Terminologies in Genetics and Plant Breeding Part -2

C 306. A tall wheat variety developed through a complex cross in 1965. This variety stillcontinues to be dominant wheat for drought (soil moisture stress) and low-fertilityconditions in some parts of the plains of India.

C banding: A cytological staining technique for chromosomes that labelsregions around the centromere with Giemsa stain; usually a bandlike and darklystained structure appears, which consists of heterochromatin; the technique isintensively used in chromosome identification and genome characterization, including structural changes and polymorphisms

C value: The DNA quantity per genome (i.e., per chromosome set); the contentof diploids is referred to as the 2C; haploid cells contain the 1C amount of DNA

C4 Pathway. A pathway of CO2 fixation in many angiosperms in which the first stableproduct of photosynthesis is C4 compounds such as aspartate, malate, andoxaloacetate (instead of 3-phosphoglycerate of the Calvin cycle). In mesophyll cells,the CO2 is assimilated by carboxylation of PEP. C4 acids so-produced are thentransferred to the bundle sheath cells, probably by diffusion. Within these cells, theCO2 released by decarboxylation enters the PCR cycle, giving origin to 3-phosphoglycerate. It is interesting to note that the C4 pathway and PCR cycle areintegrated in different cells of the same plant. From evolutionary point of view, thissystem of CO2 fixation is most efficient, as photorespiratory losses (a characteristic ofC3 plants) do not occur in this case. The initial enzyme in C4 pathway is PEPcarboxylase, which is insensitive to O2. The bundle sheath cells get only CO2 throughdecaboxylation of C4 acids, and the enzyme ribulose-1,5-diphosphate carboxylaseproduces only phosphoglyceric acid (in absence of O2). There is thus nophotorespiration.

Callus culture: The in vitro culture of callus, often as first stage in theregeneration of whole plants in culture

Callus induction: Undifferentiated plant tissue is produced at wound edges;callus can also be induced and grown in vitro by varying the ratio of hormones(eg., auxin and cytokinin) in the growth medium

Callus. An undifferentiated mass of cells, originating from an anther, microspore, planttissue ex plant, or other cellular sources, when cultured in vitro.

Callus: A cluster of undifferentiated plant cells that have thecapacity to regenerate a whole plant in some species.

Callus: Undifferentiated plant cells that are multiplied under tissue culture.

CAM. A recently discovered photosynthetic mode especially adapted to deserts calledCrassulacean Acid Metabolism. In this mode, several desert succulent plantsincluding the cacti keep their stomata closed during the hot daytime and open them inthe cool of the night. CO2 absorbed through leaf openings is stored in organic acidsand not fixed until the next day. This delayed photosynthesis greatly reduces waterloss during the day, thereby enhancing the succulent plant’s ability to maintain waterbalance and water storage.

Canalisation. A developmental buffering system reducing potential variation due togenotype or environment.

Canalised Character. A character whose phenotype is kept within narrow boundsdespite disturbing forces. Development is such that all the different genotypes havethe same constant phenotype over the range of environments that is usual for thespecies. The genetic differences are revealed if the organisms are put in stressenvironment or a severe mutation stresses the developmental system.

Cancer genes: Mutant alleles of normal genes that lead to cancer

Candidate gene approach of association mapping: Association analysis is restricted to the genomic regions having the candidate genes/QTLs for the trait(s) of interest.

Candidate Gene. A sequenced gene of previously unknown function that, because of itschromosomal position or some other property, becomes a candidate for a particularfunction such as disease determination.

Candidate gene: A gene that is expected, on the basis of previous knowledge, to be involved in the control of a trait of interest.

Candidate gene: A gene whose function suggests that it may be involved in thegenetic variation observed for a particular trait (phenotype, disease, or condition);candidate genes can be divided into two categories: positional and functional

Candidate population: In forestry, trees, which are planted to serve as a basefor forward selection or in some way selected from that for further studies; forexample, selected phenotypic selections may serve as a candidate population, which is subject to further progeny testing before reselection to the breedingpopulation; the genotypes taken into consideration for the breeding population

Capture oligo: The oligo that is complementary to the 3' side of the SNP locus and includes the polymorphic nucleotide.

Carbohydrate. A macromolecule composed of carbon, hydrogen, and oxygen.Carbohydrates are the main source of energy and are also important components ofcell wall and intercellular materials. Monosaccharides are simple sugars having thegeneral formula Cn(H2O)n. Ribose, deoxyribose, glucose, fructose, galactose,mannose, etc. are monosaccharides. Disaccharides are sugars formed by thecondensation of two hexose monomers with the loss of one molecule of water. Theyare, therefore, C12H22O11. Sucrose and lactose fall in this category. Polysaccharidesresult from the condensation of many hexose monomers, with a corresponding loss ofwater molecules. Their formula is (C6H10O5)n. The most important polysaccharides inliving organisms are starch (plants) and glycogen (liver and muscles), and cellulose,the most important structural element of the plant cell wall.

Carbon Source. A nutrient (such as sugar) that provides carbon to organisms needed forthe synthesis of organic molecules.

Carboxydismutase. Also called ribulose-1,5-diphosphate carboxylase; the primaryphotosynthetic enzyme that represents about 50% of the stromal proteins. It leads tothe integration of CO2 and H2O with ribulose-1,5-diphosphate to produce twomolecules of 3-phosphoglycerate (the first stable product of the PCR cycle). Theenzyme is highly sensitive to O2, and it also brings about oxygenation of ribulose-1,5-diphosphate to produce one molecule of 3-phophoglycerate and one molecule ofglycolate. The latter then enters photorespiratory cycle and ultimately oxidised to C02and H2O. This loss is the characteristic of PCR cycle (C3 plants). The enzymecomprises 16 sub-units (L8S8): 8 large sub-units of high molecular weight (L8), and 8small sub-units of smaller molecular weight (S8). The large sub-unit is coded by thegenes (rbc-L) present in chloroplast DNA, while the small one is produced by nucleargenes (rbc-S). The rbc-L is the highly conserved gene; only little variation has beenobserved across species.

Carcinogen. A substance that causes cancer.

Carcinogen: Physical or chemical agent which induces cancer.

Carrier. An individual who possesses a mutant allele but does not express it in thephenotype owing to the presence of its dominant counterpart. Thus the genotype Aa isa carrier of a if there is complete dominance of A over a.

