Indica-type Rice Research Articles

The OsMAPK5-OsWRKY72 module negatively regulates grain length and grain weight in rice.

Grain size and grain weight are important determinants for grain yield. In this study, we identify a novel OsMAPK5-OsWRKY72 module that negatively regulates grain length and grain weight in rice. We found that loss-of-function of OsMAPK5 leads to larger cell size of the rice spikelet hulls and a significant increase in both grain length and grain weight in an indica variety Minghui 86 (MH86). OsMAPK5 interacts with OsMAPKK3/4/5 and OsWRKY72 and phosphorylates OsWRKY72 at T86 and S88. Similar to the osmapk5 MH86 mutants, the oswrky72 knockout MH86 mutants exhibited larger size of spikelet hull cells and increased grain length and grain weight, whereas the OsWRKY72-overexpression MH86 plants showed opposite phenotypes. OsWRKY72 targets the W-box motifs in the promoter of OsARF6, an auxin response factor involved in auxin signaling. Dual-luciferase reporter assays demonstrated that OsWRKY72 activates OsARF6 expression. The activation effect of the phosphorylation-mimicking OsWRKY72T86D/S88D on OsARF6 expression was significantly enhanced, whereas the effects of the OsWRKY72 phosphorylation-null mutants were significantly reduced. In addition, auxin levels in young panicles of the osmapk5 and oswrky72 mutants were significantly higher than that in the wild-type MH86. Collectively, our study uncovered novel connections of the OsMAPKK3/4/5-OsMAPK5-mediated MAPK signaling, OsWRKY72-mediated transcription regulation, and OsARF6-mediated auxin signaling pathways in regulating grain length and grain weight in an indica-type rice, providing promising targets for molecular breeding of rice varieties with high yield and quality.

When a Crop Goes Back to the Wild: Feralization

Feral plants have been known since the inception of modern agriculture, but the genetic changes during what seemed to be a simple reversion of a domesticated form are poorly understood. Recent studies, revealing the changes occurring in weedy rice, show an unexpected degree of differentiation in these feral escapes.

Relationship between growth traits and yield formation in Indica-type rice crop

Introduction. Climatic variation is one of the causes for the decrease in yield and its variability in Indica-type rice (Oryza sativa L.). This evidences the necessity of the study of the interaction of meteorological variables with the behavior of rice cultivars, to establish the base of management of the harvest and increase of the yield. Objective. The objective of the present study was to relate the yield of rice with variables of plant growth. Materials and methods. Four rice cultivars were planted in the “dry” season of December 2004, February 2005 and January 2006, and in the rainy season of March 2006, April 2008 and 2009, in Los Palacios, Pinar del Río province, Cuba. The yield and its components, the dynamics of plant growth (LAI and dry matter), the variation of the dry matter of the internodes, peduncle, flag leaf, leaf and leaf sheath during the grain filling phase were evaluated the panicle growth in addition to the meteorological data. A multivariate analysis was used to relate the performance to the characteristics of the plants evaluated. Results. The yield was higher in the “dry” season and to obtain higher yields, the growth dynamics of the plant and the variation of the dry matter of the third internode during the grain filling were important. In both seasons, different source-sink relationships were established and these situations depended mainly on the temperature regime at which the plants were subjected. Conclusion. Breeders, in order to increase potencial yields, may fows their atttention in grow traits during vegetative stages.

Improvement and identification of genes for yield related traits in Indica-type rice

Improvement and identification of genes for yield related traits in Indica-type rice

Quantitative trait loci responsible for the difference in γ-oryzanol content in brown rice between japonica-type and indica-type rice cultivars

γ-Oryzanol is a main oleophilic component in rice bran oil and has been well recognized as a good dietary supplement for human health, as well as having uses in industrial materials. japonica-type rice cultivars generally showed significantly higher contents of total γ-oryzanol in brown rice compared with indica-type cultivars, although within-group variation was significant. The objective of this study was to explore quantitative trait loci (QTLs) responsible for the difference in the γ-oryzanol content between japonica-type and indica-type rice cultivars, using recombinant inbred lines (RILs), backcross inbred lines (BILs), and corresponding chromosome segment substitution lines (CSSLs) derived from crosses between japonica-type and indica-type. Results from RILs and BILs showed that eight QTLs were detected with R2 from .09 to .16. Nine candidate regions for QTL were also suggested from corresponding CSSLs. These QTLs from RILs and BILs and the candidate regions from CSSLs were not overlapped, although one QTLs was mapped near the boundaries of the respective candidate region. At four QTLs and three candidate regions, alleles or segments from japonica-type caused higher contents than those from indica-type. On the other hand, at the other four QTLs and six candidate regions, alleles or segments from indica-type caused higher contents than those from japonica-type, which is a reverse result to the parental differences. This result strongly suggested that alleles with increasing effects on γ-oryzanol content could be accumulated not only from japonica-type but also from indica-type, leading to a potential for increase in γ-oryzanol content in future breeding programs.

