Metode Ekstraksi Dna Cabai (Capsicum Annuum L.) Menggunakan Modifikasi Buffer Ctab (Cethyl Trimethyl Ammonium Bromide) Tanpa Nitrogen Cair

Chili pepper is an agricultural commodity having high economic value. The production and supply of Chili pepper frequently did not match the increased demand; it caused the market price fluctuated. It is important to create new varieties of Chili pepper with high production trait to overcome the scarcity. Therefore the plant breeding activities for Chili pepper should be done intensively in both conventional and molecular-based to obtain varieties of Chili pepper with expected qualities. In molecular breeding, DNA extraction is the crucial steps of the process. If extracted DNA has an excellent quality and quantity, the next processes normally could be completed with the high-quality result. To date, most methods of DNA extraction used liquid nitrogen to destroy the tough carbohydrates of plant tissue. Liquid nitrogen is nitrogen gas in a fluid state which quite difficult to be distributed to the remote laboratory wit no available storage facility. This study aimed to obtain a modified DNA extraction method, in particular for Chili pepper, which capable to produce DNA with high quality and quantity without using liquid nitrogen. The sample used consisted of eight F2 plants including their hybrid-parental of the Kencana and the 0207. This research applied modified Doyle and Doyle method for extraction. Modification of extraction buffer is done through the addition of the 1% (w/v) PVP (Polyvinylpyrrolidone) and 0.2% (v/v) β-mercaptoethanol. The results showed that the DNA extracted using this method has good quality and quantity, capable of being amplified by using SSR (Simple Sequence Repeat) primer and could be digested by restriction enzyme EcoRI. Besides, this method can reduce dependence on the use of liquid nitrogen, in particular for remote laboratories with no available storage facility

Alat Pengusang Cepat IPB 77-1 MM Untuk Penapisan Vigor Daya Simpan Benih Kedelai

Accelerated Aging Machine “IPB 77-1 MM” could be used for soybean seed screening based on the seed storability vigor. The aim of the research was to identify simple, fast and accurate accelerated aging method using accelerated aging machine IPB 77-1 MM. Two methods of accelerated aging test (physical and chemical treatment) were applied to seeds of Anjasmoro soybean variety. The best accelerated aging method was then used to screen seed storability vigor of 23 soybean varieties. Seed storability vigor of 23 soybean varieties were detected using accelerated aging machine IPB 77-1 MM and each was compared with the seed storability vigor of those stored 10 weeks in controlled storage. Results of the experiment showed that using chemical or physical treatment on accelerated aging process were able to decrease seed vigor, but chemical treatment decreased seed vigor faster, more simple and more practical. Accelerated aging machine IPB 77-1 MM could also be used for screening varietal seed storability vigor of soybean using electrical conductivity test

METODE EKSTRAKSI DNA PADA Jatropha spp. TANPA MENGGUNAKAN NITROGEN CAIR / DNA Extraction Method of Jatropha spp. without Liquid Nitrogen

Physic nut is one of potential plant which produces biofuel. It is necessary to do an intensive breeding program either conventionally or molecularly based to develop new varieties of physic nut. All this time the physic nut DNA extraction methods always used liquid nitrogen to destroy the plant tissue. Liquid nitrogen is not always available, especially in remote areas. Physic nut has high latex content which makes extraction process more difficult. The aim of this study was to find the technique of DNA extraction which can give a good result without using liquid nitrogen. This research was conducted in Molecular Biology Laboratory, ICABIOGRAD Bogor from November to Desember 2015. There were five Jatropha species from Thailand which used in this research e.g. Jatropha curcas, Jatropha podagrica, Jatropha gossypifolia, Jatropha multifida, and Baliospermum solanifolium. The extraction method used modification CTAB by addition of PVP, sodium metabisulphite, sucrose and ascorbic acid. The young leaves were used as the part to be extracted. The results showed that the modified method could produce a good quality and quantity of DNA. The banding pattern of DNA amplification clearly visible under UV light. This method can reduce the dependency of liquid nitrogen. AbstrakEkstraksi DNA merupakan salah satu ta hap penting dalam kegiatan pemuliaan berbasis molekuler. Jarak merupakan salah satu tanaman dengan kandungan getah cukup tinggi sehingga proses ekstraksi DNA cukup sulit dilakukan. Selama ini metode ekstraksi yang dikembangkan umumnya menggunakan nitrogen cair untuk menghancurkan jaringan tanaman. Nitrogen cair merupakan senyawa yang cukup sulit untuk didistribusikan ke laboratorium yang letaknya jauh dari kota. Tujuan penelitian ini adalah untuk memperoleh teknik ekstraksi DNA jarak yang mampu menghasilkan DNA dengan kualitas dan kuantitas yang baik tanpa menggunakan nitrogen cair. Penelitian ini dilaksanakan di Laboratorium Biologi Molekuler, Balai Besar Penelitian dan Pengembangan Bioteknologi dan Sumberdaya Genetik Pertanian (BB Biogen), Bogor pada bulan November hingga Desember 2015. Terdapat lima spesies jarak asal Thailand yang digunakan pada penelitian ini yaitu Jatropha curcas, Jatropha podagrica, Jatropha gossypifolia, Jatropha multifida, dan Baliospermum solanifolium. Ekstraksi DNA dilakukan melalui modifikasi buffer CTAB melalui penambahan senyawa PVP, natrium metabisulfit, sukrosa dan asam askorbat. Bagian tanaman yang digunakan berupa daun yang masih muda. Hasil penelitian menunjukkan DNA jarak yang diekstraksi dengan metode ini mempunyai kualitas dan kuantitas yang baik serta mampu diamplifikasi dengan baik. Metode ini mampu mengurangi ketergantungan terhadap nitrogen cair yang ketersediaannya terbatas di laboratorium yang lokasinya jauh dari kota.Kata kunci: Jatropha spp., ekstraksi, DNA, nitrogen cai