Carrier: (heterozygote) An individual who carries one copy of a recessive gene.

Carrying Capacity. The ability of an ecosystem, community, organism or any partthereof to maintain and sustain further growth. The amount of biomass that can besupported under inputs (accumulated organic matters) and outputs (respired organicmatters) balance is called maximum carrying capacity. No further increase in size(growth) is possible if the system has reached this theoretical limit. Increasingevidences suggest that the optimum carrying capacity (where growth rate is highest)sustainable over long periods in the face of environmental uncertainties is lower by asmuch as 50% than the theoretical limit of maximum carrying capacity.

Cartagena Protocol on Biosafety: The first international treaty dealing with themovement of genetically modified organisms (GMOs) across country borders; theprotocol was drawn up under the Convention of Biological Diversity and cameinto force in September 2003; more than 100 countries have ratified the agreement; although the biosafety protocol was pushed for by the South and drafted as a promise of legal protection against the introduction of GMOs, the weakness of its provisions means that the protocol and the national biosafety laws following its introduction are being steadily turned into tools to facilitate the introduction of GMOs

Caryogamy. The fusion of nuclei of two opposite sex cells following immediately afterplasmogamy in higher plants.

Cases: In association mapping, individuals carrying the allele of a gene responsible for a disease.

Catabolite Repression. The inactivation of an operon caused by the presence of largeamounts of the metabolic end products of that operon.

Catalyst. A substance that accelerates chemical reactions. However, the catalyst itself isnot modified in the process, so that it can be used again and again.

Cation. A positively charged ion such as Na+, K+, etc.

cDNA libraries: Libraries which store sequences copied into DNA from RNAtranscripts; typically these sequences carry only the exon information for makingproteins

cDNA Library. A library composed of cDNAs (complementary DNAs), not necessarilyrepresenting all mRNAs.

cDNA library: A population of bacterial transformants or phage lysates containing recombinant DNA molecules, in which all the mRNA species isolated from an organism or tissue are represented as cDNA inserts.

cDNA. Also called complementary DNA. Synthetic DNA transcribed from a specificRNA through the action of an enzyme called reverse transcriptase.

cDNA: A duplex DNA where one strand is identical in sequence (except for Tin place of U) and one is complementary to a particular RNA.

Cell (Hooke 1665). The smallest morphologic and physiologic unit of a living systemcharacterized by growth, individual metabolism, independent energy cycle, andreproduction.

Cell Biology. The study of structure, function, development, reproduction, and lifehistory of cells.

Cell culture: A technique for growing cells under laboratoryconditions.

Cell Cycle. The life cycle of the individual cell encompassing interphase and nucleardivision phase.

Cell cycle: The sequence of events that occurs between the formation of a celland its division into daughter cells; it is conventionally divided into G0, G1, (Gstanding for gap), S (synthesis phase during which the DNA is replicated), G2, andM (mitosis)

Cell Division. The process by which two cells are formed from one. It is the reproductionof cells by karyokinesis and cytokinesis. The process of cell division should beappropriately called cell multiplication.

Cell division: The reproduction of a cell by karyogenesis and cytogenesis

Cell envelope: The different surface components of the cell that are presentoutside the cytoplasmic membrane

Cell fusion: Fusion of two previously separate cells, occurs naturallyin fertilization; it can be induced artificially by the use of fusogens such aspolyethylene glycol; fusion may be restricted to cytoplasm, nuclei may fuse aswell; a cell formed by the fusion of dissimilar cells is referred to as a heterokaryon

Cell fusion: The formation of a hybrid cell produced by fusing two different cells.

Cell generation time: The time span between consecutive divisions of a cellcycle

Cell hybridisation: The fusion of a somatic cell in vitro and formation of viablecell hybrids

Cell Lineage. A pedigree of cells related through asexual division.

Cell Sap. The soluble phase of the cell. It may consist of at least three general fractions:(a) micromolecular (water, inorganic ions, and dissolved gases), (b) mesomolecular(all metabolic intermediates such as lipids, sugars, nucleotides, etc), and (c) freemacromolecules (mostly proteins, and RNAs).

Cell Theory (Schleiden and Schwann 1838/1839). A statement that all living organismsare composed of cells and cell products. The modern cell theory is a compilation ofseveral discoveries regarding cells, that is: (a) cells are the smallest unit of life, (b)cells are the morphological and physiological units of life, (c) the properties of agiven organism depend on those of its individual cells, and (d) cells originate onlyfrom pre-existing cells, and continuity is maintained through the genetic material.

Cell Wall. The rigid exoskeleton structure enclosing and protecting the contents of mostplant and bacterial cells.

Cell wall: The steadfast external coat that surrounds the cell

Cell: The basic structural and functional unit of a plant; it is a system surroundedby membranes and is compartmentalised into specific functional areas and/ororganelles with special tasks

Cell: The fundamental level of structural organization incomplex organisms. Cells contain a nucleus (with chromosomes) and cytoplasm with the protein synthesis machinery bounded by a membrane.

Center of diversity: A geographical location or local region where a particulartaxon exhibits greater genetic diversity than it does anywhere else; N. I. VAVILOVdeveloped this concept; he considered that the centers of diversity are also thecenters of origin of a crop species

Center of origin: An area from which a given taxonomic group of plants hasoriginated and spread and/or where wild-type species are found in greatest geneticvariation; the theory was first published by V. I. VAVILOV in 1922

Centimorgan (cM). A map unit; so-called after Thomas Hunt Morgan.

Centimorgan (cM): A unit of measure of recombination frequency. One cM isequal to 1% chance that a marker at one genetic locus will be separated from amarker at a second locus due to crossing-over in a single generation. (A unit of measure of recombination frequency. One centimorgan is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation)

Centimorgan: The distance between two genes/loci that is expected to lead to one percent crossing over between them.

Central Dogma. The hypothesis that biological information flows from DNA to RNA toprotein. Except some exception (RNA viruses), the rule is generally valid.