Root transcriptomes of two acidic soil adapted Indica rice genotypes suggest diverse and complex mechanism of low phosphorus tolerance.

Low phosphorus (P) tolerance in rice is a biologically and agronomically important character. Low P tolerant Indica-type rice genotypes, Sahbhagi Dhan (SD) and Chakhao Poreiton (CP), are adapted to acidic soils and show variable response to low P levels. Using RNAseq approach, transcriptome data was generated from roots of SD and CP after 15days of low P treatment to understand differences and similarities at molecular level. In response to low P, number of genes up-regulated (1318) was more when compared with down-regulated genes (761). Eight hundred twenty-one genes found to be significantly regulated between SD and CP in response to low P. De novo assembly using plant database led to further identification of 1535 novel transcripts. Functional annotation of significantly expressed genes suggests two distinct methods of low P tolerance. While root system architecture in SD works through serine-threonine kinase PSTOL1, suberin-mediated cell wall modification seems to be key in CP. The transcription data indicated that CP relies more on releasing its internally bound Pi and coping with low P levels by transcriptional and translational modifications and using dehydration response-based signals. Role of P transporters seems to be vital in response to low P in CP while sugar- and auxin-mediated pathway seems to be preferred in SD. At least six small RNA clusters overlap with transcripts highly expressed under low P, suggesting role of RNA super clusters in nutrient response in plants. These results help us to understand and thereby devise better strategy to enhance low P tolerance in Indica-type rice.

Genetic characterization of introgression lines with the genetic background of the Indica-type rice (Oryza sativa L.) cultivar IR 64 under irrigated lowland and upland conditions

We characterized 333 introgression lines (INLs) harboring chromosome segments from new plant type (NTP) and Japonica-type cultivars with the genetic background of the elite Indica-type rice (Oryza sativa L.) cultivar IR 64, by evaluating yield components and dry matter production under irrigated lowland (IL) and upland (UP) culture in 2011 and 2012; and elucidated the relationships between the traits and chromosome segments introduced from the donors. The panicle weight (PW), PW/total plant weight (PW/TW), number of fertile spikelets (FS), and FS/total number of spikelets per panicle (FS/TS) of the INLs increased, while the culm weight (CW) and panicle number (PN) decreased. Most INLs produced more dry matter in the UP than in the IL culture. The INLs were clustered into three groups (A–C) according to their traits in the UP culture, and four groups (I–IV) according to their traits in the IL culture. They were then sorted into six groups (A-I, A-II, B-II, B-III, C-III, and C-IV) according to the relationships between culture conditions. The INLs of group A-II had increased panicle length (PL), PW, PW/TW, FS, and TS, and these traits were stable in both IL and UP culture. In the other groups, the trait values changed with the conditions and season. Association analyses using trait phenotype and genotype data of SSR markers detected 166 quantitative trait loci (QTLs) for 10 traits, distributed on all chromosomes except 3 and 10. Of these, 81 QTLs for DH, CL, PL, CW, PW, PW/TW, PN, FS, TS, and FS/TS were newly detected. The INLs were characterized under different conditions, and dramatic trait modifications in IR64 rice were associated with these QTLs, through introgression from the donor cultivars. Thus, these INLs and QTLs will be useful in genetic studies to identify the gene(s) that modified IR64, and as breeding materials for genetic improvement of Indica-type cultivars.

저장조건, 쌀, 조리기구와 유지 종류가 밥의 저항전분 함량 변화에 미치는 영향

The changes of resistant starch (RS) contents of cooked rice with soybean and coconut oils under different storage conditions were investigated and RS contents were compared between the rice and cooker types. The japonica (Hopyeong) and the indica (Thailand) type rice were cooked (washed rice: water

Light-modulated seminal wavy roots in rice mediated by nitric oxide-dependent signaling.

