Rice Variants Research Articles

Antioxidant Profile and Antidiabetic Effect of Oryza sativa var. Pulu Mandoti “Local Golden Rice” from Enrekang (Indonesia): In Silico Approach

Diabetes affects 537 million adults globally, with 19.47 million cases in Indonesia. It arises from insufficient or ineffective insulin production, leading to complications like nephropathy. Due to the adverse effects of conventional medications, there is a growing need for safer alternatives. Functional foods and bioactive compounds show promise in managing diabetes. One such alternative is rice. Indonesia boasts a unique rice variety known as Pulu Mandoti, exclusively cultivated in the Enrekang District, Makassar, Indonesia. This delightful red rice variant offers numerous nutritional benefits. Unlike white rice, red rice is abundant in essential nutrients such as calcium, zinc, magnesium, protein, and fiber. The study focused on Pulu Mandoti, exploring its potential for antidiabetic and antioxidant activities using LC-MS analysis. Twelve (12) compounds were identified within the 1.23–14.41-min retention time range, with Compound 11 (2,2'-methylenebis(dibenzo[b,d]thiophene)) showing the strongest antioxidant potential compared to vitamin C. In molecular docking, Compound 11 exhibited the lowest binding affinity for both alpha-amylase and alpha-glucosidase (–10.5 and –8.7 kcal/mol, respectively), whereas acarbose displayed the highest binding affinity. For antioxidant analysis, Compounds 11 and 5 demonstrated the lowest binding affinities for NADPH oxidase and xanthine oxidoreductase, respectively, whereas vitamin C showed the highest. The coefficient values for drug properties similarity ranged from 0.40–0.76 for antidiabetic drugs, with Compound 5 displaying the highest coefficient value (0.76) and from 0.41–0.68 for antioxidants, with the highest value observed for antioxidant peptide A acetate.

Variation in amylose content in three rice variants predominantly influences the properties of sushi rice

Sushi rice is a ready-to-eat traditional Japanese dish seasoned with vinegar, sugar and salt that has gained popularity worldwide. There are many rice cultivars grown in the world which vary in their cooking, sensory, and processing quality. The aim of this study was to analyse chemical, physical, and functional properties of three rice varieties (Vietnamese, Italian, and Australian) to determine their suitability for sushi rice production. Rice was cooked using industry norms and vinegar was then added; samples with no vinegar were prepared for comparison. The rice was stored during 5 days at 4 °C after cooking for texture profile analysis and samples were taken on day 1 and day 5. Flour composition as well as amylose content, gelatinisation properties using differential scanning calorimeter, pasting properties using Rapid Visco Analyser, water absorption capacity (WAC), oil absorption capacity (OAC) and swelling power of extracted starch were determined. Results showed that the amylose content (16.51 to 21.37%) had a large impact on the functional and quality characteristics of the rice variants including texture, pasting, gelatinisation and WAC properties. Australian starch showed the highest amylose content, setback viscosity, final viscosity, pasting temperature and lowest gelatinisation temperature. The lower amylose content and gelatinisation temperature contributed to a softer texture in the Vietnamese rice samples over life. The added vinegar aided in keeping the texture soft during the shelf-life of the rice. Since sushi rice is usually prepared with vinegar, Italian and Vietnamese rice are better candidates for sushi rice based on their lower hardness after 5 days of storage when compared to the Australian variety.

Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared with the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice, significantly limiting their application. Here, we comprehensively examined the base editing activities of multiple evolved TadA8e variants in rice. We found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID∗Δ, and TadA-CDd outperformed TadA-E27R/N46L. A C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of TadA-N46P. In addition, a dual base editor constructed with a single protein, TadDE, enabled simultaneous, highly efficient C-to-T and A-to-G editing in rice. Collectively, our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice, providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.

Engineering disease-resistant plants with alternative translation efficiency by switching uORF types through CRISPR.