Metode Ekstraksi Dna Pada Jatropha Spp. Tanpa Menggunakan Nitrogen Cair / Dna Extraction Method of Jatropha Spp. Without Liquid Nitrogen

Physic nut is one of potential plant which produces biofuel. It is necessary to do an intensive breeding program either conventionally or molecularly based to develop new varieties of physic nut. All this time the physic nut DNA extraction methods always used liquid nitrogen to destroy the plant tissue. Liquid nitrogen is not always available, especially in remote areas. Physic nut has high latex content which makes extraction process more difficult. The aim of this study was to find the technique of DNA extraction which can give a good result without using liquid nitrogen. This research was conducted in Molecular Biology Laboratory, ICABIOGRAD Bogor from November to Desember 2015. There were five Jatropha species from Thailand which used in this research e.g. Jatropha curcas, Jatropha podagrica, Jatropha gossypifolia, Jatropha multifida, and Baliospermum solanifolium. The extraction method used modification CTAB by addition of PVP, sodium metabisulphite, sucrose and ascorbic acid. The young leaves were used as the part to be extracted. The results showed that the modified method could produce a good quality and quantity of DNA. The banding pattern of DNA amplification clearly visible under UV light. This method can reduce the dependency of liquid nitrogen

Genetic Diversity Analysis Using Resistance Gene Analog-Based Markers to Support Morphological Characterization of Shallots

Shallot (Allium cepa var. aggregatum) is one of the most important vegetable crops grown in Indonesia. The limited knowledge available on the genetic diversity and the threat of plant disease have been major problems to maintain high shallot production in Indonesia. Development of molecular markers linked to disease resistance is required for molecular breeding activity in this crop. This study aimed to assess the genetic diversity at conserved domain of resistance gene analog (RGA) in a set of 36 Indonesian shallot genotypes to complement morphological characterization. Twelve morphological and fifteen molecular markers traits were investigated in an attempt to characterize and to discriminate the Indonesian shallots genotypes. Characterization at orphological level indicated that phenotypic variance was highest for total bulb weight (TWB, cv = 99.39%) and the least for the plant height (PH, cv = 28.16%). The correlation analysis between traits showed that TWB and number of bulb (NB), TWB and bulb weight per plant (WB), NB and WB, and WB and PH were positively correlated. Molecular analysis revealed a total of 1,512 alleles with an average of 1.946 alleles per locus. The Polymorphism Information Content (PIC) values ranged from 0.253 to 0.676 and six out of 15 RGA markers were highly informative with PIC values ≥0.50. Based on cluster analysis, the 36 Indonesian shallot genotypes were clearly discriminated into six major groups. These results revealed that the RGA-based markers could support the morphological characterization in evaluating the genetic diversity of shallots.

Analisis Keragaman Genetik Kedelai Introduksi Menggunakan Marka Mikrosatelit

Soybean (Glycine max (L.) Meriil) is an important crop next to rice and corn. The development of improved varietyare important to increase national soybean production. The introduced soybean varieties is one of genetic resourcesthat can be used to create improved soybean varieties. The aim of this study was to analyze 35 introduced soybeancultivars using 15 microsatellite markers. The research was conducted in ICABIOGRAD Molecular Biology Laboratory,in January-March 2016. PCR analysis was scored as binary data and the collected data was analyzed using NTSYS andPowerMarker. Specific morphological characters from each soybean cultivar determine the genetic diversity. Significantpositive correlations were identified among morphological characters which would be helpful to improve the desiredcharacter. The result showed that 189 alleles were detected with average of 12.6 alleles per marker. The polymorphismlevel (PIC) was 0.86 (0.76-0.95). There were 12 of total markers having PIC>0.80 indicating their robustness todiscriminating soybean cultivars. The average major allele frequency was 21% and ranges from 8% (Satt100) to 39%(Satt125). Five SSRs were able to distinguish heterozygosity which varied from 0.41 (SoyF3H) to 0.82 (Satt333). Thephylogenetic analyses showed that the 35 introduced soybean cultivars were grouped into two clusters (coefficient ofsimilarity 0.82) consisting of 13 and 22 cultivars according to each genetic background without considering its countryorigin. Both the microsatellite markers and genetic diversity information in this study could be useful to assist crossingstrategy with utilizing introduced genetic materials in future soybean breeding in Indonesia