Central dogma: Refers to F. CRICK’s seminal concept that in nature genetic information generally flows from DNA to RNA to protein. (The underlying model for describing gene structure and function. It states that genes are transcribed in the nucleus into messenger RNA molecules, which are then translated into proteins on ribosomes)

Centres of Origin (Vavilov 1926). Geographical regions represented by the greatestdiversity of plant species. Vavilov considered these ares as geographical regions oforigin, especially if wild races of relevant species were also present in those regions.He identified 8 such centres. Later he concluded that this system did not hold true,and he developed a system of ecological groups based on specific traits. However,this concept has been substantially modified by Harlan (1992), who suggested toabandon the concept of centres altogether, and advocated to refer “ecological regionsrather than to centres”.

Centric constriction: The visible bight along a chromosome that bears the centromere

Centric fission: A chromosomal structural change that results in two acrocentric or telocentric chromosomes from one metacentric chromosome

Centric Fusion. A reciprocal translocation in which the large arms of two acrocentricchromosomes unite to form a metacentric chromosome. It necessarily reduces thechromosome number by one through eliminating the small translocation product,which is mostly heterochromatic. However, the number of large chromosome armsremains unchanged. Also see Robertsonian translocation.

Centric fusion: The whole-arm fusion of chromosomes by the joining together of two telocentric chromosomes to form one chromosome

Centric: Chromosomes having a centromere as opposed to acentric (having no centromere)

Centriole: In mitosis, this small spherical body forms the center of the astral rays

Centripetal Selection. Also called stabilizing selection. Selection acting against extremephenotypes, that is, selection favouring an intermediate “stable” value (phenotype).This happens more often in natural populations. Genotypes having intermediate valuefor most survival and reproductive traits are favoured owing to greater biologicalfitness. If the population has a number of different intermediate genotypes, it willcause preservation of genetic variability.

Centromere interference: An inhibitory influence by the centromere on crossing-over and the distribution of chiasmata in its vicinity

Centromere mis division: A transverse instead of lengthwise division of the centromere resulting in telocentric chromosomes

Centromere orientation: The process of orientation of centromeres during prometaphase of mitosis and meiosis that contributes to a proper segregation of chromatids or chromosomes during anaphase

Centromere. A localized region in each chromosome to which the spindle fibres appearto be attached and which seem to determine movement of chromosomes during celldivision. (Also called kinetochore by cell biologists).

Centromere: The structure to which the two halves of a chromosome, the chromatids, are joined; the centromere is generally flanked by repetitive DNA sequences and it is late to replicate

Certation: Competition between individual pollen tubes belonging to different genotypes and growing at different rates.

Certified Seed. Seed produced from the foundation or certified seed under the regulationof a legally constituted agency. This class of seed is used for commercial cropproduction. It is produced on a large scale in a way so as to meet the standard set bythe certifying agency.

Certified seed: Seed produced under an officially designated system of maintaining the genetic identity of, and provisions for, seed multiplication and distribution of crop varieties; is the progeny of breeder, select, foundation, or registered seed; it is grown in compliance with regulations determining standards of germination, freedom from diseases and weeds, and trueness to type

Certified seed: The progeny or increase from a breeder or foundation seed and approved by a certifying agency.

Chaos Theory. A small change to a complex system can result in a large and unpredictedoutcome. For example, the introduction of semi-dwarfing gene in the hexaploid wheathas resulted in short stature, increased photo-receptivity and harvest index, high yield,and the like.

Character Difference. A contrasting difference between two organisms (or two purelines) with respect to one particular character. For example, plant height is acharacter, and the two lines, one with tall and other with dwarf statures representcharacter difference.

Character. A specific property of an individual resulting from the interaction of agene(s) with the environment. A gene cannot cause a character to develop unlessproper environment is present; conversely, no amount of manipulation of anenvironment will produce a character if necessary gene(s) is absent. It is the interplayof these two agents that determine the development of the character. Geneticists usethis term as a synonym for characteristic or trait.

Character: Any propert of an individual showing heritable variation. It includes morphological, physiological biochemical and behaviourial properties.

Chargaff’s Rule. A rule that is followed in all DNA molecules. Total amount of purinebases (A+G) is always equal to the total amount of pyrimidine bases (C+T). Further,the amount of A always equals the amount of T, and C always equals G. However,(A+T) / (C+G) ratio varies across species; but within the species, it remains relativelyconstant. This rule seemed to be one of the milestones towards deciphering doublehelical model of DNA byWatson and Crick (1953).

CHAs. Chemical Hybridising Agents. These are chemical agents used to selectively killpollens of a genotype likely to be used as female parent in a hybrid-breedingprogramme (ethrel, DPX 3378, MG1 & MG2, for example). Ethrel causes femalesterility in Indian mustard when applied at the rate of 2000-3000 ppm. MG1 & MG2are carcinogenic and have residual effect too. Oxanilates @ 1500 ppm can also beapplied for the same purpose during stamen-pistil primordia stage. However, nochemicals are perfectly selective. In wheat, chemicals such as CH 9701, CH 9702, CH9708, CH 9831, and CH 9832 have exhibited acceptable levels of male-sterility. Themost suitable stage for the spray of CHAs has been found as 10-15 mm of spikelength.

Chasmogamy. One of the outbreeding devices as in rice. In this case, opening of flowerbuds follows after bursting of the anther. Thus, some extent of outcrossing (4-5%) isalmost always ensured.

Check Cross. The crossing of an unknown genotype with a phenotypically similarindividual of known genotype. The F2 segregation serves to establish whether thesame phenotypes stem from the action of identical or dissimilar alleles of the samelocus or from the action of non-allelic genes.

Chemical mutagen: A chemical capable of causing genetic mutation

Chemical-hybridizing agents (CHA): Compounds applied to plants prior to anthesis to selectively induce male sterility

Chiasma interference: The occurrence, less frequent or more frequent than expected by chance, of two or more crossing-over and chiasmata in a given segment of a chromosomal pairing configuration and/or chromosome

Chiasma terminalisation: The progressive shift of chiasmata along the arms of paired chromosomes from their points of origin toward terminal positions

Chiasma. A cross-shaped structure formed following crossing over between any twonon-sister chromatids of a pair of homologous chromosomes during meiosis. It isvisible manifestation of crossing over.

Chiasma: A cross-shaped structure forming the points of contact betweennesses chromatids of homologous chromosomes, first seen in the diplotene stage of meiotic prophase I

Chimera. A plant (rarely an animal) composed of genetically distinct tissues owing tomutation, somatic segregation or grafting. According to their structure, chimera maybe sectorial (different tissues growing side by side and occupying distinct sectors ofvarying size), periclinal (one tissue placed centrally and the second grows around it asthe covering layer), and mericlinal (actually an interrupted periclinal chimera).