Engineering disease-resistant plants can be a powerful solution to the issue of food security. However, it requires addressing two fundamental questions: what genes to express and how to control their expressions. To find a solution, we screen CRISPR-edited upstream open reading frame (uORF) variants in rice, aiming to optimize translational control of disease-related genes. By switching uORF types of the 5'-leader from Arabidopsis TBF1, we modulate the ribosome accessibility to the downstream firefly luciferase. We assume that by switching uORF types using CRISPR, we could generate uORF variants with alternative translation efficiency (CRISPR-aTrE-uORF). These variants, capable of boosting translation for resistance-associated genes and dampening it for susceptible ones, can help pinpoint previously unidentified genes with optimal expression levels. To test the assumption, we screened edited uORF variants and found that enhanced translational suppression of the plastic glutamine synthetase 2 can provide broad-spectrum disease resistance in rice with minimal fitness costs. This strategy, which involves modifying uORFs from none to some, or from some to none or different ones, demonstrates how translational agriculture can speed up the development of disease-resistant crops. This is vital for tackling the food security challenges we face due to growing populations and changing climates.

Optimal-Band Analysis for Chlorophyll Quantification in Rice Leaves Using a Custom Hyperspectral Imaging System.

Hyperspectral imaging (HSI) is a promising tool in chlorophyll quantification, providing a non-invasive method to collect important information for effective crop management. HSI contributes to food security solutions by optimising crop yields. In this study, we presented a custom HSI system specifically designed to provide a quantitative analysis of leaf chlorophyll content (LCC). To ensure precise estimation, significant wavelengths were identified using optimal-band analysis. Our research was centred on two sets of 120 leaf samples sourced from Thailand's unique Chaew Khing rice variant. The samples were subjected to (i) an analytical LCC assessment and (ii) HSI imaging for spectral reflectance data capture. A linear regression comparison of these datasets revealed that the green (575 ± 2 nm) and near-infrared (788 ± 2 nm) bands were the most outstanding performers. Notably, the green normalised difference vegetation index (GNDVI) was the most reliable during cross-validation (R2=0.78 and RMSE = 2.4 µg∙cm-2), outperforming other examined vegetable indices (VIs), such as the simple ratio (RED/GREEN) and the chlorophyll index. The potential development of a streamlined sensor dependent only on these two wavelengths is a significant outcome of identifying these two optimal bands. This innovation can be seamlessly integrated into farming landscapes or attached to UAVs, allowing real-time monitoring and rapid, targeted N management interventions.

Down-Regulation of Rice Glutelin by CRISPR-Cas9 Gene Editing Decreases Carbohydrate Content and Grain Weight and Modulates Synthesis of Seed Storage Proteins during Seed Maturation

The glutelins are a family of abundant plant proteins comprised of four glutelin subfamilies (GluA, GluB, GluC, and GluD) encoded by 15 genes. In this study, expression of subsets of rice glutelins were suppressed using CRISPR-Cas9 gene-editing technology to generate three transgenic rice variant lines, GluA1, GluB2, and GluC1. Suppression of the targeted glutelin genes was confirmed by SDS-PAGE, Western blot, and q-RT-PCR. Transgenic rice variants GluA1, GluB2, and GluC1 showed reduced amylose and starch content, increased prolamine content, reduced grain weight, and irregularly shaped protein aggregates/protein bodies in mature seeds. Targeted transcriptional profiling of immature seeds was performed with a focus on genes associated with grain quality, starch content, and grain weight, and the results were analyzed using the Pearson correlation test (requiring correlation coefficient absolute value ≥ 0.7 for significance). Significantly up- or down-regulated genes were associated with gene ontology (GO) and KEGG pathway functional annotations related to RNA processing (spliceosomal RNAs, group II catalytic introns, small nucleolar RNAs, microRNAs), as well as protein translation (transfer RNA, ribosomal RNA and other ribosome and translation factors). These results suggest that rice glutelin genes may interact during seed development with genes that regulate synthesis of starch and seed storage proteins and modulate their expression via post-transcriptional and translational mechanisms.

