which are costly to synthetize and customize. Here, we demonstrate that with a precise selection of only 40 "pseudo-random" reverse-transcription primers, it is possible to decrease the rate of undesirable abundant sequences within a library without affecting the transcriptome diversity. "Pseudo-random" primers are simple to design, and therefore are a flexible tool for enriching transcriptome libraries in rare transcripts sequences.