Chimera: A tissue containing two or more genetically distinct cell types, or an individual composed of such tissue; chimeral plants may originate by grafting, spontaneous mutation, induced mutation, sorting-out from variegated seedlings, mixed callus cultures, or protoplast fusion;

Chimera: An individual consisting of cells of two or more types.

Chimeric Genes. Genes generated through rearrangement and shuffling of other geneshaving their own coding and regulatory domains.

Chi-Square (2) Test. A statistical test used to determine the probability of obtainingobserved proportions by chance, under a specific hypothesis.

Chi-squared test (χ2 test): A significance test used to statistically assess the goodness of fit of observed data to a prediction

Chlorophyll. An asymmetrical molecule with porphyrin hydrophilic head composed offour pyrrole rings forming a complex with an Mg atom. The molecule has also a longhydrophobic phytol chain attached to one of the rings. There are several types ofchlorophyll (a, b, c, d, and e). Types a and b are found in chloroplasts of higherplants.

Chloroplast. A chlorophyll-containing organelle (plastid) in plants, serving as the site ofphotosynthesis. Besides chlorophyll, it also contains carotenoid pigments. It seems toarise from pre-existing chloroplasts. It has its own DNA, and is considered semiautonomous.

Chondroid. A cell organelle in bacteria, which is functionally equivalent to themitochondrion of higher organisms.

Chromatid aberration: Chromosomal changes produced in one chromatid as a consequence of

Chromatid bridge: A bridelike structure caused by a dicentric chromatid with the two centromeres passing to opposite poles during anaphase; the frequency of chromatid bridges in AII of meiosis is sometimes used as a measure for the level of cytological disturbances (E.g. in induced autopolyploid and allopolyploids)

Chromatid Conversion. A type of gene conversion that is inferred from the existence ofidentical sister-spore pairs in a fungal octad that shows a non-Mendelian allele ratio.

Chromatid Interference. A situation wherein the occurrence of a crossover between anytwo non-sister chromatids affects the probability of those chromatids being involvedin other crossovers in the same meiosis.

Chromatid Segregation. See double reduction.

Chromatid segregation: Segregation of two sister-chromatid segments of a chromosome

Chromatid. One of two thread-like structures formed by the longitudinal division of achromosome during prophase, and known as daughter chromosome during anaphase.

Chromatid: The two identical halves of a chromosome produced for cell division and meiosis.

Chromatin remodelling: Refers to a reshaping (at molecular scale) of chromatin, that alters specific genes so that DNA subsequently gets expressed; it can be caused by short interfering RNA (siRNA) or certain transcription activators

Chromatography: A technique used for separating and identifying the components from mixtures of molecules having similar chemical and physical properties; molecules are dissolved in an organic solvent miscible in water, and the solution is allowed to migrate through a stationary phase; since the molecules migrate at slightly different rates they are eventually separated

Chromatophore. Any particle isolated from photosynthetic bacteria, which containsphotosynthetic pigments. Chromatophores are scattered throughout the cytoplasm ofsuch bacteria.

Chromocenter: A central aggregation of heterochromatic chromosomal elements of the cell nucleus; the euchromatic chromosome arms extend from the chromocenter                                                                                              

Chromogene. Any gene localised in chromosomes as opposed to cytogene.

Chromomere. A small beadlike structure visible on a chromosome during prophase ofmeiosis and mitosis.

Chromoplast. A plastid containing coloured (yellow or orange) pigments with reducedchlorophyll content. Yellow or orange chromoplasts occur in petals, fruits, and rootsof certain higher plants. The red colour of ripe tomato fruits is due to the presence ofchromoplasts having the red pigment, lycopene, which is a member of carotenoidfamily. Chromoplasts containing pigments such as phycoerythrin and phycocyanin arefound in red and blue green algae, respectively.

Chromosomal aberration: An abnormal chromosomal complement resulting from the loss, duplication, or rearrangement of genetic material

Chromosomal Hybrid Sterility. Sterility associated with the failure of chromosomepairing and other meiotic misadventures indicating lack of structural homologybetween chromosomes of two parental species. All these upset formation offunctional gametes.

Chromosomal Inheritance. Inheritance of a genetic information contained in thechromosomes (Mendelian inheritance) as opposed to extrachromosomal inheritance.

Chromosomal. Pertaining to structure, constituents, and function of chromosomes.

Chromosome Aberration. Any type of change in the chromosome structure or number;also called chromosome mutation. It is the occurrence of cytologically visible changesin the genome. The changes may include chromosome parts, whole chromosomes, orwhole chromosome sets. The change in chromosome parts is called structuralaberrations or chromosome rearrangements. The changes in whole chromosome setsare referred to as numerical aberrations or euploidy.

Chromosome Addition. The addition of a chromosome (pair) to the normal complementof a variety. If the extra chromosome is from another species, it is called alienchromosome addition. O’Mara (1940) developed disomic addition lines by attemptinga cross between common wheat (AABBDD) and rye (RR) followed by chromosomedoubling and selecting a disomic addition line of wheat with a pair of addedchromosomes from rye (2n= 42+IrIr) in later generations.

Chromosome banding: The experimental production of differentially stained regions because of the distribution of different chromatin constituents along a chromosome

Chromosome Complement. The group of chromosomes derived from a particulargametic or zygotic nucleus. It may be composed of one (monoploid nucleus), two(diploid nucleus), or more (polyploid nucleus) chromosome sets.

Chromosome Disjunction. The separation of paired chromosomes during anaphase offirst meiotic division.

Chromosome doubling: Induced or spontaneous doubling of chromosome sets leading to rediploidization or to polyploids

Chromosome elimination: The loss of chromosomes from nuclei during certain mitotic or meiotic stages; it is common in several artificial autopolyploid sand allopolyploids

Chromosome engineering: Manipulation of whole chromosome sets, individual chromosomes, or even chromosome segments, by different means, for scientific analysis or improvement of performance of crop plants

Chromosome jumping: A technique that allows two segments of duplex DNA that are separated by thousands of base pairs (~200 kb) to be cloned together; after sub cloning, each segment can be used as a probe to identify cloned DNA sequences that, at the chromosome level, are roughly 200 kb apart

Chromosome landingDirect identification, in a single step, of the clone with DNA insert having the target gene using one or more markers located very close to the gene, made possible by high-resolution mapping, as a result of which the physical distance between the markers and the target gene is less than the average insert size of the genomic library.