Yellow-Green Leaf 19 Encoding a Specific and Conservative Protein for Photosynthetic Organisms Affects Tetrapyrrole Biosynthesis, Photosynthesis, and Reactive Oxygen Species Metabolism in Rice

Chlorophyll is the main photosynthetic pigment and is crucial for plant photosynthesis. Leaf color mutants are widely used to identify genes involved in the synthesis or metabolism of chlorophyll. In this study, a spontaneous mutant, yellow-green leaf 19 (ygl19), was isolated from rice (Oryza sativa). This ygl19 mutant showed yellow-green leaves and decreased chlorophyll level and net photosynthetic rate. Brown necrotic spots appeared on the surface of ygl19 leaves at the tillering stage. And the agronomic traits of the ygl19 mutant, including the plant height, tiller number per plant, and total number of grains per plant, were significantly reduced. Map-based cloning revealed that the candidate YGL19 gene was LOC_Os03g21370. Complementation of the ygl19 mutant with the wild-type CDS of LOC_Os03g21370 led to the restoration of the mutant to the normal phenotype. Evolutionary analysis revealed that YGL19 protein and its homologues were unique for photoautotrophs, containing a conserved Ycf54 functional domain. A conserved amino acid substitution from proline to serine on the Ycf54 domain led to the ygl19 mutation. Sequence analysis of the YGL19 gene in 4726 rice accessions found that the YGL19 gene was conserved in natural rice variants with no resulting amino acid variation. The YGL19 gene was mainly expressed in green tissues, especially in leaf organs. And the YGL19 protein was localized in the chloroplast for function. Gene expression analysis via qRT-PCR showed that the expression levels of tetrapyrrole synthesis-related genes and photosynthesis-related genes were regulated in the ygl19 mutant. Reactive oxygen species (ROS) such as superoxide anions and hydrogen peroxide accumulated in spotted leaves of the ygl19 mutant at the tillering stage, accompanied by the regulation of ROS scavenging enzyme-encoding genes and ROS-responsive defense signaling genes. This study demonstrates that a novel yellow-green leaf gene YGL19 affects tetrapyrrole biosynthesis, photosynthesis, and ROS metabolism in rice.

Physical properties of four rice cultivars grown in Indian temperate region

Setting up of non-standard unit operations could result in cracking of rice grains during milling, leading to accumulation of broken rice and generation of inferior quality product. Therefore, it is very much important to study physical properties of rice for designing of appropriate rice processing machinery that would minimise post-harvest losses during milling operation. Hence, the present investigation was aimed to study physical properties of four rice cultivars (SR-4, K-39, Mushq Budij and pigmented) grown in Kashmir. Brown and polished rice variants of the four cultivars were studied for grain dimensions, equivalent diameter (ED), geometric mean diameter (GMD), arithmetic mean diameter (AMD), volume, surface area, sphericity, aspect ratio, bulk density (BD), true density (TD), porosity, thousand kernel weight, static coefficient of friction and colour. In general, polishing of rice led to significant (p<0.05) reduction in grain dimensions, volume, surface area, thousand kernel weight (TKW), ‘a’ and ‘b’ values and static coefficient of friction (SCOF). However, there was increase in sphericity, porosity and ‘L’ values of rice kernels after polishing. Amongst cultivars, brown SR-4 rice had the largest length (6.36 mm), GMD (3.30 mm) and AMD (3.73 mm), respectively. However, polished K-39 rice had the highest BD (790.0 kg/m3), TD (1540.0 kg/m3) and porosity (48.70) amongst cultivars. Moreover, unpolished pigmented rice had the highest TKW (23.03 g). In addition, the minimum SCOF was observed when rice kernels were allowed to slide through glass surface with the lowest value observed for pigmented variety (0.40). The present research will be beneficial in fabricating machines for rice processing industry which would be helpful in eliminating post-harvest losses that occur during milling operation.