Rice (Oryza sativa L.) seminal roots from germinated seeds help establish seedlings, but the seminal root growth and morphology are sensitive to environmental factors. Our previous research showed that several indica-type rice varieties such as Taichung native 1 (TCN1) showed light-induced wavy roots. Also, auxin and oxylipins are two signaling factors regulating the wavy root photomorphology. To investigate the signaling pathway, here, we found that nitric oxide (NO) was a second messenger triggering the signal transduction of light stimuli to induce the wavy morphology of seminal roots in rice. Moreover, interactions between oxylipins and phytohormones such as ethylene and auxin participating in the NO-dependent regulatory pathway of light-induced wavy roots were examined. The order of action of signaling components in the pathway was NO, oxylipins, ethylene, and auxin.

Speciation and determination of inorganic arsenic in rice using liquid chromatography-inductively coupled plasma/ mass spectrometry: collaborative study.

An analytical method to speciate two inorganic As forms [arsenite, As(lll) and arsenate, As(V)] in indica and japonica types of rice (both husked and polished) and determine the inorganic As concentration as the sum of these two was internationally validated. The method can additionally determine two organic As compounds, monomethylarsonic acid and dimethylarsinic acid, in rice as separate LC peaks. The method is based on LC separation and inductively coupled plasma (ICP)-MS detection. The method was evaluated through the International Union of Pure and Applied Chemistry/lnternational Organization for Standardization/AOAC harmonized protocol. Sixteen laboratories from four countries participated in the study, and 13 laboratories returned valid data. Twenty test portions of 10 blind duplicates of indica and japonica type rice samples (both husked and polished) were used in this study. Repeatability RSD (RSDr) and reproducibility RSD (RSDR) were calculated at five concentrations of total inorganic As between 0.03 and 0.68 mg/kg. The RSDr was in a range of 3.8 to 7.7% and the RSDR was in a range of 10 to 36%. These performance characteristics were found to be sufficient for determination of inorganic As at or higher than 0.03 mg/kg. Applicability of the method was estimated to be in a range of 0.02-2.0 mg/kg.

Classification of Single Cereal Grain Kernel Using Shape Parameters Based on Machine Vision

The study was conducted to identify three types of non-touching grain kernels using a colour machine vision system. Images of individual cereal grain kernels were acquired using an camera. Shape feature was extracted from binary and edge images of cereal grain kernels obtained by iamge processing for classification. A total of 13 shape feature parameters, including region area, perimeter, length, width, the maximum radius, the smallest radius etc, were extracted from each kernel to use as input to the Bayesian classifier. Experimental results showed that the Bayesian classifier gave better classification with a calssificaiton accuracy of 99.67% for indica type rice, followed by 98.67% and 78.33% for japonica rice and glutinous rice using training set, respectively. The classification system was developed with Bayesian classifier that achieved an overall recognition rate of 92.22% with training data set and furthermore, a classification accuracy of 90% for the testing data set.

Sequential Monitoring of Transgene Expression Following Agrobacterium-Mediated Transformation of Rice

Although Agrobacterium-mediated transformation technology is now used widely in rice, many varieties of indica-type rice are still recalcitrant to Agrobacterium-mediated transformation. It was reported recently that T-DNA integration into the rice genome could be the limiting step in this method. Here, we attempted to establish an efficient sequential monitoring system for stable transformation events by visualizing stable transgene expression using a non-destructive and highly sensitive visible marker. Our results demonstrate that click beetle luciferase (ELuc) is an excellent marker allowing the observation of transformed cells in rice callus, exhibiting a sensitivity >30-fold higher than that of firefly luciferase. Since we have previously shown that green fluorescent protein (GFP) is a useful visual marker with which to follow transient and/or stable expression of transgenes in rice, we constructed an enhancer trap vector using both the gfbsd2 (GFP fused to the N-terminus of blasticidin S deaminase) and eluc genes. In this vector, the eluc gene is under the control of the Cauliflower mosaic virus 35S minimal promoter, while the gfbsd2 gene is under the control of the full-length rice elongation factor gene promoter. Observation of transformed callus under a dissecting microscope demonstrated that the level of ELuc luminescence reflected exclusively stable transgene expression, and that both transient and stable expression could be monitored by the level of GFP fluorescence. Moreover, we show that our system enables sequential quantification of transgene expression via differential measurement of ELuc luminescence and GFP fluorescence.