Chromosome Loss. Failure of a chromosome to become part of the daughter nucleus atcell division. Slow replication of DNA of the chromosome (compared to the restones), its slow movement towards the pole, and similar other reasons may causechromosome loss during the cell multiplication.

Chromosome Map. The graphic representation of a chromosome in which the genesbelonging to a particular linkage group are plotted according to their relativedistances. In genetic maps, recombination frequency expressed in map units is used asa measure of distance between linked genes. However, in cytological maps, genes arelocated on the basis of cytological findings obtained with the aid of chromosomemutations such as deletions, inversions, or translocations.

Chromosome map: A map showing the location of genes on a chromosome, deduced from genetic recombination and cytological experiments

Chromosome number: The specific somatic chromosome number (2n) of a given species or a crop derivative of it

Chromosome painting: Fluorescent in situ hybridisation of a specifically labelled DNA probe or probes that hybridizes to the entire chromosome of the probe’s origin; using different fluorescent dyes and probes, a pattern multi-coloured chromosomes or chromosome segments appear

Chromosome pairing: The highly specific side-by-side association of homologous chromosomes during meiotic prophase

Chromosome Rearrangement. See chromosome aberration.

Chromosome reduplication: The synthesis of all compounds that result in an identical copy of the original chromosome

Chromosome segment substitution lines: A series of homozygous lines, each having a single distinct chromosome segment from a DP in the chromosome background of RP.

Chromosome segregation: The separation of the members of a pair of homologous chromosomes in a manner that only one member is present in any post meiotic nucleus

Chromosome staining: The pre-treatment and treatment of chromosomes with different dyes in order to make them more suitable for chromosome counting or specific analyses

Chromosome Substitution. The process by which a chromosome of one variety isreplaced or substituted into the genome of another variety. If a non-homologouschromosome is substituted into the genome of another species, the process is referredto as alien chromosome substitution. Nullisomics and monosomics can be used tofacilitate such substitutions.

Chromosome substitution: The replacement of one or more chromosomes by others from another source by spontaneous events or a crossing scheme 

Chromosome Theory of Inheritance (Sutton and Boveri, 1902). The unifying theorystating that chromosomes are containing structures of genetic factors. This theoryaccounts for inheritance pattern of Mendelian traits.

Chromosome theory of inheritance: States that the chromosomes, as the carriers of genetic information, represent the material basis of nuclear inheritance

Chromosome walking: A technique combining restriction mapping, subcloning, and nucleic acid hybridization to analyze DNA inserts of a genomic library in an effort to locate the gene of interest.

Chromosome. Structural units of the nucleus that carry genes in a linear order.Chromosomes undergo drastic morphological changes during the life cycles oforganisms. Most commonly, chromosome numbers range from 6 to 25 homologouspairs in diploid condition. At the extreme, one pair has been found in certain strains ofthe horse nematode Parascaris equorum, and 630 pairs in the fern – Ophioglossumreticulatum.

Chromosome: A condensed structure found in the cell nucleus that contains the genes of that cell. The self-replicating genetic structure of cells, containing genes, which determines inheritance of traits. Chemically, each chromosome is composed of proteins and a long molecule of DNA.

Chromosome-walking technique: A procedure that is used for the determination of a gene on a particular DNA clone of a DNA library; the total DNA of a chromosome has to be available as a series of overlapping DNA fragments; such fragments are produced either by DNA shearing or by cleavage using restriction enzymes; the fragments are used for series of hybridizations; it starts with a cloned gene, which is already identified on the same chromosome; this known gene serves as a probe for detection of clones (fragments) that contain neighbouring DNA sequences;

Cis configuration: Two sites on the same molecule of DNA.

cis Dominance. The ability of a gene to affect genes next to it on the same chromosome.

Cis-acting locus: Locus that affects the activity only of DNA sequences on the same molecule of DNA; usually implies that the locus does not code for protein.

cis-trans Test. A test to determine whether two mutant sites of a gene are in the samefunctional unit or gene.

Cistron. Originally defined as a functional genetic unit within which two mutationscannot complement. Now, it is equated with the term gene as the region of DNA thatencodes a single polypeptide, tRNA or rRNA.

CK60A (Stephens and Holland 1954). A cytoplasmic-genetic male sterile linedeveloped through placing Kaffir (pure line) genome in the cytoplasmic backgroundof Milo (pure line) by repeated backcrosses in sorghum. It provided the initial choiceof male-sterile line for hybrid breeding programme after its introduction from USA.This cytoplasm is designated as A1. Other versions of male-sterile cytoplasm are alsoavailable (A2 and A3, for example).

Clade. A group of related biological taxa that includes all descendants of an often remotecommon ancestor.

Cladistics. A system of biological taxonomy that reconstructs phylogenies in terms ofsuccessive sequences of branching ancestor-descendant lineages.

Cladogenesis. Evolutionary change characterized by tree-like (dendritic) branching,illustrating phylogenetic relationships.

Classical genetics:  Branch of genetics based solely on visible results of reproductive acts. It is the oldest discipline in the field of genetics, going back to the experiments on Mendelian inheritance by Gregor Mendel who made it possible to identify the basic mechanisms of heredity.

Clean Crop. An approach of establishing a multiline variety in which all the componentslines were resistant to all the prevalent races of the pathogen(s). The aim of thisapproach was to keep the crop as free of disease as possible, and at the same time toreduce the catastrophic disease losses following shifts in the racial composition of thepathogen population.

Cleavage. Rapid cycles of DNA synthesis followed by cell division in which thecytoplasm is partitioned without growth, occurring very early in embryonicdevelopment.

Cleaved amplified polymorphic sequenceDetection of length polymorphism following restriction digestion of specifically amplified PCR products; syn., PCR–RFLP.