Relative physiological parameter appraisal on indigenous rice variety of South India (Kattuyanam) in contrary to the contemporary cultivars (Andhra Ponni) influenced by biochar

Biochar is a charred organic material that has a wide application in soil improvement and crop yield. It is significant to refurbish the traditional rice variants which belong to south india variety. This study efforts to relatively analyze the morphological characteristics of rice varieties Kattuyanam (traditional variety) and Andhra Ponni (Modern variety) exposed to varied conditions of biochar and its influence on soil fertility. The growth of the seedlings in both varieties was monitored in different conditions (only vermicompost, only biochar, vermicompost, and biochar together, without water and with water) during two different season (Spring and Winter) the biometric parameters of each were measured to determine the effect of conditions in their growth. The seedling's whole height, stem height, root height, leaf height, number of leaves, number of roots, number of auricles, and number of ligules were taken into consideration. These parameters were measured and compared with seedlings in each block of different conditions. The absolute growth rate was calculated for the parameters which are taken before four days of transplantation. The weight of the seedlings of each block was considered and the difference between the weight of the rice varieties was analyzed. Thus this work encourages a dual concept of utilizing waste to produce biochar and evaluate its soil enrichment property on traditional rice variety cultivation.

Metabolome Analysis under Aluminum Toxicity between Aluminum-Tolerant and -Sensitive Rice (Oryza sativa L.).

Aluminum (Al) solubilizes into trivalent ions (Al3+) on acidic soils, inhibiting root growth. Since about 13% of global rice cultivation is grown on acidic soils, improving Al tolerance in rice may significantly increase yields. In the present study, metabolome analysis under Al toxicity between the Al-tolerant variety Nipponbare and the Al-sensitive variety H570 were performed. There were 45 and 83 differential metabolites which were specifically detected in Nipponbare and H570 under Al toxicity, respectively. Furthermore, the results showed that 16 lipids out of 45 total metabolites were down-regulated, and 7 phenolic acids as well as 4 alkaloids of 45 metabolites were up-regulated in Nipponbare, while 12 amino acids and their derivatives were specifically detected in H570, of which 11 amino acids increased, including L-homoserine and L-methionine, which are involved in cysteine synthesis, L-ornithine and L-proline, which are associated with putrescine synthesis, and 1-aminocyclopropane-1-carboxylate, which is associated with ethylene synthesis. The contents of cysteine and s-(methyl) glutathione, which were reported to be related to Al detoxification in rice, decreased significantly. Meanwhile, putrescine was accumulated in H570, while there was no significant change in Nipponbare, so we speculated that it might be an intermediate product of Al detoxification in rice. The differential metabolites detected between Al-tolerant and -sensitive rice variants in the present study might play important roles in Al tolerance. These results provide new insights in the mechanisms of Al tolerance in rice.

Development of the PARMS Markers of the Waxy Gene and Utilization in Discriminating Wild Accessions, and Cultivated Rice (Oryza sativa L.) with Different Eating and Cooking Quality

Amylose content (AC) is the major indicator of rice eating and cooking quality (ECQ). Its synthesis in rice endosperm is mainly regulated by the protein, granule-bound starch synthase 1, which is encoded by the waxy gene (Os06g0133000, LOC_Os06g04200). The diversity of AC is largely attributable to the allelic variation at the Wx locus and the development of effective and accurate functional molecular markers to target rice variant alleles is crucial in the breeding strategy. In the present study, we developed six pairs of penta-primer amplification refractory mutation system (PARMS) markers to distinguish between Wxlv, Wxa, Wxin, Wxb, Wxmp, and Wxop,hp. These markers were successfully used to screen the genotype of large assets of genetic resources including 98 wild accessions, 55 cultivars, and 22 parental lines. Our results showed that Wxb in a low AC type was predominant in Guangxi cultivated rice as a result of cultural preference, while Wxlv in the wild accessions. Moreover, our findings surprisingly revealed the presence of Wxb in wild accession, which is a new outcome that may contribute to understanding the origin, selection and domestication processes of rice. These functional markers could be effectively used in marker-assisted breeding to improve selection efficiency of cultivars with desired AC in the early generation.