QTL analyses of heterosis for grain yield and yield-related traits in indica-japonica crosses of rice (Oryza sativa L.)

Two sets of rice materials, 166 RILs derived from a cross between Milyang 23 (Korean indica-type rice) and Tong 88-7 (japonica Rice), and BC1F1 hybrids derived from crosses between the RILs and the female parent, Milyang 23, were produced to identify QTLs for heterosis of yield and yield-related traits. The QTLs were detected from three different phenotype data sets including the RILs, BC1F1 hybrids, and mid-parental heterosis data set acquired from the definition of mid-parental heterosis. A total of 57 QTLs were identified for nine traits. Of eight QTLs detected for yield heterosis, five overlapped with other heterosis QTLs for yield-related traits such as spikelet number per panicle, days to heading, and spikelet fertility. Four QTLs for yield heterosis, gy1.1, py6, gy10, and py11, were newly identified in this study. We identified a total of 17 EpQTLs for yield heterosis that explain 21.4 ∼ 59.0 % of total phenotypic variation, indicating that epistatic interactions may play an important role in heterosis.

Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.).

Total spikelet number per panicle (TSN) is one of the most important traits associated with rice yield potential. This trait was assessed in a set of 334 chromosomal segment introgression lines (ILs: BC3-derived lines), developed from new plant type (NPT) varieties as donor parents and having the genetic background of an indica-type rice variety IR64. Among the 334 ILs, five lines which had different donor parents and showed significantly higher TSN than IR64 were used for genetic analysis. Quantitative trait locus (QTL) analysis was conducted using F2 populations derived from crosses between IR64 and these ILs. As a result, a QTL for high TSN (one from each NPT donor variety) was detected on common region of the long arm of chromosome 4. The effect of the QTL was confirmed by an increase in TSN of five near-isogenic lines (NILs) developed in the present study. The variation in TSN was found among these NILs, attributing to the panicle architecture in the numbers of primary, secondary and tertiary branches. The NILs for TSN and the SSR markers linked to the TSN QTLs are expected to be useful materials for research and breeding to enhance the yield potential of rice varieties.

Rice develop wavy seminal roots in response to light stimulus

Rice (Oryza sativa L.) seminal roots are the primary roots to emerge from germinated seeds. Here, we demonstrate that the photomorphology of the seminal roots was diverse among rice varieties, and the light-induced wavy roots were found mostly in indica-type rice varieties. The light-induced wavy morphology in rice seminal roots has been different with curling or coiling roots in some other specific conditions, such as high air humidity or high nitrogen nutrient. The efficiency of light-induced root waving was developmental stage dependent. The wavy root phenotype was caused by asymmetric cell growth around the stele. Using the inhibitors to block auxin polar transport and fatty acid oxygenation, the role of auxin and oxylipins in the morphogenesis of light-induced wavy roots was investigated. Expressions of genes encoded in the enzymes involved in fatty acid oxygenation in light-exposed roots were monitored by reverse transcriptase-polymerase chain reaction. Our results suggested that auxin polar transport was essential for inducing wavy seminal roots by light stimulus. In addition, the ketol oxylipins derived from allene oxide synthase (EC 4.2.1.92)-mediated fatty acid oxygenation function as intracellular signals for triggering the light-induced wavy root phenotype.

Proline biosynthetic gene expression in tissue cultures of rice (Oryza sativa L.) in response to saline treatment

The regulation of proline biosynthesis has been examined in callus and cell cultures of the indica-type rice cultivar Khao Dawk Mali 105 (KDML105) in response to a saline treatment (250 mM NaCl) in terms of the expression of Δ1-pyrroline-5-carboxylate reductase (OsP5CR) and members of the gene family encoding the rate-determining enzyme, Δ1-pyrroline-5-carboxylate synthase (designated OsP5CS1 and OsP5CS2). Using friable callus, growth was retarded by treatment with 250 mM NaCl within 4 days, with a significant increase in the expression of OsP5CS2 by 24 h, and a less marked induction in OsP5CS1 and OsP5CR over the same time-course. Cell suspension cultures derived from the friable callus were also treated with 250 mM NaCl and an induction in OsP5CS2 was again observed, although this was not as marked as in the friable callus, and there was no significant change in OsP5CS1 and OsP5CR expression. This is the first report that details the expression of OsP5CS1 and OsP5CS2 in tissue culture and the results show that, in common with whole plants, OsP5CS2 displays a primacy of response to saline treatment. However, this response may require a community of communicating cells, as occurs in callus tissue, rather than cell suspension cultures. This difference has implications both in terms of the biology of signaling in response to increased salinity and in the use of tissue culture to screen for saline-tolerant germplasm.