Cleaved amplified polymorphic sequences (CAPS): PCR-amplified DNA (STS, EST, or SCAR products) that is digested with restriction endonucleases to reveal polymorphisms in restriction sites

Cleistogamous: Designating a self-pollinated plant that produces inconspicuous flowers that never open (Eg. wheat or tomato)

Cleistogamy. Fertilisation within closed flowers. It is a mechanism in which flower budsdo not open at all. Therefore, it enforces self-pollination and imposing restriction tooutbreeding. However, the precision with which it works is subject to modification byboth genetic and environmental forces. True cleistogamy is exemplified in the basalinflorescences of California oatgrass (Danthonia californica), lettuce, etc. It isperhaps favoured in a dry flowering season (Mediterranean climates in spring)because such flowers remain closed during much of the pollination period.Cleistogamy inhibits desiccation of anthers and stigmas, thus promoting full seed setby self-pollination. Flowers remain open only for a brief period, providingopportunities for occasional outcrossing. In some grain legumes such as pigeonpea,cleistogamy has been found under simple genetic control (monogenic recessive trait).

Clonal propagation: The reproduction of plants through asexual means, such as cuttings, grafts, or tissue culture.

Clone. A group of individuals descended vegetatively (asexually) from a commonancestor. Organisms so derived are highly uniform and homogeneous, and geneticallyidentical to their ancestor. A number of agricultural crops are clonally propagated.Nearly all clonally propagated species are perennial outcrossers in nature, and all suchplants are highly heterozygous and conspicuously intolerant of inbreeding. They oftenexperience inbreeding depression following inbreeding (selfing). Only highly superiorclones that carry favourably interacting alleles of many different loci, much like thegenotypes of elite F1 hybrids of corn, succeed in agriculture.

Clone: A genetic replica of an organism created without sexual reproduction.

Clone: Asexual progeny of a single asexually propagated plant.

Cloning vector: DNA molecule originating from a virus, a plasmid, or the cell of a higher organism into which another DNA fragment of appropriate size can be integrated without loss of the vector’s capacity for self-replication; vectors introduce foreign DNA into host cells, where it can be reproduced in large quantities. Examples are plasmids, cosmids, and yeast artificial chromosomes; vectors are often recombinant molecules containing DNA sequences from several sources.

Cloning. Asexual production of a line of cells or organisms or segments of DNAgenetically identical to the original one.

Cloning: Asexually producing multiple copies of genetically identical cells or organisms descended from a common ancestor.

Cloning: The process of asexually producing a group of cells (clones), all genetically identical, from a single ancestor. In recombinant DNA technology, the use of DNA manipulation procedures to produce multiple copies of a single geneor segment of DNA is referred to as cloning DNA.

Clustal: A group of multiple sequence alignment tools, e.g., ClustalW, ClustalX, and Clustal Omega.

Cluster analysis: A technique of statistical analysis in which similar variances are grouped or clustered; the results of statistical calculations are often shown as dendrograms; particularly, in cross breeding the cluster analysis is used in orderto select most diverse parents for crossing

Cluster analysis: The entities with similar features are grouped into the same cluster.

C-meiosis. Also called colchicine meiosis. It is a modified meiosis that occurs followingthe action of colchicine and other spindle poisons. If spindle formation is completelysuppressed during the first or the second or both meiotic divisions, meiotic productswith more than one chromosome set result. As a rule, spindle inhibition during thefirst or second meiotic division yields two diploid meiotic products. If the spindlecannot function in both meiotic divisions, the result is a tetraploid meiotic product.Similarly in C-mitosis, complete spindle suppression leads to the formation ofrestitution nuclei with doubled chromosome numbers.

Co 205. The first successful interspecific hybrid of sugar cane released as a cultivar inIndia. It was developed by crossing a clone - Vellai - of S. officinarum with the wildspecies, S. spontaneum. One of the seedling of this interspecific cross provided Co205 that became commercially acceptable in sub-tropical India, and later replaced thethen existing varieties belonging to the species S. barberi.

Coadaptation. The selection processes that tend to accumulate harmoniously interacting(coadapted) individuals or (coadapted) alleles into the gene pool of populations. Alsothe selection processes that tend to favour individuals that have mutually beneficialphenotypic associations with each other in populations.

Coarse Cereals. A group of cereals consisting of maize, sorghum, pearl millet, ragi,barley and a host of small millets including proso and foxtail. These are nutritionallyrich cereals.

Code Dictionary. A listing of 64 possible codons and their translational meanings suchas corresponding amino acid(s), chain termination, and the like.

Coding sequence: The part of a gene that determines the sequence of amino acids of a protein, as opposed to noncoding sequences, such as promoter, operator, intron, or terminator regions

Coding strand: The strand of duplex DNA that is transcribed into acomplementary Mrna molecule

Codominance. The situation in which a heterozygote shows the phenotypic effects ofboth alleles equally.

Codominance: The expression of both alleles in the heterozygote with equaleffect on the phenotype, as opposed to recessive and dominant

Codon bias: Although several codons code for a single amino acid, a plant may have a preferred codon for each amino acid this is called codon bias

Codon. A triplet of bases of mRNA that encodes a single amino acid or specifiescommencement or termination of translation of a genetic message.

Codon: A triplet of nucleotides in a DNA or RNA moleculethat codes for one of the 20 amino acids in proteins, or for asignal to start or stop protein production. Each gene thatcodes for protein is a series of codons that gives the instructionsfor building that protein.

Codon: A triplet of nucleotides that represents an amino acid or a termination (STOP) signal.

Coefficient of co-ancestry: The degree of relatedness between pairs of individuals/lines of the sample. Alternatively, it is the probability that the alleles of a randomly chosen gene in a pair of individuals/lines are identical by descent.

Coefficient of Coincidence. The ratio of the observed number of double recombinants tothe expected number. It is a measure of the intensity of interference. Its value rangesfrom 0 (absolute interference, that is, no double recombinants) to more than 1(negative interference).

Coefficient of correlation: A number that measures the linear dependencebetween two random variables; limiting values of −1 and +1 indicate perfectnegative and perfect positive correlation, respectively; a correlation of zero suggests a complete lack of association between the two variables

Coefficient of Selection. See selection coefficient.