Strategies to generate melatonin-enriched transgenic rice to respond to the adverse effects on rice production potentially caused by global warming

Global warming is predicted to reduce the yield of rice, which feeds more than half of the world’s population. A rise in temperature will inevitably hamper rice production by causing drought and flooding. Melatonin has the capacity to ameliorate such adverse effects. Here, we propose multiple genetic means of producing melatonin-enriched, high-yield rice variants to adapt upcoming global warming.

Antifungal and defense elicitor activity of Potassium phosphite against fungal blast disease on ptxD-OE transgenic indica rice and its acceptor parent

In rice farming, the blast disease caused by Magnaporthe oryzae (T.T. Hebert) M.E. Barr. is one of the primary production constraints worldwide. The current blast management options such as blast-resistant varieties and spraying fungicides are neither durable nor commercially and environmentally compatible. In the present study, we investigated the antifungal and defense elicitor activity of potassium phosphite (Phi) against M. oryzae on elite rice cultivar BPT5204 (popularly known as Samba Mahsuri in India) and its transgenic rice variant (ptxD-OE) over-expressing a phosphite dehydrogenase enzyme. The Phi was evaluated both preventively and curatively on rice genotypes where the preventive spray of Phi outperformed the Phi curative application with significant reductions in both rice blast severity (35.67–60.49%) and incidence (22.27–53.25%). Moreover, the application of Phi increased the levels of photosynthetic pigments (Chlorophyll and Carotenoids) coupled with increased activity of defense enzymes (PAL, SOD, and APx). Besides, Phi application also induced the expression of defense-associated genes (OsCEBiP and OsPDF2.2) in the rice leaf. Furthermore, the Phi application reduced the reactive Malondialdehyde (lipid peroxidation) to minimize the cellular damage incited by Magnaporthe in rice. Overall, the present study showed the potential of Phi for blast suppression on rice as an alternative to the current excessive use of toxic fungicides.

The morphological and physiological studies Gorontalo local upland rice treated with drought and shade stresses

Crop growth and production are strongly affected by abiotic and biotic stresses. Survival rate frequently been used to evaluate rice drought tolerance with a low survival rate of rice plants undergoing drought stress leading to low yields. The aim of this research was to obtain Gorontalo local upland rice variants that are tolerant against drought and shade stresses by considering the morphological and physiological characteristics. The research was conducted in Bulotada Barat Village, Sipatana District, Gorontalo, from January to August 2017. Employing the randomized block design with three replications, the research consisted of two treatment factors. The first factor is the accession, which consists of two tolerant accessions; two moderately tolerant accessions, two drought-sensitive accessions, and two shade-sensitive accessions. The second factor pertains to the drought and shade stresses which consist of drought + 25% shade stress, drought + 50% shade stress, and a control. Irrigation in the drought control specimen was given until inundation reached 1.5 cm. In a drought-stressed situation, irrigation was given when the groundwater reached -30 to -35.9 kPa. The Ponda Merah accessions were the accessions that were tolerant against drought and shade stresses. The morphological characteristics of Gorontalo local upland rice that showed tolerance against drought and shade stresses were longer roots (33.20 cm), heavier dry weight (38.82 gr), a thinner leaf (186,56 cm2.g-1), and a higher yield (4,90 gr.cluster−1). The physiological characteristic of the Gorontalo local upland rice that showed tolerance against drought and shade stresses was the sugar content (0,73 g.g-1) which was higher than the other treatment.

A perspective on the benefits of consumption of parboiled rice over brown rice for glycaemic control.

