RICECAP GLOSSARY
A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z
Aadult plant resistance – resistance to pathogens that is manifested in mature plants but not in the younger, seedling stages.
amylose content- amylose is a polysaccharide made of linear chains of 100-1000 glucose residues. Amylose content is used to represent the starch fraction of milled rice, or the amount of starch in the grain that determines its eating and cooking quality. Low-amylose varieties are moist, sticky, and glossy after cooking; high-amylose varieties are dry and fluffy.
anther culture- The aseptic culture of immature anthers to generate haploid plants from microspores via androgenesis, used in generation of double-haploid plants.
awn. A bristlelike extension, present in some rice varieties, of varying length originating from the outer glume of the rice spikelet.
bioinformatics- bioinformatics describes any use of computers to handle biological information. In practice the definition used by most people is narrower; “bioinformatics” can be a synonym for "computational molecular biology" - the use of computers to characterize the molecular components of living things. [Damian Counsell, bioinformatics.org]
blast – a plant disease caused by the ascomycete fungus Pyricularia grisea (aka P. oryzae), in temperate flooded and tropical upland (rainfed) rice cropping systems. Rice blast is characterized by the appearance of lesions on leaves, nodes, and panicles. In suitable conditions, lesions expand rapidly and coalesce, leading to complete drying/death of infected leaves. Most damage occurs when the fungus grows in the area below the seed head, causing it to break. Magnaporthe oryzae is the sexual/perfect stage of the fungus.
brown rice - rice kernels where only the hulls have been removed but the bran remains. This type of rice can be eaten and is often found in health food and specialty stores.
bulked segregant analysis- A method to obtain markers linked to a target trait, in which DNA samples, prepared from a number of individuals of each of two contrasting phenotypes, are separately pooled and used to generate contrasting DNA fingerprints. DNA fragments unique to one pool become candidates for a marker linked to the gene controlling the trait.
CAP - USDA/CSREES program - Coordinated Agricultural Project
centiMorgan (cM)- Unit of distance on a genetic map, based on recombination frequencies. For small recombination fractions, cM and % recombination frequency are nearly equivalent. A distance of one cM between two loci corresponds to about a 1% chance that they will inherit alleles from different grandparents due to crossing over in the most recent generation.
chalkiness – the level of chalk-like appearance in endosperm. Chalkiness is undesirable as it detracts from appearance and uniformity, and generally results in lower mill yields because grains tend to break easily.
D
degree of milling - the extent of bran removal from brown rice.
doubled haploid (DH)- a plant with the full chromosome complement that results from spontaneous or induced chromosome doubling of a haploid cell or plant, usually after anther or microspore culture.
equilibrium moisture content (EMC) - the moisture content that rice will come to after an extended period of exposure to air at set temperature and relative
EST (expressed sequence tag) A partial cDNA sequence, derived from a single sequencing reaction run. Useful for (1) assigning putative function to a cDNA without the need of obtaining a full length sequence, and (2) designing PCR primers to amplify gene portions. Allows a large number of cDNAs to be characterized by restricting sequencing to a single run for each clone.
forward genetics- The traditional approach to genetics, which starts with a phenotype and then identifies the gene(s) or mutation that control or cause that trait. Contrast with reverse genetics, in which one goes from a gene/sequence to then determining phenotype.
functional genomics- an area of study aimed at determining the function of genes and the proteins they encode in determining traits, physiology or development of an organism. Generally the term is used for an experimental approach utilizing computational and high-throughput technologies at the level of whole genomes.
gene chip- usually refers to a specific form of oligonucleotide array, produced by Affymetrix with photo- lithographicmasking techniques used in semiconductor manufacture. Used to produce arrays with up to 400,000 distinct oligonucleotides.
head rice - The are 3/4 or longer whole milled kernels separated from the total milled rice. Depending on the grain tyupe, whole milled kernels are spearated using special sized screens. The weight of whole milled kernels or head rice is expressed as a percentage of the original rough rice sample. For example, if you start with 100 lbs. of rough rice and mill it, then separate out whole milled kernels and broken milled kernels, you may obtain values like 62 lbs. of whole milled rice (head rice) and 11 lbs. of broken milled rice (brokens.) Together these represent 73 lbs. of total milled rice from the original sample. As percentages, this means the sample yielded 62% head rice, 11% brokens and 73% total milled rice. The rest of the sample would have been bran and hulls.
head rice yield (HRY) - mass percentage of rough rice that remains as head rice
High-throughput- in genetic studies, a methodology utilized to quickly screen large numbers of individuals (genotypes) for a particular trait. “High-throughput” can be strictly defined as any process where large amounts of samples or information passes through a system from input to output. In addition to being used in discussion of genomic studies, the term is commonly applied in the fields of computer systems, pharmaceutical discovery, and combinatorial chemistry.
