bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of soybean (Glycine max [L.] Merr.) mutants and improved varieties having diverse drought tolerance character using SSR marker
Authors: Nugroho K , Kosmiatin M , Husni A , Tasma I M , Lestari P 
Published: May 2020

Abstract
Global climate change has a huge impact on the agricultural world. The water scarcity that happened in some areas can lead to decreased food production, including soybean in Indonesia. Indonesia has a number of soybean genotypes with diverse drought tolerance which have been obtained using various approaches and could be one of the alternatives in responding to the problem. This study aimed to identify soybean mutant genotypes generated from in vitro selections and improved varieties using Simple Sequence Repeat (SSR) markers. A total of 10 mutant lines and 20 improved varieties from Indonesia were genotyped using 10 SSR markers adopted from literatures and ten newly designed SSR markers. The research was conducted in ICABIOGRAD molecular biology laboratory from November 2017 to February 2018. The amplicons were scored as binary data and analyzed using NTSYS and PowerMarker softwares. The new SSR markers were designed based on the variants searched from the IAARD genome database (www.genom.litbang.pertanian.go.id) and showed unambiguous amplicons. The results showed that adopted SSR markers were able to detect more alleles, a higher range of major allele frequency, gene diversity, heterozygosity and Polymorphism Information Content (PIC) compared to the newly designed markers. Phylogenetic analysis showed that all of the soybean mutants were grouped in the same cluster with the parent (Sindoro). This molecular marker-based information of soybean mutants along with the improved varieties in this study could be useful for assisting breeding strategy in screening parental lines to develop drought tolerant soybean varieties in the future.
Diversity analysis in soybean (Glycine max [L.] Merrill) mutant lines grown in saline soil using agronomic traits and RAPD markers
Authors: Agam M G S A S , Kusmiyati F , Anwar S , Herwibawa B 
Published: May 2020

Abstract
Soybean is one of the strategic food crops in Indonesia, but its production is far below the demand due to inadequate area for soybean cultivation. Shifting soybean cultivation to marginal land such as saline soil has been suggested as a realistic solution to increase soybean production. Development of soybean variety tolerant to salinity is the key step to support the cultivation of soybean in saline soil. The objective of this research was to evaluate the genetic diversity in mutant soybean lines generated using gamma rays based on agronomic traits and RAPD markers. A total of 200 irradiated seeds of cultivar Detam-3 were planted in saline soil with electrical conductivity of 1.2–4.3 dS/m. Agronomic traits were evaluated on plants until harvesting time. Genetic analysis using two RAPD markers (OPAA-02 and OPAA-14) was done on 11 plants of each radiation treatment. The results showed that 54 plants survived in saline soil. High level of variation based on agronomic traits was observed in these plants. RAPD analysis revealed 60% and 83.3% polymorphism among 11 plants for OPAA-02 and OPAA-14 markers, respectively.
Targeted mutation of GA20ox-2 gene using CRISPR/Cas9 system generated semi-dwarf phenotype in rice
Authors: Santoso T J , Trijatmiko K R , Char S N , Yang B , Wang K 
Published: May 2020

Abstract
Recently, the engineered CRISPR/Cas9 system has been applied to rapidly and efficiently modify the targeted gene(s) in a wide variety of plants. Recent studies of successful targeted mutagenesis using the CRISPR/Cas9 system with a single gRNA expression in rice plants have been reported. GA20ox-2 is a gene encoding an oxidase enzyme involved in the biosynthesis of gibberellin and linked to sd1 locus. A previous study revealed that mutation of this gene resulted in shorter stature of rice plant due to defects in the gibberellin’s signalling pathway. Here, we studied targeted mutation of OsGA20ox-2 gene in rice using the CRISPR/Cas9 system with the expression of two gRNAs. In this study, we introduced a single plasmid vector of CRISPR/Cas9 system harboring dual gRNAs to modify OsGA20ox-2 gene in a rice model cv. Kitaake via Agrobacterium-mediated transformation. Targeted mutagenesis of OsGA20ox-2 gene using CRISPR/Cas9 generated nine mutated rice lines with a mutation frequency of 90%. Most mutated lines (50%) had mutations in both OsGA20ox-2 gRNA. They resulted in homo-diallelic mutation type with 44 bp deletion, while three lines were heterozygous, one line was homo-diallelic with 2 bp insertion, and one line had no mutation. The K15 mutated rice line was identified as a homozygous two-nucleotide insertion and had the semi-dwarf phenotype, demonstrating that OsGA20ox-2 gene had been disrupted.
Transformation using RNAi technology for developing potato lines resistance to late blight (Phytophthora infestans)
Authors: Listanto E , Riyanti E I , Ambarwati A D 
Published: May 2020

