Oryza Nivara Research Articles

Evolutionary Systems Biology Identifies Genetic Trade-offs In Rice Defense Against Above- and Belowground Attackers.

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, and O. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different above- and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), respectively, and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at the KSL8 and MG1 loci on chromosome 11. KSL8 encodes the first committed step towards biosynthesis of either stemarane- or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking out KSL8-jap and CPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance to S. frugiperda and decreased resistance to M. incognita. Furthermore, MG1 resides in a haplotype that provided resistance to M. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungus Magnaporthe oryzae and other pests and pathogens. Finally, KSL8 and MG1 alleles are located within trans-species haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms at KSL8 and MG1 may be maintained through complex and diffuse community interactions.

Molecular Evolution of Rice Blast Resistance Gene bsr-d1

Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating plant blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice varieties. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica, with the bsr-d1 resistance allele being unique to indica. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our comprehension of resistance gene variation and expedite the resistance breeding process.

Molecular Mapping and Transfer of Quantitative Trait Loci (QTL) for Sheath Blight Resistance from Wild Rice Oryza nivara to Cultivated Rice (Oryza sativa L.).

Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F2 population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts.

Fine mapping of interspecific secondary CSSL populations revealed key regulators for grain weight at qTGW3.1 locus from Oryza nivara.

The online version contains supplementary material available at 10.1007/s12298-024-01483-0.

Functional Cookies Based on Brown Rice (Oryza nivara) and Black Rice (Oryza sativa L. indica) as A Healthy Snack for Adolescent with Obesity

Functional Cookies Based on Brown Rice (Oryza nivara) and Black Rice (Oryza sativa L. indica) as A Healthy Snack for Adolescent with Obesity

Genome-wide characterization and functional analysis of heat shock transcription factors in wild and cultivated rice (Oryza sativa L.)

Due to domestication, the genetic diversity in cultivated rice is lower than that of wild rice species. Recent progress in sequencing the genomes of wild and cultivated rice genus is an important step in identifying their genetic differences associated with abiotic and biotic stresses-resistant ability. Thus, in this study, heat shock transcription factor (Hsf) genes in 6 wild rice accessions, including Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate and Oryza rufipogon, and 1 cultivated rice variety Nipponbare were firstly identified, and the evolution of rice Hsf genes were analyzed. Totally, 22, 23, 24, 24, 25, 25 and 25 Hsf genes were identified in the 7 tested rice genomes, Oryza barthii, Oryza glumaepatula, Oryza meridionalis, Oryza nivara, Oryza punctate, Oryza rufipogon and Oryza sativa, respectively. The evolutionary analysis of Hsf genes revealed that Oryza rufipogon was the immediate ancestral progenitor of Oryza sativa. The variation in the number of Hsf genes between wild and cultivated rice genotypes was mainly due to segmental duplication and whole genome duplication (WGD) events, which might contribute to the different stress-tolerant ability between the wild and cultivated rice varieties. Secondly, the function of the Hsf genes in wild and cultivated rice in response to salinity stress was compared. Under salt stress, four Hsf genes, HsfA2b, HsfB4b, HsfB4c and HsfB4d, were exclusively down-regulated in Oryza rufipogon shoots. Whilst, another four Hsf genes, HsfA7a, HsfB2c, HsfC1b and HsfC2b, were up-regulated in the shoots of both the cultivated rice and its ancestral progenitor Oryza rufipogon. Meanwhile, genomic comparison results showed that 1, 1, 5 and 5 nsSNPs were detected in these 4 Hsf genes respectively, which might alter the functions of these genes. RT-qPCR results further confirmed the expression profile of one of these 4 Hsf genes, HsfB2c. The expression pattern of this gene in the cultivated rice variety in response to salt stress was similar with the previously known salt stress-tolerant gene, WRKY28. This indicated that these 4 Hsf genes might be among the conserved genes related to salt stress tolerance in the wild and cultivated rice. In summary, these results provide novel clues to the further functional studies of Hsf genes in rice for breeding programs.