horizontal resistance- partial resistance to multiple races of a pathogen; it is usually race-nonspecific and a quantitative trait (as opposed to vertical resistance).
indica - one of the two major ecogeographical races of Oryza sativa (see also japonica). The major type of rice grown in the tropics and subtropics. It has broad to narrow, light green leaves and tall to intermediate plant stature (except for the semidwarf). Indica plants tiller profusely. Grains are long to short, slender, somewhat flat, and awnless. Indica grains shatter easily and have 23-31% amylose content. They grow mostly in the Philippines, India, Pakistan, Java, Sri Lanka, Indonesia, central and southern China, African countries, and other tropical regions.
japonica - one of the two major ecogeographical races of O. sativa (see also indica).A group of rice varieties from northern and eastern China grown extensively in some areas of the world. It has narrow, dark green leaves, medium-height tillers and short to intermediate plant stature. It is found in the cooler zones of the subtropics and in the temperate zones. Grains are short, roundish, spikelets awnless to long-awned, panicles low-shattering, and have 0-20% amylose content.
javanica - designation for the bulu and gundil varieties of Indonesia and many upland rices. They belong to the japonica race of O. sativa. Rice varieties with broad, stiff, light green leaves. It is low-tillering and has a tall plant stature. Grains are long, broad, and thick, awned or awnless. Javanica grains are low-shattering and have 0-25% amylose content.
Mmarker-assisted selection (MAS) The use of DNA markers for selection of desired individuals within a population, by linking the molecular marker to a desired trait. To be of maximal use, the markers should be closely linked to one or more target loci, which may often be quantitative trait loci. (for review, see Goff and Salmeron, Scientific Amer., August, 2004).
microarray- (aka DNA chip) usually refers to a miniaturized array of a large number (into the thousands) of unique DNA sequences spotted robotically onto glass slides or other solid substrate. Microarrays are used to simultaneously study large numbers of genes and their regulation, by probing with labeled nucleic acids taken from biological samples. Can also refer to miniaturized arrays of proteins or other types of molecules.
milled rice - Rice kernels that have been milled to remove the bran, leaving "white" or milled rice. After removal of broken kernels, whole milled rice is the type most often found in stores for normal cooking. Broken kernels from milled rice are often sold for processing purposes like dog food, etc.
milled rice yield (MRY) - The weight of milled rice, both brokens and whole rice kernels, that remains after hulls and bran are removed from 100 lbs of rough rice. Sometimes this is also referred to as Total Milled Rice or Total Milled Rice Yield.
milling quality - A value used in the rice industry to represent the percentage of head rice and total milled rice obtained from a given rough rice sample. For example, a rough rice sample is taken from a load of rice and milled. It yields 609T head rice, 10% brokens and thus 70% total milled rice. Milling quality would be expressed as 60/70 or head rice/total milled rice, with the broken percentage understood to be 10. The price that a farmer receives for rough or paddy rice can be greatly affected by the milling quality and a minimum standard for number 2 paddy rice is 55/70 milling quality to avoid discounts. Milling quality can be affected by many factors such as harvest moisture and diseases.
milling yield - The estimate of the quantity of head rice (whole rice or nearly whole kernels) and of total milled rice that can be produced from a unit of rough rice. It is generally expressed as a percentage.
MPSS (massively parallel signature sequencing) a method for identifying and quantifying many mRNA molecules simultaneously from a single sample. MPSS produces short (16-20 base) sequence tag from a defined position within an mRNA, and measures the relative abundance of these tags in a library to estimate gene expression profiles. MPSS utilizes technology commercialized by Lynx Therapeutics, Inc. (for an example of application see: Meyers, et al., (2004) Nature Biotech. 8:1006-1011).
oryzanol –a group of natural compounds extracted from rice bran, made up of ferulic acid esters of triterpene alcohol and sterols. Clinical studies indicate that consumption of oryzanol can lower serum cholesterol in humans.
QTL (quantitative trait loci) Genetic loci where allelic variation is associated with variation in a quantitative trait. The presence of QTL is inferred from genetic mapping. Total variation is partitioned into components linked to a number of discrete, mapped chromosome regions.
reverse genetics- Going from a gene/DNA sequence, often discovered via high- throughput sequencing and bioinformatics technologies, to its biological function. Reverse genetic methods are more amenable to whole genome, high- throughput analysis than is forward genetics. Contrast with forward genetics, in which one goes from a heritable phenotype to discovery of a gene/sequence.
rice blast – a plant disease caused by the ascomycete fungus Pyricularia grisea (aka P. oryzae), in temperate flooded and tropical upland (rainfed) rice cropping systems. Rice blast is characterized by the appearance of lesions on leaves, nodes, and panicles. In suitable conditions, lesions expand rapidly and coalesce, leading to complete drying/death of infected leaves. Most damage occurs when the fungus grows in the area below the seed head, causing it to break. Magnaporthe oryzae is the sexual/perfect stage of the fungus.