A set of near-isogenic lines of Indica-type rice variety CO 39 as differential varieties for blast resistance

Twenty-seven near-isogenic lines (NILs) with the genetic background of a blast-susceptible variety, CO 39, were developed by repeated backcrossing as a first set of a large number of differential varieties (DVs) with Indica-type genetic background. The NILs included 14 resistance genes—Pish, Pib, Piz-5, Piz-t, Pi5(t), Pik-s, Pik, Pik-h, Pik-m, Pik-p, Pi1, Pi7(t), Pita, and Pita-2—derived from 26 donor varieties. The reaction patterns of NILs against 20 standard isolates from the Philippines were similar to those of blast monogenic lines with the same resistance gene, except for those against two isolates that are avirulent to Pia in the genetic background of CO 39. A genome-wide DNA marker survey revealed that chromosome segments were introgressed in the regions where each resistance gene was previously mapped and most of the other chromosome regions in each NIL were CO 39 type. Segregation analysis of resistance and co-segregation analysis between resistance and DNA markers using F3 populations derived from the crosses between each NIL and the recurrent parent, CO 39, revealed a single-gene control of resistance and association between resistance and target introgressed segments. The morphological characters of each NIL were almost the same as those of the recurrent parent except for some lines, suggesting that these NILs can be used even under tropical conditions where Japonica-type DVs are not suitable for cropping. Thus, these NILs are useful not only as genetic tools for blast resistance study but also as sources of genes for breeding of Indica-type rice varieties.

Studies on the germination characteristics of indica-type rice. I. The physiology and ecology of germination under the environmental conditions provided by different depths of water.

Studies on the germination characteristics of indica-type rice. I. The physiology and ecology of germination under the environmental conditions provided by different depths of water.

Physico-chemical characteristics and non-starch polysaccharide contents of Indica and Japonica brown rice and their malts

Brown rice malt from Indica and Japonica type rice were prepared and their nutrient composition as well as non-starch polysaccharide (NSP) contents and also some of the physico-chemical characteristics were determined. The activity of α- and β-amylases in the ungerminated (native) rice was negligible but increased considerably on germination. Malting altered the chemical composition of both Indica and Japonica rice to a small extent but caused noticeable changes in the pasting characteristics. The free sugars and water-soluble non-starch polysaccharide (NSP) contents of the malt samples were considerably higher than the native samples. The carbohydrate elution profile of native and malted rice on Sepharose CL-2B revealed partial degradation of starch. However, the electrophoresis patterns of the native and malt samples were comparable but exhibited decrease in their band intensity. The study revealed that, controlled germination or malting causes considerable changes in the physico-chemical and bio-chemical properties of both Indica and Japonica rice.

Variation in free amino acid profile among some rice (Oryza sativa L.) cultivars

The free amino acid (FAA) concentration of rice is becoming an increasingly important grain quality factor because of its apparent influence on the organoleptic acceptability of cooked rice. To determine the variability of this character among rice cultivars the FAA profiles of 49 cultivars were determined using Pico-Tag method. Among these 13 cultivars were selected to determine variation in FAA accumulation pattern after 24-hour germination treatment. The results show significant variation in the concentrations of total as well as individual FAAs among cultivars. There were also significant differences between indica- and japonica-type cultivars in the concentrations of some FAAs. The ratio of the total concentration of aspartate-derived to glutamate-derived FAAs (A/G ratio) evaluated for the japonica group (0.68) was significantly lower than that for the indica group (1.07). This suggests that typically, japonica-type rice grains tend to accumulate more Glu-derived than Asp-derived FAAs. Other results show a decline in the A/G ratios of both groups in response to germination treatment, with the indica group exhibiting a more rapid response. These results appear to suggest key differences in the FAA accumulation patterns of japonica- and indica-type rice grains especially with respect to the contents of aspartate-derived and glutamate-derived amino acids.