Terminologies in Genetics and Plant Breeding Part -12

Ochre Codon. One of the stop codons, UAA.

Ocimene. A volatile terpene found in certain legumes. Its amount varies among clones,and thus ocimene content may be altered by breeding, suggesting that clones withimproved attractiveness for honeybee visitation could be developed.

Octad. A group of eight ascospores contained in an ascus. It is produced in species inwhich the tetrad normally undergoes a post-meiotic mitotic division.

ODV. Other Distinguishable Varieties; seeds of other varieties with distinct appearancepresent in a seed lot of designated variety.

OECD. Organization for Economic Cooperation and Development. OECD wasdeveloped after the Second World War in Europe. The scheme developed for uniformtechnology and standard methods and practice for seed production and certificationfor forage moving in international trade was taken over by OECD in 1962. Since then,it adopted and implemented schemes for certification of different kinds of seedsincluding those of cereals, sugar beet, forestry, and the like. The basic objective ofOECD seed scheme is to encourage use of seed of high quality in the participatingcountries. The scheme authorizes use of labels and certificates for seed produced andprocessed for international trade according to the seed principles. The scheme is openon voluntary basis to members of organization as well as to other member countriesof United Nations. If a country adopts OECD seed schemes, it is obliged to ensurethat the rules of the scheme are strictly observed.

Off - Season Nursery. A place wherein a breeding strain is grown in a season not suitedto its normal rearing. The off-season planting serves the purpose of advancinggenerations, e.g., growing of off-season wheat and chickpea at Wellington (TamilNadu) and Dharwad (Karnataka), respectively.

Off-type: An individual differing from the population norm in morphologicalor other traits; the term also includes escapes and contaminants (eg. seeds that donot conform to the characteristics of a variety, uncontrolled self-pollination duringproduction of hybrid seed, segregates from plants, etc.)

Okasaki Fragment. A small segment of single-stranded DNA synthesized as a part ofthe lagging strand in DNA replication. The strand of the original DNA being used asthe template for lagging strand is unfolded in 3’ to 5’ direction; however, replication166always proceeds in the opposite direction (5’ to 3’ direction). This is why laggingstrand is synthesized in fragments (while the leading strand continuously).

Oligogene. Major gene.

Oligogenic. Of characters controlled by one or a few genes.

Oligonucleotide ligation assay (OLA): A PCR-based method for SNP typing; it is a ligase mediated gene detection system which uses exact 3′ matching of aprimer to one of the SNP allele; if this happens, the other labeled oligonucleotidethat binds to the nucleotide immediately next to the SNP on the other side wouldbe joined to the primer by ligase; the resulting sample can then be tested for thepresence of the label

Oligonucleotide ligation assayAssay for SNP genotyping based on the hybridization of a pair of oligos with the target PCR products, followed by ligation of the two oligos by DNA ligase.

Oligonucleotide microarraysOligonucleotides synthesized at a very high density (up to one million oligonucleotides/cm2) directly on thin wafers of silicon glass. Syn., DNA chips.

Oligonucleotide. A short segment of synthetic DNA.

Oligonucleotides: Small single-stranded segments of DNA typically 20-30nucleotide bases in size which are synthesized in vitro.

Oncogene. The cancer-causing gene; a gene whose expression leads to the production ofa cancer. Oncogenes are usually mutated forms of normal cellular genes.

Oncogene: A gene, one or more forms of which is associated with cancer. Manyoncogenes are involved, directly or indirectly, in controlling the rate of cell growth.

One Gene – One Enzyme Hypothesis (Beadle and Tatum 1941). A hypothesis statingthat each gene controls the synthesis or the activity of only a single protein withcatalytic activity (enzyme). With the developments in biochemical genetics, theprinciple has been verified and modified. The modified version is one cistron – onepolypeptide.

Ontogeny. The course of development of an individual organism, organ, or an organelle.

OntologiesControlled vocabularies shared by database communities working on different taxa.

On-Types. Plants that conform to the standard type in question with respect to acharacteristic or group of characters. For example, several on-type progenies arebulked to form the pure-seed lot during purification of a variety through massselection.

Opal Codon. One of three stop codons, UGA.

Open reading frameA correct reading frame that begins with an initiation codon and ends with a termination codon.

Open-Pollinated Corn. Corn propagated from seed produced by uncontrolledpollination.

Open-Pollinated Progeny Test. A test for GCA by evaluating progenies derived fromseed produced on selected plants outcrossed with other plants of the same population.Usually used in forage species.

Open-reading frame (ORF): The mRNA region between the start and stopcodon

Operator. A DNA region at one end of an operon that acts as the binding site forrepressor protein.

Operator: A region of DNA at one end of an operon that acts as the binding sitefor a specific repressor protein and so controls the functioning of adjacent cistrons

Operon. A set of adjacent structural genes (whose mRNA is synthesized in one unit) andthe adjacent regulatory signals that affect transcription of the structural genes.

Operon: A set of adjacent structural genes whose mRNA is synthesized in onepiece, together with the adjacent regulatory genes that affect the transcription ofthe structural genes; it is under the control of an operator gene, lying at one endof it

Oppositional Factor Hypothesis (East and Mangelsdorf, 1925). A hypothesis putforward to account for gametophytic incompatibility in Nicotiana spp. It states that167the incompatible allele in the style opposes the penetration of pollen tubes with thesame allele.

