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Recently, a dual or multiple origin of domesticated rice has been the prevailing opinion among rice scientists because rice is clearly differentiated into two major varietal groups, indica and japonica, and several minor groups. Molecular clock studies that suggested that divergence in the A-genome wild rice genepool occurred prior to domestication gave further weight to the opinion that rice had...
Regulatory small RNAs (approximately 20 to 24 nt in length) are produced through pathways that involve several key evolutionarily conserved protein families; the variants of these proteins found in plants are encoded by multigene families and are known as Dicer-like, Argonaute, and RNA-dependent RNA polymerase proteins. Small RNAs include the well-known classes of microRNAs (miRNAs, ~21 nt) and the...
The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community. This paper outlines a set of standard procedures for describing...
Increasing the iron (Fe) and zinc (Zn) concentrations of staple foods, such as rice, could solve Fe and Zn deficiencies, which are two of the most serious nutritional problems affecting humans. Mugineic acid family phytosiderophores (MAs) play a very important role in the uptake of Fe from the soil and Fe transport within the plant in graminaceous plants. To explore the possibility of MAs increasing...
Opportunities abound to apply crop science to solving many of the world’s food problems. International agricultural research centers (IARCs) provide a window through which students can see the need for improved agricultural productivity and briefly experience the rewards of working on difficult but important issues. In today’s world of highly technical graduate education, students find it difficult...
Plants have evolved delicate mechanisms to cope with environmental stress. Following exposure to environmental stimuli, extracellular signals are perceived and transmitted through signal transduction cascades. Upon receipt and transmission of the signals, a number of stress-related genes are induced, leading to stress adaptation in plant cells. Rice, which is a critical food grain for a large portion...
Metabolomics is a recently developed technology for comprehensive analysis of metabolites in organisms. Plant metabolites that are produced for the growth, development, and chemical defense of plants against climatic alterations or natural predators are also useful to us as nutrients or medicines; hence, it is important to comprehend the amounts and varieties of plant metabolites. Besides providing...
Flowering time is a key trait for geographical and seasonal adaptation of plants and is an important consideration for rice breeders. Recently identified genetic factors provide new insights into this complex trait. The list of genes involved in flowering and their functions tells us that the molecular basis of day-length measurement includes both of the evolution of unique factors and the regulatory...
Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The...
Research into rice—the world’s most important food crop—is crucial for the development of technologies that will increase productivity for farmers who rely on rice for their livelihood. This is particularly the case throughout the developing countries of Asia and is also true for much of Latin America and, increasingly, Africa. The benefits of such increased productivity will flow through to rice-growing...
Rice domestication involved a complex process of selection by ancient humans, leading to the development of a new species, Oryza sativa, during the last 10,000 years. Recent rice genome research and the cloning of domestication-related genes have provided novel knowledge about the domestication process, although recent reviews have revealed more complexity than previously suspected. Some of this additional...
The genic colinearity of grass genetic maps, physical maps, and contiguous genomic sequences has been a major contributor to almost two decades of study into the structure and evolution of grass genomes. This research has led to the discovery of all of the major phenomena responsible for the rapid evolution of flowering plant genomes. These processes include polyploidy, transposable element (TE) amplification,...
One of the great advantages of the fully sequenced rice genome is to serve as a reference for other cereal genomes in particular for identifying genes linked to unique traits. A trait of great interest is reduced lignocellulose in the stem of related species in favor of fermentable sugars as a source of biofuels. While sugarcane is one of the most efficient biofuel crops, little is known about the...
Accurate sequencing of the rice genome has ignited a passion for elucidating mechanism for sequence diversity among rice varieties and species, both in protein-coding regions and in genomic regions that are important for chromosome functions. Here, we have shown examples of sequence diversity in genic and non-genic regions. Sequence analysis of chromosome ends has revealed that there is diversity...
Iron deficiency is a major cause of reduced crop yields worldwide, particularly in calcareous soils. Unlike barley, rice is highly susceptible to iron deficiency because of a low capacity to secrete mugineic acid family phytosiderophores (MAs), which are iron chelators secreted by graminaceous plants. We present an approach toward the generation along with field trials of transgenic rice lines exhibiting...
Coordinated transcriptional modulation of large gene sets depends on the combinatorial use of cis-regulatory motifs in promoters. We postulate that promoter content similarities are diagnostic for co-expressing genes that function coherently during specific cellular responses. To find the co-expressing genes we propose an ab initio method that identifies motif families in promoters of target gene...
The increasing world population and global climate change have made optimizing crop plant return both crucial and urgent. Furthermore, improved understanding of crop yield potential as well as the implementation of related crop management strategies might be important components of a new green revolution. Notably, grain size (weight) and grain number are both essential components of crop yield potential;...
Proteomics techniques have identified a vast number of proteins that participate in the growth of plants or their adaptation to environmental stresses. Functional analysis of those proteins will contribute to the development of high-yielding crops through artificial manipulation of the basic life phenomena of plants or through the assessment of their stress tolerance. The conditions in almost all...
Plant roots have a large range of functions, including acquisition of water and nutrients, as well as structural support. Dissecting the genetic and molecular mechanisms controlling rice root development is critical for the development of new rice ideotypes that are better adapted to adverse conditions and for the production of sustainably achieved rice yield potential. Most knowledge regarding the...
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