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Identifikasi famili gen putatif penyandi protease inhibitor dengan pendekatan in silico komparatif pada genom Hevea brasiliensis Muell. Arg (Identification of putative gene family encoding protease inhibitors by in silico comparative analysis in Hevea brasiliensis Muell. Arg genome) Irfan MARTIANSYAH; Riza Arief PUTRANTO; Nurul KHUMAIDA
Menara Perkebunan Vol. 85 No. 2 (2017): 85 (2), 2017
Publisher : INDONESIAN OIL PALM RESEARCH INSTITUTE

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22302/iribb.jur.mp.v85i2.257

AbstractProtease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].

Peranan GA3 terhadap Kerontokan dan Kualitas Buah Jeruk Pamelo Berbiji dan Tidak Berbiji Kalsum, Ummu; Slamet Susanto; Ahmad Junaedi; Nurul Khumaida; Heni Purnamawati
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 49 No. 3 (2021): Jurnal Agronomi Indonesia
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

Kerontokan buah sering terjadi dan menyebabkan rendahnya panen buah. Informasi penggunaan hormon GA3 dalam menekan kerontokan buah pada jeruk pamelo masih belum tersedia. Riset ini bertujuan untuk mengkaji peranan GA3 terhadap kerontokan dan kualitas buah jeruk pamelo berbiji dan tidak berbiji. Penelitian ini dilaksanakan pada Desember 2019 sampai Juni 2020 di Desa Tambakmas, Kecamatan Sukomoro Kabupaten Magetan. Desain percobaan menggunakan rancangan tersarang, dimana faktor utama adalah kultivar (Bali Merah 1 dan Bali Merah 2) dan faktor tersarang adalah penyemprotan GA3 (tanpa disemprot GA3, penyemprotan GA3 pada 1 minggu setelah antesis (MSA) dan penyemprotan GA3 pada 1 dan 3 MSA). Bali Merah 1 tergolong pada pamelo berbiji, sedangkan Bali Merah 2 adalah pamelo tidak berbiji. Peubah pengamatan meliputi konsentrasi GA3 buah pada 4, 5, dan 6 MSA, final set, jumlah buah rontok, bobot dan diameter buah, bagian dapat dimakan (BDD), padatan terlarut total (PTT), asam tertitrasi total (ATT), rasio PTT/ATT dan vitamin C. Hasil menunjukkan bahwa penyemprotan GA3 meningkatkan final set namun tidak memberikan pengaruh nyata pada bobot buah, diameter buah, ATT, rasio PTT/ATT dan kandungan vitamin C. Penyemprotan GA3 pada 1 dan 3 MSA menekan jumlah buah rontok serta meningkatkan konsentrasi GA3 buah pada 4, 5, dan 6 MSA, BDD dan PTT buah. Kata kunci: asam tertitrasi total, final set, padatan terlarut total, Vitamin C

Adaptasi Tanaman Kedelai Terhadap Intensitas Cahaya Rendah : Karakter Daun untuk Efisiensi Penangkapan Cahaya La Muhuria; Kartika Ning Tyas; Nurul Khumaida; , Trikoesoemaningtyas; Didy Sopandie
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 34 No. 3 (2006): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

This research was conducted to identify some leaf characters related to light capture efficiency. It used split plot design with sub plot nested at the main plot. The main plot was light intensity consisted of two levels: I100 = light intensity 100% and I50 = light intensity 50%, while the sub plot was soybean genotype consisted of G1 = Pangrango, G2 = Ceneng, G3 = Godek, and G4 = Slamet. Leaf characters measured were : leaf total area, specific leaf area, trifoliate leaf area, leaf hairs (trichome) density, leaf thickness, length of palisade, chlorophylls content (chlorophyll a, b, and ratio a/b), and the greenness intensity. The result of research indicated that Ceneng has lower total leaf area, higher specific and trifoliate leaf area, less leaf hair density, thinner leaf, shorter palisade, higher greenness intensity, higher chlorophyll content (a and b), and also lower ratio chlorophyll a/b. Key words: Light capture efficiency, light intensity, tolerant genotype, sensitive genotype, soybean