The effect of alginate extract on the properties of brown rice (Oryza nivara) ice cream

The production of ice cream with the basic ingredients of brown rice milk is carried out to increase the consumption of antioxidants derived from brown rice (Oryza nivara). This is because the plant is less consumed due to its rough texture. The recent development of brown rice ice cream (BRICE) is intended to expand the use of the plant into a common commodity. Previous investigations have established that stabilizers are required in ice cream production, although only a few used natural stabilizers such as alginate. Therefore, this study aimed to determine the effect of adding the different concentrations of alginate from brown seaweed Laminaria sp. on the physical characteristic, namely melting power, viscosity, overrun, total dissolved solids, chemical properties, which include protein, fat, as well as antioxidant activity and hedonic level of BRICE. The concentration of alginate used was at 0.025%, 0.05%, 0.075%, and 0.1%, while the data collected were analyzed using analysis of variance (ANOVA) and Duncan’s test. The result showed that the addition of different alginate concentrations had a significant effect on the value of the parameters observed.

Mapping of a novel recessive brown planthopper resistance gene bph46 from wild rice (Oryza nivara)

Mapping of a novel recessive brown planthopper resistance gene bph46 from wild rice (Oryza nivara)

Mapping for yield related traits in rice reveals major effect QTL qFLA1.1 from Oryza nivara increases flag leaf area

Mapping for yield related traits in rice reveals major effect QTL qFLA1.1 from Oryza nivara increases flag leaf area

Increasing The Growth and Yield of Red Rice (Oryza nivara) Through The Addition of Nanosilica Fertilizer to The Rooftop Farming System

One type of rice that is rich in potential nutritional content is brown rice, but the production of this type of rice is still far behind compared to other types of rice. Therefore, special efforts are needed to support production, one of which is through the use of superior varieties accompanied by the fulfillment of the right nutrients, especially the Si nutrient. This research aims to determine the effect of adding nanosilica on the growth and yield of red rice. This research used a factorial randomized block design consisting of 2 factors, namely variety (consisting of two levels V1 = Pamera, V2 = Pamelen) and nanosilica concentration (consisting of five levels S0: 0 mL L-1 (control); S1: 7, 5 mL L-1; S2: 10 mL L-1; S3: 12.5 mL L-1; S4: 15 mL L-1.). The results of the research concluded that applying nanosilica colloid to the Pamera and Pamelen varieties at a concentration of 15 mL L-1 was able to increase plant length and number of tillers, as well as speeding up the flowering age of red rice. However, giving nanosilica had no effect on harvest age and yield components.

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara.

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

Linkage mapping and quantitative trait loci detection for seedling vigor and grain size in advanced backcross introgression lines from wild accessions of Oryza nivara

Linkage mapping and quantitative trait loci detection for seedling vigor and grain size in advanced backcross introgression lines from wild accessions of Oryza nivara

Growing Conditions and Varietal Ecologies Differently Regulates the Growth-regulating-factor (GRFs) Gene Family in Rice.

Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among the rice cultivation practices, aerobic methods are water efficient but result in significant yield reduction relative to non-aerobic cultivation. Therefore, mechanistic insights into aerobic rice cultivation are important for improving the aerobic performance of rice. This study aimed to examine the evolution of GRFs in different rice species, analyse the phenotypic differences between aerobic and non-aerobic conditions in three rice varieties, and assess the expression of GRFs in these varieties under both aerobic and non-aerobic conditions. This study comprehensively examined the GRFs gene family in 11 rice species (Oryza barthii, Oryza brachyantha, Oryza glaberrima, Oryza glumipatula, Oryza sativa subsp. indica, Oryza longistaminata, Oryza meridionalis, Oryza nivara, Oryza punctata, Oryza rufipogon, Oryza sativa subsp. japonica) focusing on phylogenetic analysis. Additionally, the expression patterns of 12 GRFs were investigated in three distinct genotypes of O. sativa subsp. indica rice, under both non-aerobic and aerobic conditions. Three major phylogenetic clades were formed based on conserved motifs in the 123 GRFs proteins in eleven rice species. Further, novel motifs were identified especially in O. longistaminata indicative of the species level evolutionary differences in rice. Among the trait performance, the number of tillers was reduced by ~ 36% under aerobic conditions, but the reduction was found to be less in CR Dhan 201, an aerobic variety. Besides, three GRFs namely GRF3, GRF4, and GRF7 were found to be distinct in expression between aerobic and non-aerobic conditions. Three GRF genes namely GRF3, GRF4, and GRF7 could be associated with the aerobic adaptation in rice.

Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers (Nilaparvata lugens (Stål)) Derived from Oryza nivara.

The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from Oryza nivara, has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as bph39(t) and bph40(t), contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the bph39(t) and bph40(t) loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (STPKR), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of STPKR from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of STPKR (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of Nipponbare. Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the STPKR gene with respect to BPH resistance controlled by bph39(t) and bph40(t). Functional markers specific for STPKR have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.

Genome-Wide Identification, Evolution, and Expression Analysis of the WD40 Subfamily in Oryza Genus.

The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development.

Conservation and molecular identification of traditional rice varieties collected from Kerala using matK and rbcL DNA barcode markers

Varietal identification of economically significant crops has acquired great importance in the global market especially in the terms of protection of plant varieties. Kerala is the home to several different specialty traditional rice varieties which is vital sources of nutritional and therapeutic properties. Traditional rice landraces are an integral part of the nutrition, medicine, and culture of Kerala. Most of these varieties possess similar morphological characteristics but differ in their nutritional and medicinal properties. It has become a challenge for a non-taxonomist to identify and recognize the traditional rice varieties accurately. DNA barcoding has been considered a standard method to identify species or variety which utilizes a unique pattern of variation in the DNA of the species. It can be adopted as a routine and faster approach to determine the molecular taxonomy when compared to morphological identification approaches. Currently, the most intensively applied two DNA barcode loci are maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL) for plant identification. But, the efficacy of these two loci in discriminating plant species may vary. Hence, in this study fifty-four traditional rice varieties collected from the Wayanad district of Kerala were used to generate and compare the two standard DNA barcode regions for plant matK and rbcL via PCR amplification. The varieties collected were varying in the husk color from black; red to brown and the brown rice varieties not display any morphological variation. The study identified that among the two selected markers rbcL was observed to have the potential to discriminate the intra and interspecific regions of the studied rice varieties and this would have been utilized to generate DNA barcodes for each variety. This study separates and identifies 28 traditional rice varieties among the 54 studied varieties as Oryza nivara, the wild progenitor of Asian cultivated rice. Along with other supporting information the data presented here could be used as a reference to check the authenticity and varietal purity of commercially significant rice varieties in the future.

Formulasi dan uji aktivitas sediaan lotion tabir surya ekstrak etanol 96% bekatul beras merah (Oryza nivara)

Brown Rice Bran (Oryza nivara) contains phenolic compounds, flavonoids, tannins, steroids, or terpenoids that can function as an antioxidant activity that can protect the skin from the adverse effects of UV rays of the sun. Extraction was carried out by maceration method using 96% ethanol as solvent. The viscous extract obtained was then subjected to phytochemical screening and SPF test and made into three different concentrations, 5%, 10%, and 15%, which would then be formulated into a sunscreen lotion dosage form. The resulting preparations evaluated the physical quality of lotion preparations in the form of organoleptic tests, homogeneity tests, pH tests, dispersibility tests, and SPF tests of preparations. The results of the SPF test extract with concentrations of 5%, 10%, and 15% showed that the protection produced was in the ultra-category with SPF values respectively 31.1, 40.1, and 45.1. The results of the physical evaluation of the preparation of sunscreen lotion with brown rice bran extract showed that the lotion produced was not homogeneous, and the results of the pH test and dispersion test still met the requirements. Testing the SPF value of lotion preparations showed that the protection produced by each formula was in the maximum to ultra-category with SPF values of 11.7, 14.1, and 16.4, respectively.

