Indonesian Rice Cultivars Research Articles

Identifying Single Nucleotide Polymorphisms (SNPs) in <i>OsFER1</i> and <i>OsFER2</i> Genes Linked to Iron accumulation in Pigmented Indonesian Rice (Oryza sativa L.)

Iron (Fe) is an essential micronutrient for the well-being of plants, animals, and bacteria. In plants, iron plays a pivotal role in a myriad of metabolic processes, encompassing redox reaction, photosynthesis, respiration, chlorophyll synthesis, and nitrogen fixation. For humans, iron is indespensable for several metabolic functions, particularly in the synthesis of haemoglobin. Iron deficiency can lead to health issues on a global scale, therefore identifying key crops, such as rice for providing sufficient iron in diet intake is very important. In rice, the maintenance of iron homeostasis is orchestrated by various genes, with OsFER1 and OsFER2 acting as iron accumulator genes in leaves, stems, flowers, and grains. The primary objective of this study was to ascertain the single nucleotide polymorphisms (SNP) in the OsFER1 and OsFER2 and to assess the iron content in Indonesian local rice cultivars. To achieve this, we examined partial sequences of OsFER1 and OsFER2 to identify SNPs in the Indonesian rice cultivars used (Cempo Ireng, Pari Ireng, Hitam Kalsel, Merah Pari Eja, and Ciherang). Concurrently, the iron content in the seeds was quantified using Atomic Absorption Spectrophotometry (AAS). The analysis revealed that the OsFER1 gene sequence, specifically exon 5, exhibited a SNP in the form of a transition. In contrast, the OsFER2 gene sequences, specifically in intron 2 displayed SNPs in the form of insertions. Notably, the iron content in the seeds was highest in Cempo Ireng (black rice), while it was lowest in Merah Pari Eja (red rice) and Ciherang (non-pigmented rice). Importantly, the identified SNPs in these partial gene sequences did not exert any discernible influence on iron levels or the formation of ferritin protein.

Anatomical characteristics of the upland local Indonesian rice cultivars as structural protection against drought

Anatomical characteristics of the upland local Indonesian rice cultivars as structural protection against drought

Exogenously applied Casuarina equisetifolia leaf extracts act as an osmoprotectant on proline accumulation under drought stress in local rice from Indonesia.

The effects of exogenously supplied osmoprotectants in crops have not yet been extensively studied. In this study, an osmoprotectant containing a high concentration of proline (2.5g mol-1 FW) was obtained from a Casuarina equisetifolia leaf extract. The effect of the extract was evaluated in local Indonesian rice cultivars Boawae Seratus Malam (BSM), Gogo Jak (GJ), Situ Bagendit (SB) (drought-tolerant), Kisol Manggarai (KM) and Ciherang (drought-susceptible) cultivars under drought at the morphological, physiological, and genetic levels. Under drought, the KM showed an increased level of OsWRKY, OsNAC, OsDREB1A, and OsDREB2A expression after application of the osmoprotectant, leading to the activation of proline synthesis genes including OsP5CS1, OsP5CR, and OsProDH, while the tolerant cultivars (BSM, GJ, and SB) showed no difference. The content of chlorophyll, carotenoids, anthocyanins, ascorbate peroxidase, catalase, and superoxide dismutase activities also increased in GJ and KM, during drought stress and applied osmoprotectants, but remained low in the BSM. We conclude that the foliar application of osmoprotectants derived from C.equisetifolia caused an accumulation of proline in susceptible plants. The existence of these extracts stabilizes leaf cells and supports photosynthetic compartments and carbon assimilation in plants, leading to growth.