Karakter Morfo-Fisiologi Daun, Penciri Adaptasi Kedelai terhadap Intensitas Cahaya Rendah , Kisman; Nurul Khumaida; , Trikoesoemaningtyas; , Sobir; Didy Sopandie
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 35 No. 2 (2007): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

The main objective of this study was to identify the leaf morpho-physiological characters as markers for adaptation of soybean to low light intensity. The field experiment was conducted using split plot design with 3 replications. First factor was soybean genotype consisted of shade tolerant genotypes (Ceneng, Pangrango) and sensitive genotypes (Godek, Slamet). Second factor was low light intensity consisted of: L0 = control (under full sun light), L1 = 5 days under 50% shading (exposed after 21 days after planting/DAP), L2 = 5 days under dark condition (exposed after 21 DAP), L3 = 3 days 50% shading + 5 days sun light (exposed after 18 DAP), dan L4 = 3 days 50% shading + 3 days sun light + 5 day dark conditions (exposed after 15 DAP). The 50% shading was made artificially using black plastic paranet with 50% light transmitted. Results of this study showed that under the conditions of low light intensity, leaf morpho-physiological characters of soybean that could be used as markers for adaptation were leaf area, specific leaf weight, and chlorophyll content. Leaves of shade tolerant genotypes were wider and thinner and also contained higher chlorophyll especially for chlorophyll b than that of shade sensitive genotypes under low light intensity. Key words : Low light intensity, tolerant genotype, leaf area, chlorophyll, specific leaf weight

Pola Pewarisan Adaptasi Kedelai (Glycine max L. Merrill) terhadap Cekaman Naungan Berdasarkan Karakter Morfo-Fisiologi Daun , Kisman; , Trikoesoemaningtyas; , Sobir; Nurul Khumaida; Didy Sopandie
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 36 No. 1 (2008): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

The objective of this study was to analyze the inheritance pattern of soybean adaptation to shade stress based on leaf morpho-physiological characters. Genetic materials used in this study consisted of 22 plants of low irradiance (LI)-tolerant genotype (Ceneng) and 22 plants of LI-sensitive genotype (Godek); 21 plants of F1 (Ceneng x Godek); and 114 plants of F2 populations (derived from F1). These populations were planted under shading of paranet 50%. The population was arranged in a Randomized Complete Block Design with two replicates. Analysis of inheritance of soybean adaptation involved estimation of heritability (broad sense) and gene action. Results of this study showed that: adaptation of soybean to low light stress based on characters of yield per plant was highly heritable (68% of broad sense) with partial dominant mode of action. Characters of leaf area and specific leaf weight were highly (68% of broad sense) and moderately (48% of broad sense) heritable, respectively, with additive mode of action. Soybean adaptation based on leaf physiological characters (chlorophyll contents) was highly heritable (70% - 86% of broad sense) in epistatic mode of action. Key words: Soybean, leaf morpho-physiological character, heritability, gene action

Perbaikan Teknik Kultur Embrio Kelapa Kopyor (Cocos nucifera L.) Asal Sumenep Jawa Timur Melalui Penambahan Bahan Aditif dan Pengujian Periode Subkultur , Sukendah; , Sudarsono; , Witjaksono; Nurul Khumaida
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 36 No. 1 (2008): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

