Seleksi Marka SCAR untuk Identifikasi Dini Jenis Kelamin Tanaman Pepaya (The Selection of SCAR Markers for Early Sex Identification of Papaya)

<p>Identifikasi dini terhadap jenis kelamin tanaman pepaya merupakan hal penting yang dapat membantu petani dalam budidaya tanaman pepaya. Identifikasi kelamin pepaya berdasarkan marka morfologi dan fisiologi telah dilakukan, namun beberapa hasilnya masih bias karena faktor lingkungan. Identifikasi kelamin tanaman pepaya menggunakan marka molekuler bisa lebih cepat dan akurat. Penelitian tersebut telah banyak dilakukan, salah satu di antaranya adalah marka berbasis sequence characterized amplified region (SCAR) dan beberapa primer SCAR telah dihasilkan untuk identifikasi kelamin pepaya. Penelitian bertujuan untuk menyeleksi primer SCAR yang efektif dalam mengidentifikasi seks tanaman pepaya. Penelitian dilakukan pada bulan November 2018 sampai Juni 2019 di Laboratorium Molekuler dan Uji Mutu Kebun Percobaan Sumani Balai Penelitian Tanaman Buah Tropika di Solok. Primer SCAR yang diseleksi adalah W11,T12, PKBT5, Napf2, dan SDp. Tanaman referensi sebagai sampel umur 11–12 bulan adalah tanaman betina, jantan, dan hermaprodit masing-masing lima tanaman dari pepaya lokal dan Merah Delima. Hasil penelitian menunjukkan bahwa lima primer SCAR yang diuji hanya dapat membedakan tanaman betina dengan tanaman jantan dan hermaprodit tetapi belum dapat membedakan antara tanaman jantan dengan hermaprodit. Konsistensi pola amplifikasi dihasilkan dari primer SCAR W11, Napf2, dan T12 dengan posisi 800 bp. Primer SCAR W11, Napf2, dan T12 selanjutnya dapat digunakan sebagai marka untuk identifikasi kelamin tanaman betina dengan tanaman jantan dan hermaprodit.</p><p><strong>Keywords</strong></p><p>SCAR; Identifikasi; Pepaya; Jantan, Hermaprodit </p><p><strong>Abstract</strong></p><p>The determination of sex expression of papaya plants is important to farmers in its cultivation. The identification of papaya plant sex based on morphological and physiological characters have been previously carried out, however, the results were still biased due to environmental factors. Many studies have been carried out to identify this plant sex, such as the use of molecular and SCAR markers, based on sequence characterization on amplified regions. This research aims to select the SCAR primers that are effective in identifying papaya plant sex. The study was conducted from November 2018 to June 2019, at Laboratory of Molecular and Quality Testing of the Indonesian Tropical Fruit Research Institute in Solok. The selected SCAR primers were W11, T12, PKBT5, Napf2, and SDp, using a total of five female, male, and hermaphrodite plants are reference aged 11–12 month from local papaya and cv. Merah Delima. The five SCAR primers tested were only able to differentiate females from male and hermaphrodite plants. The consistency of the amplification pattern was obtained from the SCAR W11, T12, and Napf2 primers at 800 bp. In conclusion, SCAR W11, Napf2, and T12 primers are used as markers to distinguish female plants from male and hermaphrodite.</p>

Resistance of Capsicum annuum genotypes against various isolates of Phytophthora capsici from Java, Indonesia

Wartono, Wiyono S, Syukur M, Giyanto, Lestari P. 2019. Resistance of Capsicum annuum genotypes against various isolates of Phytophthora capsici from Java, Indonesia. Biodiversitas 20: 3723-3730. Phytophthora capsici Leonian is one of the pathogenic oomycetes that can reduce chilli production worldwide. In this study, Indonesian local chilli genotypes were evaluated for their resistance to P.capsici on chilli in Java, under controlled conditions. P. capsici used in this study consisted of four isolates derived from chilli plants in Java Island. The chilli genotypes tested were 38 local chilli (Capsicum annuum L.) originated from Indonesia and 3 introduced C. annuum. Inoculation was carried out by drenching 5 ml suspension of zoospore (1 x 104) on the growing medium suitable for the oomycetes around the plant. Disease symptom was measured at 21 days after inoculation. Salicylic acid and b-1.3-glucanase analyses were conducted to 7-week old plant with specific interval. Molecular characterization to complement disease assay was carried out using SCAR primers (OpD04,717-F/D04,717-R). Significant differences were found in genotypes, isolates, and interactions between chilli genotypes x P. capsici isolates. Four tested isolates had different levels of virulence ranging from moderate (CpnsCK1, KdrRM3, WnsbCk) to high (WnsbCK2). The chilli genotypes revealed high partial resistance to P. capsici, as demonstrated by six genotypes resistant to CpnsCK1, two genotypes to KdrRM3, and one genotype resistant to WnsbCK1. Resistance of one of chilli pepper, Ungara was positively associated with an increase of salicylic acid and b-1.3-glucanase. There is no association between the SCAR marker with resistance of chilli to P. capsici suggested these pathogens from Java are probably controlled by another locus which is not detected by this SCAR marker.