The shifting genetic diversity pattern of Indonesian rice improved varieties from 1943-2019 based on historical pedigree data

Abstract. Anas, Damayanti F, Kadapi M, Carsono N, Sari S. 2022. The shifting genetic diversity pattern of Indonesian rice improved varieties from 1943-2019 based on historical pedigree data. Biodiversitas 23: 4649-4656. For rice plants in Indonesia, stagnation in increasing crop yields due to a reduction in genetic diversity is a significant issue. The issue of using the same parents in breeding programs and consumer preferences for a single main variety are among the causes of the narrowing of rice plants' genetic diversity. The purpose of this study is to figure out which ancestors are significant and how the genetic diversity of improved Indonesian rice cultivars has changed over time. Changes in the genetic background of the Indonesian rice gene pool were decided using pedigree analysis by calculating the coefficient of parentage (COP) among varieties. There are 280 ancestors in the rice gene pool. The pedigree map exemplifies the complexities of rice breeding in Indonesia. The four classical ancestors of DGWG, Taichung Native1, China, and Latisail had a noteworthy influence on all irrigated rice plant types (11.22%) and upland rice plant types (8.30%) in the gene pool. The dominance of the phenomenal variety IR64 has been continued by Inpari 32, which is a direct derivative of Ciherang. In the meantime, Inpago9, Luhur 2, and UPLRI ancestors set the foundation for the upland rice plant type. Inpara7 and Inpara9, along with their IRRI-introduced parents (IRRIpara4 and IRRIpara5), had a significant impact on Indonesian tidal rice plants. The A1, Hipa7, and Hipa3 varieties are heavily influenced by the hybrid rice plants of Indonesia.

The Relationship between Pollen Viability and Filled Grains in Native Indonesian Rice Cultivars under High Temperature at Flowering Stage

Background: The research was conducted to screen rice cultivars with resistance ability to high-temperature conditions and analyze the relationship between pollen viability and filled grain of native Indonesia rice cultivars. Methods: The rice seeds were germinated, sown into a tray and then transplanted into pots filled with sandy loam and compost 3:1. After 20% of flowering, four pots of each cultivar were kept under ambient temperature (28-32°C) and the other four pots were transferred to high-temperature (33-38°C) conditions. Pollen stainability and pollen germination were conducted using IKI solution and by germinating them under in vitro conditions respectively before being viewed under the light microscope. Yield characters were analyzed to obtain a relationship with pollen viability. Result: Percentage of pollen germination, filled and empty grains of rice cultivars significantly differed between the two conditions by t-test. Ciherang and Sigeudop were two resistant cultivars for high-temperature treatment, with filled grain percentage more than 85%. There was a strong relationship between pollen germination and filled grains at ambient temperature (r=0.95; p less than 0.01) and high temperature (r=0.94; p less than 0.01). Rice cultivars that show high pollen germination under high-temperature conditions would produce a high percentage of filled grains.

Screening of Indonesian rice cultivars against bacterial leaf blight disease under acidic soil condition

Marginal lands, which often have poor soil, are largerlyfound in North Sumatra, Indonesia. Acidic soil, one of margial lands, become an obstacle for agiculture including rice growing. Additionally, bacterial leaf blight disease which is caused by Xanthomonas oryzae pv oryzae, is also the main problem for rice production in Indonesia and worldwide. This study was aimed to screen rice cultivars that were tolerant to acidic soils and showed resistance to bacterial leaf blight (X. oryzae pv. oryzae).This research was conducted at the Screenhouse in Faculty of Agriculture, Universitas Sumatera Utara from July to November 2020. This experiment was designedas factorial Randomized Block Design (RBD) by 3 factors, i.e. Factor 1:rice cultivars (Inpari 30, Inpara 5, Inpago 9 and InpagoUnsoed 1); Factor 2: soil pH (control (pH 6.8) and pH 4.0); Factor 3:isolate of X.oryzae pv oryzae (Xoo 1) with three replications. The results showed that all cultivars grown in acidic soil were susceptible to bacterial leaf blight diseases, while all cultivars grown in control soil pH were moderately susceptible. Disease incidence for all cultivars were 100% starting from the fifth week after planting. Plant growth in acidic soil was affected more severely than that of on neutral soil, while the highest disease severity was 75 % (Inpari 30).