Rice is a staple food for over 3.5 billion people worldwide. The nutritional content of rice varies with different post-harvest processing techniques. Major varieties include brown rice (BR), white rice (WR) and parboiled rice (PBR). While consumption of BR is advocated due to its higher nutritional content compared to other varieties, some studies have indicated lower post-prandial blood glucose (PPBG) levels when PBR is consumed. This apparent benefit of PBR consumption is not well publicised and no commentaries on underlying mechanisms are available in literature. In this review, we looked into differential nutrient content of PBR, as compared to BR and WR, and tried to understand how their consumption could be associated with glycaemic control. Various roles played by these nutrients in mechanisms of insulin secretion, insulin resistance, nutrient absorption and T2DM-associated inflammation were reviewed from literature-based evidence. We report differential nutritional factors in PBR, with respect to BR (and WR), such as higher calcium and selenium content, lower phytic acids, and enriched vitamin B6 which might aid PBR's ability to provide better glycaemic control than BR. Our interpretation of reviewed literature leads us to suggest the possible benefits of PBR consumption in glycaemic control and its inclusion as the preferred rice variant in diets of T2DM patients and at-risk individuals.

Comparative response of Malaysian weedy rice (Oryza sativa) initial growth towards the allelopathic potential of Leucaena leucocephala (Lam.) de Wit and Dicranopteris linearis (Burm. f.) Underw

The infestation of weedy rice has becoming a threat which leads to competition between weedy rice and commercial rice for nutrient uptake. Weedy rice management is more dependent on the herbicides application that can contribute to various environmental problems. Thus, this study was conducted to assess the allelopathic potential of two invasive plants namely L. leucocephala and D. linearis in controlling the growth of weedy rice. The allelopathic potential was evaluated through laboratory bioassay namely the dish pack method, sandwich method and plant box method to determine the allelopathic potential on the seedling growth of two weedy rice variants collected in Peninsular Malaysia (designated as WRE and WRN) and MR220 CL2 rice variety. Highest concentration of L. leucocephala leaf litter (50 mg) inhibited the radicle elongation of MR220 CL2, WRN and WRE by 49 %, 51 % and 83 % compared to control, respectively. Through the dish pack method, the volatile compound from D. linearis leaf were found to disrupt the radicle growth of MR220 CL2, WRN and WRE by 21 %, 29 % and 25 % of the control at the nearest distance (41 mm) of the bioassay plants with the D. linearis leaf. Compared with D. linearis, the root exudate from L. leucocephala exhibited higher inhibitory effect towards the bioassay species. Overall, the findings from this study showed that the allelopathic potential of L. leucocephala was more preferable to be investigated further for sustainable weedy rice management in the future by infusing the biological approach.

An inferred functional impact map of genetic variants in rice

Interpreting the functional impacts of genetic variants (GVs) is an important challenge for functional genomic studies in crops and next-generation breeding. Previous studies in rice (Oryza sativa) have focused mainly on the identification of GVs, whereas systematic functional annotation of GVs has not yet been performed. Here, we present a functional impact map of GVs in rice. We curated haplotype information for 17 397 026 GVs from sequencing data of 4726 rice accessions. We quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918 848 non-redundant missense GVs. Furthermore, we generated high-quality chromatin accessibility (CA) data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5 067 405 GVs for CA in regulatory regions. We characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different directions. Finally, we demonstrated how the functional impact map could be used to prioritize causal variants in mapping populations. This impact map will be a useful resource for accelerating gene cloning and functional studies in rice, and can be freely queried in RiceVarMap V2.0 (http://ricevarmap.ncpgr.cn).

Black rice cultivar from Java Island of Indonesia revealed genomic, proteomic, and anthocyanin nutritional value.

