Rice

https://thericejournal.springeropen.com/

List of Papers (Total 603)

Detection of Novel QTLs Regulating Grain Size in Extra-Large Grain Rice (Oryza sativa L.) Lines

Background Grain size is an important trait that affects rice yield. Although many genes that contribute to grain size have been cloned from mutants or by quantitative trait locus (QTL) analysis based on bi-parental mapping, the molecular mechanisms underlying grain-size determination remain poorly understood. In this study, we identified the lines with the largest grain size and...

The Nipponbare genome and the next-generation of rice genomics research in Japan

The map-based genome sequence of the japonica rice cultivar Nipponbare remains to date as the only monocot genome that has been sequenced to a high-quality level. It has become the reference sequence for understanding the diversity among thousands of rice cultivars and its wild relatives as well as the major cereal crops that comprised the food source for the entire human race...

Reference genes for accurate gene expression analyses across different tissues, developmental stages and genotypes in rice for drought tolerance

Background Quantitative reverse transcription PCR (qRT-PCR) has been routinely used to quantify gene expression level. This technique determines the expression of a target gene by comparison to an internal control gene uniformly expressed among the samples analyzed. The reproducibility and reliability of the results depend heavily on the reference genes used. To achieve...

Lodging Resistance of Japonica Rice (Oryza Sativa L.): Morphological and Anatomical Traits due to top-Dressing Nitrogen Application Rates

Background Lodging in rice production often limits grain yield and quality by breaking or bending stems. Excessive nitrogen (N) fertilizer rates are the cause of poor lodging resistance in rice, but little is known about the effect of top-dressing N application rates on the mechanical strength of japonica rice plants, especially how the anatomical structure in culms is affected...

Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice

Brown planthopper (BPH) is the most devastating pest of rice. Host-plant resistance is the most desirable and economic strategy in the management of BPH. To date, 29 major BPH resistance genes have been identified from indica cultivars and wild rice species, and more than ten genes have been fine mapped to chromosome regions of less than 200 kb. Four genes (Bph14, Bph26, Bph17...

Genetic Variability in Phosphorus Responses of Rice Root Phenotypes

Background Low phosphorus availability is a major factor limiting rice productivity. Since root traits determine phosphorus acquisition efficiency, they are logical selection targets for breeding rice with higher productivity in low phosphorus soils. Before using these traits for breeding, it is necessary to identify genetic variation and to assess the plasticity of each trait in...

Rice panicle plasticity in Near Isogenic Lines carrying a QTL for larger panicle is genotype and environment dependent

Background Panicle architectural traits in rice (branching, rachis length, spikelet number) are established between panicle initiation and heading stages. They vary among genotypes and are prone to Genotype x Environment interactions. Together with panicle number, panicle architecture determines sink-based yield potential. Numerous studies analyzed genetic and environmental...

Proteomic and Glycomic Characterization of Rice Chalky Grains Produced Under Moderate and High-temperature Conditions in Field System

Background Global climate models predict an increase in global mean temperature and a higher frequency of intense heat spikes during this century. Cereals such as rice (Oryza sativa L.) are more susceptible to heat stress, mainly during the gametogenesis and flowering stages. During periods of high temperatures, grain filling often causes serious damage to the grain quality of...

Marker assisted pyramiding of two brown planthopper resistance genes, Bph3 and Bph27 (t), into elite rice Cultivars

Background Brown planthopper (BPH) is the most destructive insect in rice production. Breeding of resistant cultivars is the most cost-effective and environment-friendly strategy for BPH management; however, resistant cultivars are currently hampered by the rapid breakdown of BPH resistance. Thus, there is an urgent need to use more effective BPH resistance genes or pyramiding...

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

Background Rice (Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a...

Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance

Background The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was...

The existence of C4-bundle-sheath-like photosynthesis in the mid-vein of C3 rice

Background Recent studies have shown that C4-like photosynthetic pathways partly reside in photosynthetic cells surrounding the vascular system of C3 dicots. However, it is still unclear whether this is the case in C3 monocots, especially at the molecular level. Results In order to fill this gap, we investigated several characteristics required for C4 photosynthesis, including C4...

QTLs for Resistance to Major Rice Diseases Exacerbated by Global Warming: Brown Spot, Bacterial Seedling Rot, and Bacterial Grain Rot

In rice (Oryza sativa L.), damage from diseases such as brown spot, caused by Bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by Burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °C). Therefore, the need for cultivars carrying genes for resistance...

Development of Cytoplasmic Male Sterile IR24 and IR64 Using CW-CMS/Rf17 System

BackgroundA wild-abortive-type (WA) cytoplasmic male sterility (CMS) has been almost exclusively used for breeding three-line hybrid rice. Many indica cultivars are known to carry restorer genes for WA-CMS lines and cannot be used as maintainer lines. Especially elite indica cultivars IR24 and IR64 are known to be restorer lines for WA-CMS lines, and are used as male parents for...

Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought

BackgroundWith the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and...

Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars

BackgroundThe most sustainable approach to control rice blast disease is to develop durably resistant cultivars. In molecular breeding for rice blast resistance, markers developed based on polymorphisms between functional and non-functional alleles of resistance genes, can provide precise and accurate selection of resistant genotypes without the need for difficult, laborious and...

Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.)

Background Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains.ResultsThe...

Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response

Background Rice is one of the most important food crops for humans. To improve the agronomical traits of rice, the functions of more than 1,000 rice genes have been recently characterized and summarized. The completed, map-based sequence of the rice genome has significantly accelerated the functional characterization of rice genes, but progress remains limited in assigning...

Kinetic Analysis of Zinc/Cadmium Reciprocal Competitions Suggests a Possible Zn-Insensitive Pathway for Root-to-Shoot Cadmium Translocation in Rice

Background Among cereals, rice has a genetic propensity to accumulate high levels of cadmium (Cd) in grains. Xylem-mediated root-to-shoot translocation rather than root uptake has been suggested as the main physiological factor accounting for the genotypic variation observed in Cd accumulation in shoots and grains. Several evidence indicate OsHMA2 – a putative zinc (Zn...

Association of SNP Haplotypes of HKT Family Genes with Salt Tolerance in Indian Wild Rice Germplasm

Background Rice is one of the most important crops for global food security but its productivity is adversely affected by salt stress prevalent in about 30 % of the cultivated land. For developing salt-tolerant rice varieties through conventional breeding or biotechnological interventions, there is an urgent need to identify natural allelic variants that may confer salt tolerance...

Rice: The First Crop Genome

Rice was the first sequenced crop genome, paving the way for the sequencing of additional and more complicated crop genomes. The impact that the genome sequence made on rice genetics and breeding research was immediate, as evidence by citations and DNA marker use. The impact on other crop genomes was evident too, particularly for those within the grass family. As we celebrate 10...

The Rice TCM5 Gene Encoding a Novel Deg Protease Protein is Essential for Chloroplast Development under High Temperatures

BackgroundHigh temperature affects a broad spectrum of cellular components and metabolism in plants. The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms. Deg proteases are required for the survival of Escherichia coli at high temperatures. However, it is still unclear whether rice Deg proteases are required for chloroplast development...

Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

BackgroundRice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce...

Potential Yield Increase of Hybrid Rice at Five Locations in Southern China

BackgroundA number of field studies have demonstrated that the yield potential of hybrid rice cultivars is higher than that of inbred cultivars, although the magnitude of difference between hybrid and inbred cultivars at different yield levels has not been described. The objective of this study is to compare the yield increase potential at different yield levels between hybrid...