Konstruksi Vektor Biner Mengandung Gen Hibrid cryIB-cryIAa untuk Transformasi Agrobacterium Tanaman Padi (Oryza sativa L)

This study aimed to obtain binary vectors carrying cryIB-cryIAa hybrid gene suitable for Agrobacterium-mediated transformation of two Indonesian rice cultivars, Rajalele (Javanica) and Cisadane (Indica). Introduction of hybrid Bt toxin, encoded by cryIB-cryIAa hybrid gene with different binding receptor in the insect gut driven by maize ubiquitin promoter, was intended to reduce the possibility of the appearance of stem borer resistant to Bt toxin. A HindIII fragment containing the ubi cryIB-cryIAa hybrid gene was excised from pBKS ubi cryIB-cryIAa and cloned into the HindIII site of binary vector pCAMBIA 1301, 1303, or 1304. Restriction analysis of recombinant plasmids confirmed the insertion of the gene and demonstrated that the gene inserted in two orientations. The recombinant plasmids were transformed into electrocompetent Agrobacterium tumefaciens EHA105 by electroporation. Embryogenic calli of Rajalele and Cisadane were co-cultivated with A. tumefaciens EHA 105 harbouring binary vector pCAMBIA 1301, 1303, or 1304 containing ubi cryIB-cryIAa. GUS histochemical assay revealed that high transformation efficiency (75-100%) on both cultivars were obtained from embryogenic calli transformed with pCAMBIA 1303 or 1304.

Glycemic index of ten commercially Indonesian rice cultivars

Ten Indonesian rice cultivars (Inpari 32, Sintanur, Inpago Unsoed 1, Sulutan Unsrat 2, Memberamo, Way Apo Buru, Bestari, Pepe, Situ Bagendit, and Logawa) were analysed for glycaemic index (GI). Wistar rats were randomly selected and after overnight fast were given a portion containing 0.44 g available carbohydrate of different cultivars cooked rice (test foods) or glucose (reference food) on separate occasions. Blood glucose responses were determined at fasting and during the postprandial periods over the next 2 h and we calculated the incremental area under the blood glucose response curve (IAUC). GI value was determined by dividing IAUC for test foods by IAUC for reference food and multiplying by 100. There were significant differences (p < 0.001) between GI values for Inpari 32 (74.54 ± 4.68), Sintanur (91.36 ± 1.28), Inpago Unsoed 1 (94.11 ± 5.93), Sulutan Unsrat 2 (83.56 ± 5.87), Memberamo (92.78 ± 3.69), Way Apo Buru (71.53 ± 7.71), Bestari (87.76 ± 12.69), Pepe (70.61 ± 10.69), and Situ Bagendit (81.81 ± 5.63) rice cultivars and all classified as high GI. However, Logawa (54.39 ± 1.49) cultivar was classified as low GI. Therefore, we have an urgent need to develop low GI rice cultivars via breeding technologies.

Profile of phenolic compounds in Indonesian rice (Oryza sativa) varieties throughout post-harvest practices

Apart from being a foremost source of calories for a large part of the world’s population, cultivated rice (Oryza sativa) provides beneficial effects for human health through several bioactive compounds, including phenolics. Therefore, to earn this advantage, it is essential to retain the phenolics through appropriate post-harvest practices. In this paper, the profile of 10 individual phenolic compounds contained by rice grains after drying, dehusking and polishing processes were studied. A number of Indonesian rice cultivars from indica and javanica subspecies were acquired from conventional (IR-64, Umbul-umbul and Pandanwangi) and organic farming (Batang Lembang, Pandanwangi, black- and red-pigmented rice) were studied. Additionally, the effect of polishing degree on individual phenolics content in the grain was also evaluated. The level of phenolics decreased, also their relative values dramatically changed throughout a series of post-harvest processes. Moreover, changes on the composition of phenolic acids and its aldehydes in the grain have been described. p-Coumaric acid reflects the greatest differences on the phenolic composition during the course of post-harvest practices that altered from 48% to 8% portion to the total phenolics in paddies and polished grains, respectively. However, phenolics content in black-pigmented rice appeared to be the most persistent in the rice matrix. Since the profile of individual phenolics has also been evaluated on different polishing degrees (70%, 80%, 90% and 100% bran removal), the distribution of these compounds in the whole grain rice was effectively disclosed. These variations in the compositions and quantities of phenolics revealed the effect of post-harvest practices, varietal differences as their distribution in the grain.