Genetic Diversity of Jatropha spp. Germplasm Based on Morphological and Molecular Markers

Germplasm of Jatropha spp. with high genetic diversity is needed to develop a new superior variety of Jatropha spp. Morphological and molecular characterizations are important to support development of their superior hybrid varieties. The aims of this study were to identify Jatropha spp. accesion potential for genetic improvement using morphological characters and analyze their genetic diversity using SSR markers. A total of eight genotypes of Jatropha spp. originated from several localities in Indonesia and Thailand was observed. Results showed that accessions of Jatropha spp. were varied in morphological and molecular characters. Based on principle component analysis, characters of stem color, leaf veins, leaf shapes, flower position, total branch number, productive branch number, petiole color, and petal color contributed most to the total diversity. Based on oil seed content, potential accessions identified for further genetic improvement were J. podagrica (34.63%) and J. curcas (29.64%). The results of molecular analysis showed that high allele variation (3–7 alleles) was observed among Jatropha spp. accessions with an average allele number of 4.12 and the average Polymorphism Information Content (PIC) value was 0.57 (0.46–0.77). Three SSR markers showed PIC value >0.5 indicating that these markers were informative for genetic diversity detection of Jatropha spp. The phylogenetic analysis showed that seven accessions of Jatropha spp. could be divided in two groups at similarity coefficent of 0.53. Results of genetic diversity analysis in this study should be useful for proper identification and selection for appropriate parents to assist in breeding of Jatropha spp. in Indonesia

Keragaman Genotipik dan Fenotipik 48 Aksesi Kedelai Introduksi Asal Cina

Sebagai salah satu komoditas tanaman pangan penting di Indonesia setelah padi dan jagung, kedelai memerlukan upaya peningkatan keragaman genetik dengan cara introduksi aksesi dari negara lain terutama Cina sebagai salah satu negara asal kedelai di dunia. Marka simple sequence repeat (SSR) dapat digunakan untuk analisis keragaman genetik antaraksesi kedelai introduksi. Tujuan penelitian ini adalah mempelajari keragaman genotipik dan fenotipik 48 aksesi kedelai introduksi asal Cina menggunakan 15 marka SSR. Analisis DNA dilakukan menggunakan PCR dan data hasil PCR menggunakan marka SSR dianalisis menggunakan perangkat lunak XLSTAT, NTSYS, dan PowerMarker. Data karakter morfologis diperoleh dari basis data Germplasm Resources Information Network (GRIN), United States Department of Agriculture (USDA) (www.ars-grin.gov). Data ini digunakan sebagai data keragaman fenotipik yang diperlukan untuk menunjang hasil karakterisasi molekuler. Hasil penelitian menunjukkan bahwa terdapat keragaman karakter morfologis dan molekuler antaraksesi kedelai yang dipelajari. Berdasarkan hasil analisis komponen utama, karakter tinggi tanaman, bobot 100 biji, hasil biji, warna pusar biji, warna trikoma, warna bunga, dan warna polong berkontribusi besar terhadap keragaman total. Analisis molekuler menggunakan marka SSR menunjukkan bahwa terdapat variasi alel yang cukup tinggi (9–25 alel) di antara aksesi kedelai dengan rerata jumlah alel 15,6, sedangkan rerata nilai Polymorphism Information Content (PIC) sebesar 0,89 (0,84–0,94). Seluruh marka SSR memiliki nilai PIC>0,5 yang menunjukkan bahwa marka tersebut informatif untuk studi keragaman genetik kedelai dengan rerata nilai diversitas gen sebesar 0,90. Hasil analisis filogenetik dan analisis koordinat utama menunjukkan bahwa 48 aksesi tersebut mengelompok menjadi tiga dengan koefisien kemiripan 0,84. Pada penelitian ini dilakukan pula uji asosiasi antara marka SSR dan karakter morfologis. Asosiasi yang signifikan ditemukan pada tujuh lokus marka SSR. Persentase keragaman total yang dapat dijelaskan oleh marka SSR tersebut, yaitu 17,25–78,45%. Marka GMES2225 dan Sat_286 berasosiasi dengan warna kulit biji, sedangkan marka GmF35H berasosiasi dengan tinggi tanaman. Informasi keragaman genetik akan sangat bermanfaat sebagai langkah awal untuk kegiatan seleksi tetua persilangan dengan sifat yang diinginkan dalam membantu program pemuliaan kedelai di Indonesia