Coefficient of Variation. A measure of relative dispersion for the purpose of comparingtwo or more statistical series. The series may differ in respect of standard deviation,means or both or may differ in units. However, cv, which is a percentage, andtherefore, unitless can be used to compare variability present in them. Numerically, itis standard deviation expressed as the percentage of mean [cv = (σ/μ) x 100]. Itremains unaltered by a change in scale; but it is altered by a change of origin, whichaffects the mean but not the standard deviation. The cv, as used in breedingexperiments, expresses experimental error as the percentage of mean. Numerically, cv= [(σ2e)½/ μ] x 100. It indicates the degree of precision with which the treatmentsare compared, and is a good index of the reliability of the experiment. Thus higher thecv value, the lower is the reliability of the experiment. The cv varies greatly with thetype of experiment, the crop being grown, the crop season, and the charactermeasured.

Coefficient of variation: The standard variation expressed as percentage of themean

Coenocytes: An organism or a portion thereof that is multinucleate; the nucleiare not each separate in one cell, such as in some protoplast or cell fusion products

Coenospecies. Two or more taxonomic species with the common evolutionary origin.Only limited gene exchange can occur between coenospecies. Usually sterile hybridsare produced by hybridisation.

Coenzyme. Usually a non-protein compound of low molecular weight required for theaction of some enzymes. For example, dehydrogenases require a nicotinamideadeninedinucleotide (NAD+) to function. In many coenzymes, as in NAD+, theessential components are vitamins, particularly those of the B group.

Cofactor. A metal or a prosthetic group (in case of conjugated proteins) required by theenzymes for their activity.

Cohorts. Progenies from different crosses in the same generation included forsimultaneous evaluation in the test nursery.

Coincidence. See coefficient of coincidence.

Colcemid. A synthetic equivalent of colchicine. It is used to induce polyploids usually inanimals.

Colchicine (Blakeslee and Avery 1937). An alkaloid drug used to induce polyploidy inplant species. However, at a lower concentration, it also acts as a mutagen. It isextracted from seeds or corms of the autumn crocus (Cochicum autumnale L.), amember of family Liliaceae. It acts as spindle poison and thus arrests formation ofspindle fibres during cell division. In the absence of spindle fibres, separation ofdaughter chromosomes and their migration to the opposite poles does not occur. Thusit leads to a cell with doubled chromosome complements. For induction of polyploid,it is applied to meristematic regions of the plant by wetting with an aqueous solution,by spraying on in an emulsion or by rubbing on in a lanolin paste. It is effective whenapplied to germinating seeds, or to young seedlings, roots, or to growing points suchas shoots or buds. The concentration, duration and temperature of the treatment allaffect the outcome. After application, the chemical arrests spindle formation in thedividing cell and prevent separation of the daughter chromosomes and their migrationto the opposite poles. Thus the cell becomes polyploid. Following induction,polyploid tissue may be identified on account of its larger cell size and morechloroplasts in the guard cells. Some other chemicals that can induce polyploidy arecolcimid (used more frequently in case of animal cells), acenapthene, chloral hydrate,ethyl-mercury-chloride, sulphanilamide, chloroform, ethyl alcohol, and the like.

Colchicine: A poisonous alkaloid drug (C22H25NO6) that is obtained frommeadow saffron (Colchicum autumnale); it has a disruptive effect on microtubularactivity; thus, it affects tissue metabolism generally, and mitosis and meiosis inparticular; it is used for induction of polyploidy

Colchiploidy: Polyploidy induced by application of colchicines

Colinear markersMarkers located in the same linear order in two different chromosomes of the same species or in chromosomes of two different species.

Colinearity. The exact point-by-point relationship between the order of amino acidsalong the polypeptide chain and the order of corresponding codons along thepolynucleotide chain of the nucleic acid.

Colony. A visible clone of cells.

Color classificationIn image analysis, extraction of the object, i.e., the plant, from the original RGB image.

Combination breeding: A breeding method that utilises the genetic diversityof individuals or varieties in order to create and to select new phenotypes on thebasis of genetic recombination of useful characters of parental materialcombinedin the hybrid

Combined marker-assisted selectionMAS is used in combination with phenotypic screening/selection.

Combining Ability. The ability to produce superior hybrids when crossed with otherappropriate inbreds.

Combining ability: Capacity or ability of a genotype to transmit superiorperformance to its crosses

Combining ability: The performance of a line with others in across.

Commensalism. A kind of interaction in biotic community in which one population(commensal) benefits but the second (host) is unaffected.

Common Phenolics. Phenolic compounds found in plants. These are present in smallconcentration in both resistant and susceptible plants; but their synthesis oraccumulations appear to be accelerated following infection. These are toxic to thepathogens, and their production and accumulations proceed at a faster rate afterinfection in a resistant variety than in the susceptible one.

Community. In ecological sense, all the populations occupying a given area.

Comparative (gene) mapping: Localisation (mapping) of a common set of DNAprobes onto linkage maps of different species; the results of these comparisonsindicate substantial conservation of blocks of genes and even large segments ofchromosomes between species; this approach shows synteny of markers amongrelated species or genera; such maps have been established for cereals (wheat,maize, oats, rye, rice, sorghum, millet) and Solanaceae, such as potato, tomato,and paprika

Comparative genomic hybridisation (CGH): A molecular cytogenetic techniquethat allows detection of DNA sequence copy number changes throughout thegenome in a single hybridisation

Comparative mapping: A comparative study of linkage maps of different species.

Comparative positional candidate gene: A gene that is likely to be located inthe same region as a DNA marker that has been shown to be linked to a singlelocustrait or to a quantitative trait locus (QTL), where the gene’s likely location inthe genome of the species in question is based on its known location in the mapof another species (i.e. is based on the comparative map between the two species)

Compensating trisomic: An aneuploid individual with an extra chromosome in which a missing standard chromosome is compensated for by two novelinterchange chromosomes; the two novel chromosomes carry two different armsof the missing chromosome

Competition Effect. Interdependence of adjacent plants because of their common needfor limited available resources such as sunshine, soil nutrients, moisture, CO2, O2, andthe like. Non-planted borders, varietal and fertilizer competition, and missing hillstypes of competition effects are taken into account. Removing border plants from plotmeasurements, grouping homogeneous treatments and stand correction are a fewtechniques of controlling competition effects from the agricultural experiments.

Competition. The endeavour of two or more organisms (genotypes) of the same or ofdifferent species to gain access to a factor(s) or a thing that is in short supply. In plantbreeding, such competition is usually for survival and reproduction of individuals inthe population.