Abstract

Phytophthora infestans (Mont.) de Bary causes late blight, a major disease of potato and tomato that causes production loss at about 10–100% in Indonesia. Breeding for late blight resistance in potato has been carried out in this country to minimize fungicide application. The objective of this study was to generate potato lines resistant to P. infestans through RNAi method. A series of studies were conducted, including confirmation of RNAi construct insertion in Agrobacterium tumefaciens and PCR analysis, transformation of two potato cultivars using A. tumefaciens carrying the RNAi fragment, in addition to selection and molecular analysis of selected plantlet using Polymerase Chain Reaction (PCR). The RNAi plasmid construct was confirmed via PCR analysis using specific primers for 35s and Tnos fragment, and resulted in 500 bp and 250 bp for fragment of 35s and Tnos, respectively. Transformation was performed on 733 Granola’s internode explants and 569 Atlantic’s internode explants. The transformation process produced 282 explants from Atlantic, while Granola did not produce any transformants. The level of transformation efficiency of Atlantic on selection medium containing hygromycin was 49.61%. Following regeneration step, the 282 selected explants produced 167 plantlets. Based on PCR reaction using specific primers for hpt gene, 14 plantlets were PCR positive and contained hpt fragment. Overall, Agrobacterium tumefaciens-mediated transformation on potato internode explants was successful. Therefore, the selected transformants should be further tested using bioassay for resistance to P. infestans.
Genetic resources management of local tidal rice in Riau province
Authors: Sinaga P H , Yunita R , Sutrisna N 
Published: May 2020

Abstract
There are at least 19 major groups of local tidal rice cultivars distributed in Pelalawan District which were not pure. This study aimed to report the progress of collaboration research among Riau AIAT, Pelalawan District Government and farmers has developed in situ and ex situ conservation of the local tidal rice cultivars from the year 2007 to 2018. Positive mass selection in Karya population has resulted in KN1-79 line with a yield potential of 6.74 t/ha dry milled grain (DMG), whereas in Cekau population has resulted in C1/KB line with a yield potential of 8.60 t/ha DMG. KN1-79 and C1/KB line have been released as Karya Pelalawan variety and Cekau Pelalawan variety, respectively. Both varieties have been registered by Center of Plant Variety Protection. The drawback of these local cultivars is late in maturity. Karya Pelalawan was crossed to Fatmawati and produced varieties Bono Pelalawan and Mendol Pelalawan which have early maturity character. Cekau 34 was crossed with Cisantana and produced Inpara Pelalawan with new characters such as early maturing, aromatic grain and tolerant to iron toxicity and salinity. Participatory plant breeding has promoted the released varieties to be widely and rapidly distributed as well as easily accepted by farmers. By promoting the ownership of local cultivars to the local government, local cultivars could be as a regional identity. Thus, it has been shown that Pelalawan District Government was actively involved in the development of released cultivars derived from local rice cultivars.
The use of specifically adapted genetic resources for regional economic development
Authors: Moeljopawiro S 
Published: May 2020

Abstract
Genetic resources are essential sources for further varietal improvement as well as directly used of their products due to their prime quality product in a particular region but not in other regions. Genetic resources grown for some time in a region probably have been improved their adaptability to the environment. The resourses could be used to develop new varieties adapted to a specific location. If every region has that kind of variety, it will, in turn, improve national productivity of that commodity. Besides, genetic resources having specific adaptability to a specific location and producing a prime quality needed by the consumer may also be useful to boost the economy of that particular region. This kind of products is generally known as the Geographical Indication (GI) products. A GI must identify a product as originating in a given place. Examples of products protected with GI that improve the local economy are: (1) GI Kintamani arabica coffee which before the protection involving 40 groups of farmers (1,750 workers), the price of coffee IDR 25,000.00/kg. After the protection, the farmers’ groups become 60 involving 2,640 workers and the price increase to IDR 75,000.00/kg, (2) Muntok white pepper, the price after protection is IDR 170,000.00/kg, whereas the price before protection was IDR 40,000.00/kg. The use of genetic resources in varieties improvement required a tremendous amount of effort and funds, while GI required effort in maintaining quality of products and funds for the promotion of product.
Genetic diversity of red rice varieties originating from West Java and Banten based on SSR marker related to palatability
Authors: Susiyanti  , Nurmayulis  , Eris F R , Kartina A M , Maryani Y , Aryani T 
Published: May 2020