Black rice is considered to be functional food containing anthocyanins as bioactive compounds. This study examined the genomic and proteomic patterns in local black rice from Java Island, Indonesia, with attention to the mechanism of anthocyanin synthesis. Three kinds of black rice from Java Island, including black rice from East Java (BREJ), black rice from Central Java (BRCJ), and black rice from West Java (BRWJ), were studied in comparison to white rice (WREJ) and red rice (RREJ). Genomic profiling was done by simple sequence repeat (SSR) analysis, and sequencing of red coleoptile (Rc) and glycosyltransferase (GT) genes, followed by in silico analysis. Total anthocyanin was investigated by ultra-high performance liquid chromatography- diode array detector (UHPLC-DAD). The proteomic profiles were determined by liquid-chromatography and mass spectrometry of tryptic peptides. The SSR profiles showed a specific band in each black rice variant. The Rc gene exon-2 sequences were similar in the three black rice cultivars. The GT gene sequence was identified as a new variant that correlates with the purple stem, leaf, bran, and whole grain morphology seen exclusively in the BRWJ cultivar. The anthocyanin composition in Java black rice is diverse. The highest cyanidin level was seen in BRWJ and the highest level of peonidin-3-O-glucoside in BREJ. Proteomic profiling of the black rice cultivars demonstrated that the expression of proteins that might be related to the levels of anthocyanin synthesis varied. These studies conclude that the genomic, proteomic and anthocyanins composition of Java black rice cultivars may be used the improvement of their functional nutrition values.

Phenotypic Characteristics of Weedy Rice Variants of Central Mindanao

The presence of different weedy rice (WR) have already been reported in other areas of the Philippines. However, reports documenting its presence and phenotypic characteristics in Central Mindanao are not yet available. This study investigated the incidence, biology, and phenotypic characteristics of WR in Central Mindanao. Survey and collection were conducted in rice field areas of South Cotabato, North Cotabato, Sultan Kudarat, and Maguindanao from 2016–2017. Eight WR variants with distinct grain characteristics were identified and designated in 2016 DS (dry season); 24 variants in 2016 WS (wet season); 31 variants in 2017 DS; and 24 WR variants in 2017 WS. The most prevalent variants were WR-SuK3 (2016 WS), WR-SuK2 (2016 DS), WR-Min15 (2017DS), and WR-SuK3 (2017 WS). Germination test and characterization were conducted at the Philippine Rice Research Institute, Maligaya, Science City of Muñoz, Nueva Ecija. The collected WR variants had variable grain characteristics that affect grain quality and germinated earlier than cultivated rice, which makes WR more competitive. Under screenhouse conditions, all variants matured earlier and had better agronomic characteristics than cultivated rice (NSIC Rc 222). Identified agronomic characters of WR collected from Central Mindanao will be useful for advising control strategies to farmers.

Spike-Stalk Injection Method Causes Extensive Phenotypic and Genotypic Variations for Rice Germplasm

Genetic diversities or favorable genes within distantly related species are the important resources for crop genetic improvement and germplasm innovation. Spike-Stalk injection method (SSI) has long been applied in rice genetic improvement by directly introducing genetic materials from non-mating donor species, while its inheritance patterns and the underlying mechanisms are poorly elucidated. In this study, a rice variant ERV1 with improved yield-related traits was screened out in the way of introducing genomic DNA of Oryza eichingeri (2n=24, CC genome) into RH78 (Oryza sativa L. 2n=24, AA genome) using SSI method. Genome-wide comparison revealed that the genomic heterozygosity of ERV1 was approximately 8-fold higher than RH78. Restriction-site associated DNA sequencing technology (RAD-seq) and association analysis of the ERV1 inbred F2 population identified 5 quantitative trait loci (QTLs) regions responsible for these yield-related traits, and found that genomic heterozygosity of ERV1 inbred lines was significantly lower than ERV1, while spontaneous mutation rate of the ERV1 inbred lines was significantly higher than ERV1. Our results preliminarily uncovered the inheritance patterns of SSI variant rice, and the potential genomic regions for traits changes, which yielded novel insights into the mechanisms of SSI method, and may accelerate our understanding of plant genome evolution, domestication, and speciation in nature.