RiceCAP - The RiceCAP project is supported by the USDA National Research Initiative Competitive Grants Program. Program funding is from the USDA, Cooperative State Research, Education, and Extension Service (CSREES) in the area of Applied Plant Genomics Coordinated Agricultural Program (APG-CAP). The RiceCAP project is entitled "A coordinated research, education, and extension project for the application of genomics discoveries to improve rice in the United States"
RIL (recombinant inbred line)- An RIL is formed by crossing two inbred strains, followed by repeated selfing or sibling mating to create a new inbred line whose genome is mosaic of the parental genomes.
RNAi - RNA interference: A gene silencing phenomenon whereby double-stranded RNAs trigger the specific degradation of a homologous mRNA. The specific dsRNAs are processed into small interfering RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA- induced silencing complex (RISC). Useful as an application for specific suppression of an individual gene.
rough rice - rice grain as harvested from the field with hulls intact; often referred to as "paddy rice"
SAGE (serial analysis of gene expression)- is a method for comprehensive analysis of gene expression patterns in a given tissue or treatment. It is based on the sequencing of short segments (9-17 nucleotide) portions of cDNAs that have been ligated together into large concatemers. SAGE assumes that the abundance of a give “tag” for a gene correlates with the abundance of that transcript in a sample. (For more information see http://www.sagenet.org/ or http://cgap.nci.nih.gov/SAGE/SAGEInformation )
semi-dwarf- a plant with reduced height due to a genetic factor(s). The development of semi-dwarf varieties led to the widespread use of shorter, more productive varieties of rice that allowed the 'green revolution' in the 1960s. (for a short commentary, see: Salamini, (2003) Science, 302: 71-72.)
sheath blight- a plant disease caused by the fungus Rhizoctonia solani. It has become the most prevalent rice disease in the southern U.S. Symptoms of the disease generally appear as plants enter the late-tillering or early internode-elongation stages. The disease can progress up the plant and causes white/gray lesions on leaves. Lodging can be observed during severe infestations, particularly in tall rice varieties.
somaclonal variation- genetic or epigenetic changes induced during the callus phase of in vitro cultured plant cells -- sometimes visible as a changed phenotype in regenerated plants.
SNP (single nucleotide polymorphism) - Pronounced “snip”. A genetic marker resulting from variation in sequence at a particular position within a DNA sequence. SNPs can result from a base transition (A for G, T for C), transversion (G or A for T or C) or single-base deletion. Such variation is extensive throughout all genomes.
synteny – genes or sequences occurring in the same order on chromosomes of different species; can be used as a tool for genetic mapping in related organisms.
T-DNA- The DNA segment of the tumor-inducing plasmid present in pathogenic Agrobacterium tumefaciens, that is transferred to plant cells and inserted into the plant’s DNA as part of the infection process. Used as a vehicle for transferring genes into the genome during the production of transgenic plants.
TILLING (Targeting Induced Local Lesions IN Genomes) - The end-product of the TILLING process is a plant (and its offspring) that has been identified with a change in a specific gene of interest -- that plant line is then useful to determine the overall effect/role of that gene on properties of the plant.
TILLING is a high-throughput method to identify specific gene knockouts in mutant populations, useful as a tool of reverse genetics. TILLING utilizes PCR-based screening of plants generated through chemical mutagenesis (generally via ethyl methane sulfonate (EMS) treatment), often resulting in the isolation of missense and nonsense mutant alleles of the targeted gene(s). TILLING permits the high-throughput identification of mutations in target genes without production of genetically modified organisms and it can be an efficient way to identify mutants in a specific gene that might not confer a strong phenotype by itself.
For more information, visit: http://www.anawah.com/solutions/tilling.htmlTransposon (transposable element) - A DNA element that can move from one chromosomal location in the genome to another.
vertical resistance- complete resistance to some races of a pathogen but not to others, It is usually conferred by a major resistance (R) gene as a qualitative trait. (as opposed to horizontal resistance).
VIGS (virus-induced gene silencing)- a method to transiently interrupt gene function of a specific, target gene through RNA interference--uses a plant virus as a vehicle for introduction of the interfering RNA.