Abstract
West Java and Banten Provinces have diverse local red rice varieties/accessions to support national food security, not only in terms of quantity but also the quality of rice. Good eating quality is closely related to palatability. Palatability is a property that is directly related to the quality of rice feeding, aroma, appearance, taste and texture. This study aimed to analyze the genetic diversity and DNA fingerprint profiles of local red rice accessions from West Java dan Banten using molecular markers related to palatability. A total of 12 red rice accessions and four local red rice accessions from Banten and West Java Provinces were estimated their genetic diversity, respectively. The SSR primers used were Ams (linked with aspartate aminotransferase), GPA (glucosamine-fructose-6-phosphate aminotransferase), GBSS1 (granule-bound starch synthase), CBG (nano cyanogenic β-glucosidase), SS1 (starch synthase), SBE1 (glucosidic linkage of a-polyglucan), RM510 (gel consistency), RM13 (protein content) and RM410 (aromatic). The dendrogram showed two main groups of red rice accessions. The first group consisted of Mayang, Tambleg, Sengkeuhan, Pare Jaketra, Jalawara Hawara, Gadok, Carogol, Beureum Batu, Waren, Segubal, Tampai Beureum and Leger Pondok (similarity reached 80.5%). The second group consists of Kapundung, Cere Beureum and Cireh Hideung with a similarity of 79.5%.
Tiller profile diversity of upland rice germplasm in ICABIOGRAD gene bank
Authors: Afza H , Andarini Y N , Risliawati A 
Published: May 2020

Abstract
Tillering ability is an important agronomic trait that determines the yield of rice. Tiller type in rice is categorized as primary, secondary and tertiary tiller which produces panicle at generative phase. Tillering ability as well as the tiller type varies between varieties, especially among germplasms. Our study aimed to identify the tiller profile diversity of upland rice germplasm in ICABIOGRAD Genebank. A total of 100 accessions of local upland rice varieties were planted in a randomized completely block design with two replications under greenhouse condition. The number of tiller from each type was observed weekly from 35 to 63 days after sowing (DAS). The result of the study showed that the number of primary tiller increased slowly from 35 DAS until 63 DAS. After 49 DAS there was no significant addition in secondary tiller number. Generally, the average mean number of tertiary tiller accross the accessions was far below compared to the number of primary and secondary tiller. The highest number of primary tiller, i.e. 8, was expressed by Pae Daye Indolobye (North Sulawesi), Padi Pulut Pute Iteung (East Kalimantan) and K. Puyuk (Central Kalimantan). Up to 22 secondary tillers were formed by Gadabung, a local upland rice variety from Central Kalimantan. Information on tillering ability of local upland variety will benefit rice breeder for selecting appropriate accessions as a gene source for breeding.
Development of physical color reference for Indonesia paddy collection
Authors: Hidayatun N , Sabran M , Ramadhani A , Widaningsih N A 
Published: May 2020

Abstract
One of the objectives of genebank management is to maintain the genetic identity of its collection. In order to maintain the genetic identity, it is important to check new seed against a reference collection. A simple morphological character for determining the reference collection is the color of lemma and palea. Lemma and palea is a pair of bract-like organ in the floret and have similar pattern of pigmentation and therefore can be treated together. The color of lemma and palea determine the seed color. To develop reference collection for grain color characterization of rice germplasm in the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) Genebank, 1,000 sample of seeds produced from different year of regeneration are characterized based on the lemma and color categories of the IRRI guidelines for the characterization and evaluation system. Samples of each category were then arranged and photographed. From 11 categories of lemma and palea color described in the guidelines, there are six color categories available from genebank rice collection, whereas five color categories were not found. The six available color categories were straw, golden, brown spot in the straw background, brown line in the straw background, brown, orange-brown and black. Five color categories were not found in the collections i.e. red-purple, purple spots on straw, purple line on straw, purple and white. This material reference could be used for characterization of Indonesian rice. The seeds of the absent categories might need to be aquisitated to the genebank to complete the reference collection.
The performance of growth and yield component of soybean varieties in Margodadi village, Ambarawa sub-district, Pringsewu regency, Lampung province, Indonesia
Authors: Mustikawati D R , Endriani  
Published: May 2020

Abstract
Efforts to increase soybean production require superior varieties which are stable in every agroecology production center. Therefore, it is necessary to perform field evaluation of several new released soybean varieties. The aim of this study was to evaluate the growth and yield potential of soybean varieties developed by Indonesian Legume and Tuber Crops Research Institute (ILETRI) Malang in a field experiment. Four soybean varieties (Devon 1, Dering 1, Gema and Gepak Kuning) were sown in Margodadi Village, Ambarawa Sub-district, Pringsewu Regency, Lampung Province, Indonesia from May to August 2017. Plots were arranged in randomized complete block design with six replicates. The variables observed were crop emergence at 7 DAS sowing, plant height and number of pods at harvest, pest attack on 1-month-old plants and at harvest, and seed yield. The results showed that Gepak Kuning gave the highest yield (2.13 t/ha), which indicated that this variety is suitable to be planted and developed in the location of the study.
Inventory and morphological characterization of local upland rice in the highlands of South Sumatra province
Authors: Sasmita P , Kodir K A 
Published: May 2020