Growth Characteristics of Two Indonesian Rice Cultivars under Several Submergence Durations

Growth Characteristics of Two Indonesian Rice Cultivars under Several Submergence Durations

Expression analysis of antioxidant genes in response to drought stress in the fl ag leaf of two Indonesian rice cultivars

The objective of this study was to analysis the expression of antioxidant genes in response to droughtstress in Indonesian rice. The malondialdehyde (MDA) content and the expression of Cu-ZnSod1, cCu-ZnSod2,MnSod1, cApxa, cApxb, chl-sApx, Cat1, Cat2, Cat3, Gr1, Gr2, and Gr3 genes were assayed in the rice fl ag leaf ofCiherang and Situ Bagendit cultivars subjected to control, mild and severe drought during the grain fi llingphase. Increase in MDA content of Ciherang treated to mild and severe drought was almost two-fold andthree-fold respectively, while MDA content in Situ Bagendit subjected to mild and severe drought increasedapproximately one-fold and two-fold as compared to the control. The semi quantitative reverse transcriptionpolymerase chain reaction (sqRT-PCR) analysis showed that the expression of cCu-ZnSod1, MnSod1, Cat2, Gr3genes of Ciherang, and cCu-ZnSod2, MnSod1, cApxa, cApxb, chl-sAPX, Cat2 and Gr1 genes of Situ Bagendit increasedin fl ag leaf of plant treated to drought. Expressions of cApxb, chl-sApx, Cat3 of Ciherang and Cu-ZnSod1 and Gr2genes of Situ Bagendit were not changed signifi cantly by drought stress. Decreased expression was shownby cCu-ZnSod2, cApxa, Cat1, Gr1 and Gr2 genes of Ciherang, and Cat1, Cat3 and Gr3 genes of Situ Bagendit. Theresults indicated that the activity of oxidative defense was regulated by four genes; cCu-ZnSod1, MnSod1, Cat2,Gr3 in Ciherang, and eight genes; cCu-ZnSod1, cCu-ZnSod2, MnSod1, cApxa, cApxb, chl-sApx, Cat2 and Gr1 in SituBagendit. Therefore, differences in the number of antioxidant genes controlling oxidative defense systemmight determine the difference of the oxidative defense capacity between both cultivars in response to droughtstress during grain fi lling.

Metagenomic of Actinomycetes Based on 16S rRNA and nifH Genes in Soil and Roots of Four Indonesian Rice Cultivars Using PCR-DGGE

The research was conducted to study the metagenomic of actinomycetes based on 16S ribosomal RNA (rRNA) and bacterial nifH genes in soil and roots of four rice cultivars. The denaturing gradient gel electrophoresis profile based on 16S rRNA gene showed that the diversity of actinomycetes in roots was higher than soil samples. The profile also showed that the diversity of actinomycetes was similar in four varieties of rice plant and three types of agroecosystem. The profile was partially sequenced and compared to GenBank database indicating their identity with closely related microbes. The blast results showed that 17 bands were closely related ranging from 93% to 100% of maximum identity with five genera of actinomycetes, which is Geodermatophilus, Actinokineospora, Actinoplanes, Streptomyces and Kocuria. Our study found that Streptomyces species in soil and roots of rice plants were more varied than other genera, with a dominance of Streptomyces alboniger and Streptomyces acidiscabies in almost all the samples. Bacterial community analyses based on nifH gene denaturing gradient gel electrophoresis showed that diversity of bacteria in soils which have nifH gene was higher than that in rice plant roots. The profile also showed that the diversity of those bacteria was similar in four varieties of rice plant and three types of agroecosystem. Five bands were closely related with nifH gene from uncultured bacterium clone J50, uncultured bacterium clone clod-38, and uncultured bacterium clone BG2.37 with maximum identity 99%, 98%, and 92%, respectively. The diversity analysis based on 16S rRNA gene differed from nifH gene and may not correlate with each other. The findings indicated the diversity of actinomycetes and several bacterial genomes analyzed here have an ability to fix nitrogen in soil and roots of rice plant.

Growth Characteristics of Indonesian Rice Cultivars under Several Durations of Deep Water Treatment

Growth Characteristics of Indonesian Rice Cultivars under Several Durations of Deep Water Treatment