Sex Determination in Nutmeg Seedlings Using Scar Primers

Myristica fragrans H. is a dieocious plant with male and female flowers on different trees. At the juvenile stage of nutmeg, their sexes is not morphologically identified until at the flowering stage. However, the female is more economical than the male plants. This challenge is making the work of nutmeg farmers difficult and also inhibiting the development of the spice and flavouring industry in Ghana. Hence, the use of molecular technique to characterize male and female nutmeg plants. SCAR markers are easy, specific, and reliable and have a high sense of reproducibility than other markers. Two different primers (F-Napf-76, R-Napf-77 and F-Napf-70, R-Napf-71) were used for the PCR amplification. It was revealed that the total genomic DNA of samples from both mature plant and seedlings of nutmeg were of good quality and was much concentrated by giving good DNA bands. Although there were no distinctions among the bands, they all lie at the same level (0.3kbp) indicating that the samples were of similar molecular weight. However, double PCR amplification was not seen in all samples when run on a 1% agarose gel but single amplifications were observed.

SCAR MARKER DEVELOPMENT FOR THE CORRECT IDENTIFICATION OF IRIS ENSATA

Objective: The objective of this research was to develop the RAPD based SCAR marker for the correct identification of the Iris ensata Thunb. (I. ensata) plant from its adulterants.Methods: Five samples of I. ensata. from the different geographical area were used in this study. The plant genomic DNA was isolated with the CTAB method with some modification (as dried samples were also used). After that, polymorphism was checked with the help of the 10-mer random primers of OPAA and BG series. Then, the bands of interest were eluted and cloned into pGEMT easy vector for the sequencing. Finally, the sequence is used to develop the SCAR primers (Ir-f andIr-R) specific for I. ensata and the developed primers also validated with respect to the market samples.Results: A putative 580 bp sequence specific for Iris ensata was identified from the randomly amplified polymorphic DNA (RAPD) analysis. To overcome the main limitation of RAPD it has been converted into SCAR markers. So that, this specific band was then eluted, cloned and sequenced. After that, SCAR primers (Ir-F and Ir-R) were synthesized by using this sequence. For the validation of the synthesized SCAR primers, they were tested with respect to the market samples. The amplicon of 260 bp was produced by the SCAR primers in the authentic I. ensata but market samples did not produce any bands with the synthesized SCAR primers.Conclusion: The results of this study show a high level of polymorphism in the RAPD pattern of the different accessions of the plant. Furthermore, this study results in the successful development of the RAPD based SCAR marker for the identification of the I. ensata.

BEAUVERIA BASSIANA CHARACTERIZATION AND EFFICACY GRASSHOPPER /ANGARACRIS

The B. bassiana is a fungus of manyarthropods, including more than 200 species of insects and acaridae. When spores of the fungus come into contact with the body of an insect host, they germinate, enter the body, and grow inside, eventually killing the insect. Two local strains, including B. bassiana-G07, which was isolated from grasshopper Oedaleusasiaticus, died on natural infection, and B. bassiana-G10, which was isolated from grasshopper Caliptomus abbreviates, died of soil borne infection, were detected and it was identified as species B. bassiana by PCR. SCAR primers OPB9 F/R677 and OPA15 F/R441 was specific to of B. bassiana. The highest infection rate by B. bassiana-G07and mortality was observed in variants of both concentrations 2.1 x 108 conidia/ml, 2.1 x 109 conidia/ml; where mortality reached 86.3-100%.Mongolian Journal of Agricultural Sciences Vol.13(2) 2014: 96-100

RAPD Marker Conversion into a SCAR Marker for Rapid Identification of Johnsongrass [Sorghum halepense (L.) Pers.]

Johnsongrass [Sorghum halepense (L.) Pers.] is a malignant weed in the world, threatening biodiversity at invaded habitats in more than 50 countries. Because of similarity in morphological characters, S. halepense and its relatives, S. almum, S. nitidum, S. propinquum, S. sudanense, and S. bicolor, etc. was difficult to identify. As a supplementary methodolgy for morphology identification, a molecular detection method was established. Sequence Characterized Amplified Regions (SCAR) marker is a recent established, reliabile, and stable molecular marker based on RAPD maker, an effective way for germplasm identification. In this study, one specific band of S.halepense was screened by 163 pairs of RAPD primers. According to the sequences of the band, a pair of special SCAR primers SH1/SH2 was designed and verified by 65 Sorghum DNA samples from all over the world. The results showed SCAR primers SH1/SH2 can be used to distinguish S.halepense and its relatives rapidly with three exceptions of Australia geotypes.

Eastern Filbert Blight-resistant Hazelnuts from Russia, Ukraine, and Poland

Stable genetic resistance to the fungal disease eastern filbert blight (EFB), caused by Anisogramma anomala, is vital for sustainable production of European hazelnut (Corylus avellana) in eastern North America. In this study, new hazelnut germplasm from the Russian Federation, Ukraine, and Poland (a total of 1844 trees from 66 seed lots) was subjected to A. anomala under field conditions over at least five years in New Jersey. Plants were then rated for the presence of EFB using an index of 0 (no disease) through 5 (all stems containing cankers). Nuts of the resistant trees were evaluated to identify plants with improved kernel characteristics. Genomic DNA of these trees was also screened with sequence-characterized amplified region (SCAR) markers generated by the primers BE-03, BE-33, and BE-68, which are closely linked to the single dominant R-gene of ‘Gasaway’, to assess the resistant seedlings for the presence of this well-known source of resistance. At final evaluation, 76 trees remained free of disease with nine expressing only minor symptoms (rating 1 or 2). The resistant trees spanned 24 different seed lots representing all three countries. The remaining trees ranged from moderately to severely infected with 81% of the total collection rating 5. Several of the resistant trees were found to produce commercial-sized (≈12 mm diameter), round kernels that blanched well. Although the results of the ‘Gasaway’ SCAR primers were inconclusive, the diverse collection origins and disease phenotypes provide evidence that novel sources of resistance were likely identified in this study. These new plants should broaden the genetic base of EFB-resistant C. avellana hazelnut germplasm available for breeding.