The success of culturing of "Kopyor" coconut (matured coconut with broken meat particles due to abnormal formation of endosperm) through embryo culture depends on the medium used. A revised protocol on medium embryo culture was done to increase embryo germination and plantlet production of kopyor coconut obtained from Sumenep. Embryos excised from mature nuts were cultured in solid Eeuwens basal media supplemented with 150 ml coconut water, 150 ml coconut milk, 50 mg/l thio-urea, and 100 mg/l thio-urea. Germinating embryos were transferred to solid Eeuwens basal media containing 100, 150, and 200 ml/l coconut water. Subsequent transfers of the germinating embryos to fresh media to complete seedling development were done at different periods of subculture, i.e., 1, 2, 3, and 4 months. The highest viability of kopyor embryo was shown by 150 ml/l coconut water, about 95% embryos in this medium germinated. At plantlet phase, addition of coconut water did not give a positive result to the growth of kopyor plantlets. However, coconut water could increase the complete plantlet, i.e., plantlet with shoot and good root. Growth and number of kopyor plantlets obtained were the best when the plantlets transferred into fresh medium every 2 months. Key words: Embryo culture, kopyor coconut, additive agents, period of subculture

Aktivitas Kitinase dan Peroksidase dari Ekstrak Protein Daun, Akar, Kalus dan Tunas In Vitro Trichosanthes tricuspidata Lour. Dewi Sukma; Roedhy Poerwanto; , Sudarsono; Nurul Khumaida; Suryo Wiyono; I Made Artika
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 36 No. 1 (2008): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

A number of Trichosanthes species has been reported as a source of bioactive protein associated with defense mechanisms such as chitinase. Chitinase and peroxidase of crude protein extracted from leaves, roots, in vitro calli and shoots of T. tricuspidata had been analysed. Calli were induced on MS medium containing combinations of 1 µM NAA + 1 µM BA (K1), 2 µM NAA + 2 µM BA (K2), 3 µM NAA + 3 µM BA (K3), or 4 µM NAA + 4 µM BA (K4). Shoots were cultured in MS with 1 mg/l of BA, while leaves and roots were harvested from six-month old plants grown on the field. Results of the experiment suggested that K1-K4 medium could be used to induce calli although weight of calli from all medium composition was not significantly different (0.19-0.31 g/explant/4 weeks). Calli from K1 medium had the highest of total crude protein content (3.24 mg/ml). The highest of chitinase activity was found in in vitro shoots (6.51 mM pNP/hour/mg protein) and the highest peroxidase activity was in the plant roots (0.25 ∆ 420/minute/mg protein). Key words: in vitro calli, shoots, crude protein, chitinase and peroxidase activities

Pembentukan Galur Haploid Ganda Padi Gogo dengan Sifat-Sifat Tipe Baru melalui Kultur Antera Reny Herawati; Bambang S. Purwoko; Nurul Khumaida; Iswari S. Dewi; Buang Abdullah
Jurnal Agronomi Indonesia (Indonesian Journal of Agronomy) Vol. 36 No. 3 (2008): Buletin Agronomi
Publisher : Indonesia Society of Agronomy (PERAGI) and Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, Indonesia

The breeding of upland rice with New Plant Type characters in relatively short time can be done by using anther culture technique. The technique has been recognized as a rapid and efficient technology for crop improvement. Plant materials used in this research were F1 crossing P1 (Fatmawati x Way Rarem), P2 (Fatmawati x SGJT-28), P3 (Fatmawati x SGJT-36), P4 (Way Rarem x Fatmawati), P5 (SGJT-28 x Fatmawati), and P6 (SGJT-36 x Fatmawati). Media for calli induction (N6) and regeneration (MS) were according to Dewi methods (2003). The results of this study indicated that P3 (Fatmawati x SGJT-36) and P6 (SGJT-36 x Fatmawati) from resiprocal crosses gave better response in anther culture than the others crosses for their calli induction and green plant regeneration. From the six F1 crosses, 348 (53.5%) spontaneous doubled haploid (DH) pure lines were obtained, six lines from Farmawati x Way Rarem, 13 lines from Fatmawati x SGJT-28, 187 lines from Fatmawati x SGJT-36, three lines from Way Rarem x Fatmawati, five lines from SGJT-28 x Fatmawati, and 134 lines from SGJT-36 x Fatmawati. These lines should be evaluated and characterized for their agronomical and morphological traits. Key words: Anther culture, doubled haploid, callus induction, green plant regeneration

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