Abstract
South Sumatra has various types of local rice in various agroecosystems that have the potential as plant genetic resources (PGR) of food crops. At present, the existence of the PGR has been diminished due to genetic erosion. Inventory and characterization of local rice genetic resources were carried out in the highlands of South Sumatra during 2014–2017. The study was conducted in Muara Enim, Ogan Komering Ulu, Pagar Alam, and Lahat Regencies. The objective of the study was to inventory and characterize the PGR. The method used was exploration and desk study. Purposive sampling was applied. Morpho-agronomic characterization was carried out in situ and ex situ. Morphological observations were carried out by visually observing the parts of leaves, stems, panicles and unhulled seeds of the rice accessionsin the location. Morphological characteristics were analyzed descriptively by tabulation. Inventory result showed 17 varieties of local upland rice were spread across four regencies. Local upland rice varieties originating from the regencies with different biophysical characteristics showed differences in morphological characteristics. Among the 17 local varieties, 3 varieties were characterized, namely Setangkai, Barokah and Ayek Keruh. Morpho-agronomic characterization results showed that there was a high diversity of rice accessions collected from different locations in South Sumatra.
Characterization of 337 exon-based single nucleotide polymorphisms (SNPs) unique to the Indonesian soybean varieties
Authors: Tasma I M , Satyawan D , Rijzaani H 
Published: May 2020

Abstract
Genome resequencing of five Indonesian soybean varieties resulted in a total of 2,597,286 single nucleotide polymorphisms (SNPs), 257,598 insertions, and 202,157 deletions. Out of those SNPs, only 95,207 (2.15%) were located in the protein-coding region (exon). The objective of this study was to characterize 337 exon-based SNPs unique to the Indonesian soybean varieties. The study was conducted by taking SNP samples located in the exons using criteria of gene fragments containing the SNPs that were sequenced at least five times within each of the soybean varieties. Out of 95,154 gene-based SNPs detected, only 337 SNPs met the criteria. Each of the soybean varieties was genotyped with the 337 SNP loci, and the genotypic data were scored and analyzed. Results showed that 59 SNPs were common to all five soybean genotypes. A total of 43, 41, 25, 32 and 28 SNPs loci were unique to soybean genotype Davros, Grobogan, Malabar, Tambora and B3293, respectively. These unique SNPs can function as DNA fingerprints for each variety. Out of 59 common SNPs, 24 SNPs were mutations that change the amino acid sequence of the encoded proteins. These genes with amino acid change may have high economic values such as those controlling soybean adaptation in tropical climate, photoperiod insensitivity, disease and insect resistance genes. Expression analyses of the genes with amino acid change showed variation in the expression pattern across different soybean tissues. Functional genomic analysis is necessary to isolate genes useful for breeding purposes.
Utilization of trichoderma sp. and pseudomonas fluorescens as biofertilizer in shade-resistant soybean
Authors: Miftahurrohmat A , Sutarman  
Published: May 2020

Abstract
This study aims to obtain Trichoderma fungi and Pseudomonas fluorescens bacteria obtained from soybean planting fields and test their ability as biofertilizer agents to assist soybean growth until the end of the vegetative phase. From the soybean crop field, Trichoderma fungi and P. fluorescens (Pf) were isolated. After purification, observations were made to determine morphological physical characteristics both macroscopically and microscopically. Pf bacterial isolates were tested for their performance characteristics to ensure that bacteria were not pathogenic. For work power testing, as a biofertilizer agent, a factorial experiment was prepared in a completely randomized design (CRD). As the first factor, Trichoderma consists of without and with Trichoderma, while the second factor is Pf bacteria consisting of without and with Pf. The experiment was repeated four times so that 16 experimental units were obtained. The variables observed were plant height, number of leaves, stem diameter, and time of initial average flower appearance. Data were analyzed by ANOVA followed by HSD testing on a 5% test tarf. The results showed that the fungi Trichoderma sp. obtained by having single-celled, smooth-walled conidia measuring 3.2 x 2.0 µm, green with irregular upright hyaline conidiophores. As for P. fluorensence does not cause foul symptoms in test potatoes which are non-pathogenic. Fungi Trichoderma sp. TC-Jro-02 isolates and Pseudomonas fluorescens bacteria which were applied as biofertilizer agents were each increasing and inhibiting growth in plant height, leaf number, stover dry weight, and dry weight of soybean root of Dena varieties grown in shade up to 30 days after planting. Interactions between them affect the dry weight of stover and the dry weight of plant roots. The bacterial activity of Pseudomonas fluorescens inhibits the effect of the performance of Trichoderma fungi in supporting the growth of soybean plants in the shade.