Red Rice (Oryza Nivara) Growth and Yield are Impacted by Seedling Age and the Concentration of Liquid Organic Fertilizer

This study aims to ascertain how seedling age and liquid organic fertilizer content interact and correlate with red rice growth and production. This study was conducted in Karya Mulya village, Kesambi district, Cirebon, West Java, from December 2020 to April 2021. The factorial randomized block design (RBD) research methodology was used. Plant height, tiller count, leaf color, number of active tillers, number of panicles per clump, panicle length, number of grains per panicle, weight of 1000 grains, dry weight of grain harvested per plot, and dry weight of grain milled per plot were the key observations. The findings indicate that at 35 days following planting, there was an interaction between seedling age and liquid organic fertilizer concentration on leaf greenness. While the number of tillers 35 days after planting was affected by seedling age independently. When applied 42 days after planting, liquid organic fertilizer had an impact on the number of productive tillers, the number of panicles per clump, the length of the panicle, the number of grains per panicle, the weight of 1000 grains, the dry weight of the grain harvested per plot, and the dry weight of the grain ground per plot.

The effects of red rice flour (Oryza nivara) substitution on the making of bolu cukke traditional cake

Bolu cukke is a traditional cake typical of Soppeng district, South Sulawesi which is made from wheat flour. Along with the increasing consumption of wheat flour, the process of importing wheat in Indonesia has also increased. Wheat flour consumption can be reduced by using gluten-free local food, such as red rice. The aim of this investigation was to identify the best formulation of bolu cukke made from red rice flour based on organoleptic tests, chemical characteristics, and to compare commercial bolu cukke and the best treatment product. The method in this study consisted of several stages, namely organoleptic tests, proximate tests, and antioxidant activity. The results obtained in this study, namely the organoleptic test yielded the best treatment with the formulation of 75% red rice flour: 25% wheat flour, followed by chemical analysis based on the T-Test which showed that the water content, protein content, carbohydrate content and antioxidant activity had a significant effect on the ash and fat content did not significantly affect the use of red rice flour. The conclusion obtained is that the value of chemical characteristics in the best treatment consists of a water content value of 16.70%; ash content 1.56%; fat content 15.51%; protein content 8.08%; carbohydrate content of 58.15% and antioxidant activity based on IC50 1923.692 ppm, whereas without using red rice flour it has a water content value of 22.32%; ash content 1.49%; fat content 17.93%; protein content 8.53%; carbohydrate content of 49.73% and antioxidant activity based on IC50 3003.337 ppm.

Aplikasi Pestisida Nabati dan Trichokompos terhadap Penyakit Bercak Daun (Cercospora oryzae) pada Padi Beras Merah di Lahan Basah

Cultivation of brown rice (Oryza nivara L.) in wetlands continues to expand because its consumers continue to increase. This study aims to determine the ability of Trichocompost and a solution of botanical pesticides from kalakai, babadotan and purun tikus in controlling brown spot disease caused by the fungus Cercospora oryzae on brown rice plants in wetlands. Based on the results of observations, the application of trichocompost and purunrat solution was able to reduce the incidence of leaf spot disease from 95.1% in controls to 76.5%. The results of disease intensity showed that the application of trichocompost and kalakai solution was able to reduce disease intensity from 19.55% in controls to 14.10%. The application of trichocompost and babadotan solution increased the number of grains of rice from 216.60 grains in the control to 243.20 grains. The application of Trichocompost and kalakai solution increased the weight of 100 grains from 1.79 g to 2.10 g. The application of only trichocompost, Trichocompost and kalakai solution, trichocompost and babadotan solution, and trichocompost and purunrat solution have the same ability to reduce the incidence and intensity of Cercospora disease. All treatments tested were unable to increase plant height growth.