Optical mapping: An enabling technology for whole genome analysis, whichinvolves the capture of individual DNA molecules, obtained directly fromgenomic DNA, followed by digestion in situ by selected restriction endonucleases;the resulting fragments are then visualised directly to produce detailed opticalrestriction maps; this methodology allows patterns of sequence variation tobe detected across entire genomes, without the need for DNA amplification,and, unlike other genomewide scanning methods, provides detailed haplotypeinformation by analysing individual DNA molecules or issued patents claim thesame invention

Order Effects. The effects associated with the sequence in which parents are crossed toproduce three-way (triallel) or double cross (quadriallel) hybrids. A critical analysis ofthe combining ability effects of higher order provides evidence for the relativesignificance of the order in which the parents have been arranged to produce doublecross hybrids. It results as a consequence of epistasis. For instance, if two inbred lines,A and B, are derived from one source and lines C and D from another, the highestyieldingdouble cross is likely to be obtained from pairings of the type (A × B) × (C ×D).

Order. A systematic category that follows the class but precedes family.

ORF. Open Reading Frame. A section of sequenced piece of DNA that begins with astart codon (AUG) and ends with a stop codon (any one of UAG, UGA and UAA). It ispresumed to be the coding sequence of a gene.

Organ culture: The growth in aseptic culture of plant organs, such as rootsor shoots, beginning with organ primordia or segments and maintaining thecharacteristics of the organ

Organelle. A subcellular structure of characteristic size, shape, and specialized function,for example, mitochondria, chloroplast, endoplasmic reticulum or nucleolus.

Organic agriculture: A concept and practice of agricultural production thatfocuses on production without the use of synthetic inputs and does not allow theuse of transgenic organisms. USDA’s National Organic Program has establisheda set of national standards for certified organic production which are availableonline.

Organic conservation breeding: Varieties that are of conventional origin areconserved and propagated by cultivation under organic standards; relevant toolder varieties which should be conserved as a genepool for future breeding effortsand to varieties of high importance

Organism. The unit of a continuous lineage with an individual evolutionary history.

Organogenesis. The process of the production of organ systems in animalembryogenesis.

Orthologous genes: Genes of different species performing the same function.

Orthologous genes: Homologous genes that have become differentiatedin different species derived from a common ancestral species; as opposed toparalogous genes

Orthologous sequencesSequences from different species that originated from the same ancestral sequence.

Osmoregulation. The adjustment of osmotic potential. Under water deficit condition,there is reduction in the osmotic potential of crop plants. This reduction may stemfrom either a net increase in the cell solute concentration or the loss of water from thecell. Thus a genotype having capacity for osmoregulation can maintain turgor pressurewhich is necessary for normal cell function and growth. Low osmotic potential canalso result in lowering of the level of leaf water potential, which triggers stomatalclosure in response to water deficit. Osmotic adjustment during seed-filling periodcould help maintain photosynthesis under water stress, resulting in improved droughtresistance and yield. Considerable genotypic differences for osmotic adjustment havebeen found in sorghum and other crops.

Outbreeding. Mating between relatives occurring less commonly than would occur bychance. Said in another way, it is a mating system in which mating is betweenindividuals less closely related than individuals mating at random. The overallconsequence of outbreeding is to prevent differentiation of populations. Also callednegative inbreeding.

Outbreeding: The crossing of plants that are not closely related genetically, incontrast to inbreeding, in which the individuals are closely related

Outcross. A cross, usually natural, to a plant of different genotype.

Outcrossing: Cross-pollination between plants of different

Overcompensatory Interaction. An interaction between two or more genotypes suchthat they cooperate each other to mutual advantage. Cooperating genotypes have ahistory of mutual selection. This kind of interaction is expected to approach towardsstable equilibrium. This system is something akin to a system involving heterozygoteadvantage over homozygotes, and properties similar to that of favourable epistaticinteractions between or among different loci.

Overdominance Hypothesis. An assumption based on the superiority of heterozygotecompared to homozygous parents. The superiority increases in proportion to theamount of heterozygosity. The implication is that the two different alleles in theheterozygote (A1A2) perform different functions, and that the sum of their differentproducts is superior to the single product produced by either allele in homozygousstate (A1A1/ A2A2). There are in fact at least some evidences at which theheterozygote (for blood group) is indeed superior to homozygotes. However, formetric traits, what is observed as overdominance is not the real one because the levelof dominance is overestimated due to repulsion phase linkages.

Overdominance hypothesisHeterozygotes at certain loci are superior to the two homozygotes for the locus leading to heterosis.

Overdominance. Dominance such that the heterozygote falls outside the range of aparent with greater phenotypic value, AB blood group compared to AA and BB groupsin humans, for example. True overdominance (single locus heterozygote advantageover homozygotes) is almost certainly rare; however, dominance and/ or epistasistogether with linkage are capable of simulating overdominance.

Overdominance: The phenomenon in which the character of the heterozygotesis expressed more markedly in the phenotype than in that of either homozygote usually the heterozygote is fitter than the two homozygotes; this can give riseto monohybrid heterosis when the hybrid vigor is obtained by crossing parentsdiffering in a single specified pair of allelic genes

Overgo probesGene-specific oligonucleotide-based probes designed from ESTs.

Overlapping DNA: A special type of gene organization; one DNA sequencemay code for different proteins; it is performed by two open reading frames which subsequently act

Oxidative Phosphorylation. ATP synthesis by phosphorylation of ADP using the energyprovided by electron transfer during aerobic respiration.