Competitive Ability. The ability of one species or a genotype to succeed in a mixture. Itdepends on the ability to (a) produce a greater proportion of offspring to the nextgeneration at the expense of the others, (b) reduce the number of its counterpartswithout being changed, and (c) avoid the others without necessarily having an effecton it.

Complementarity: The chemical affinity between specific nitrogenous bases asa result of their hydrogen bonding properties. The property of two nucleic acidchains having base sequences such that an antiparallel duplex can form where theadenines and thymines (or uracils) are opposed to each other, and the guaninesand cytosines are opposed to each other.

Complementary Action. Gene action such that two nonallelic genes may be required toproduce a single effect, that is, each gene complements to the action of the other tomake the final product (function). Wherever it operates, a 9:7 ratio is obtained [9 (AB-):7 (A-bb, aaB- & aabb)] in F2 generation. If the whole population is advanced tothe F3 generation, the ratio gets changed to 25: 39. (Can you work out?)Complementation. The production of a wild-type phenotype when two differentmutations are combined in a diploid or a heterokaryon.

Complementary DNA (cDNA): A single-stranded DNAmolecule that is complementary to a specific RNA moleculeand synthesized from it. Complementary DNAs are importantlaboratory tools as DNA probes and for isolating andstudying individual genes.

Complementary DNA (cDNA): DNA that is synthesised from a messengerRNA template; the single-stranded form is often used as a probe in physicalmapping

Complementary homopolymeric tailing: The process of addingcomplementary nucleotide extensions to different DNA molecules, for example, dG (deoxyguanosine) to the 3′-hydroxyl ends of one DNA molecule and dC(deoxycytidine) to the 3′-hydroxyl ends of another DNA molecule to facilitate, after mixing, the joining of the two DNA molecules by base pairing between thecomplementary extensions

Complementary sequences: Nucleic acid base sequences that can form adouble-stranded structure by matching base pairs; the complementary sequenceto G-T-A-C is C-A-T-G.

Complementary. Of genes that interact to produce a distinct qualitative effect comparedto their individual effects separately.

Complementary: The opposite or “mirror” image of a DNAsequence. A complementary DNA sequence has an A forevery T, and a C for every G. Two complementary strands ofsingle-stranded DNA will join to form a double-strandedmolecule.

Complementation Test. See cis-trans test.

Complementation test: A genetic test to determine if two mutations withsimilar phenotypes are allelic (occur in the same gene) or are nonallelic (occurin separate genes); individuals homozygous for each mutation are crossed; if themutations are allelic, the offspring will have the mutant phenotype; if they arenonallelic the offspring will be heterozygous for both alleles and will have thewildtype phenotype

Complementation: The production of a wild-type phenotype when twodifferent mutations are combined in a diploid or a heterokaryon.

Complete Block Designs. Statistical designs for conducting agricultural experiments inwhich each block (replication) includes a complete set of treatments. CRD, RCBDand LSD are the examples of complete block designs. These designs are suited forexperiments with a small number of experiments.

Complete diallel: A mating design and subsequent progeny test resulting fromthe crossing of a certain number of parents in all possible combinations includingselfs and reciprocals; because of severe inbreeding depression in the selfs, theseare often skipped, nevertheless the test is still called a full diallel

Complete line conversionMarkers used for foreground as well as background selections in a backcross program.

Complete linkage mapA linkage map containing sufficiently large number of genetic markers so that every point in the genome of the species is genetically linked to at least one marker.

Complete penetrance: The situation in which a dominant gene always producesa phenotypic effect or a recessive gene in the homozygous state always producesa detectable effect

Completely Randomised Design. The experimental design in which the treatments areassigned completely at random so that each experimental unit has the same chance ofreceiving any one treatment. For CRD, any difference among experimental unitsreceiving the same treatment is considered as experimental error; hence, it isappropriate only for experiments with homogeneous experimental units such aslaboratory experiments, where environmental effects are relatively easy to control. Forfield experiments, where there is generally large variation among experimental plotsowing to soil fertility gradient (for example), the CRD is rarely used.

Completely randomized design: The structure of the experiment in a completelyrandomized design is assumed to be such that the treatments are allocated to theexperimental units completely at random

Complex Loci. A cluster of two or more closely linked and functionally related genesconstituting a pseudoallelic series. It may contain one operon.

Complex Loci. A cluster of two or more tightly linked but functionally related genesconstituting a pseudoallelic system. These genes may be regulated in a coordinatedmanner.

Complex Trait. A trait whose inheritance can be explained by the interaction of severalgenes plus the environment.

Complexity reduction of polymorphic sequences: Genomic DNA is digested with two restriction enzymes and the complexity is reduced by selective amplification procedure of AFLP.

Complexity: Of a genome or DNA preparation, the total number of different sequences present in the genome/DNA.

Complon. A complementation unit.

Component Compensation (Adams, 1967). The increase in one individual componentof a complex trait accompanied by a corresponding decrease in the other. Forinstance, the increase in the number of grains/spike is often accompanied by thedecrease in seed weight so that total grain yield may remain unaffected. This occursowing to a physiological balance between source and sink. It has been shown thatcomponent compensation (and negative correlation) arises in response to competitionbetween developmentally flexible components. In the presence of a stress, componentcompensation is nearly complete; in its absence, component compensation (which, inturn, indicates partial independence of genetic component traits of a complexcharacter) is partial, albeit not zero.

Composite Breeding Approach. A breeding strategy that involves a number of specificprocedures and modifications to meet short-term and long-term breeding objectives.

Composite cross: A population derived from the hybridization of severalparents, either by handpollination or by the use of male sterility

Composite interval mappingIt first carries out single marker analysis, then builds multiple QTL model, and uses QTLs present in the other marker intervals as cofactors in the model.

Composite transposon: A transposable element formed when two identical ornearly identical transposons insert on either side of a nontransposable segment ofDNA, such as the bacterial transposon Tn5

Composite variety: A plant population in which at least 70% of progeny resultfrom cross of the parent lines

Composite: A plant of the immense family Compositae, regarded as comprisingthe most highly developed flowering plants bot; a mixture of genotypes fromseveral sources, maintained by normal pollination

Composite-cross population: A population generated by hybridizing morethan two varieties and/ or lines of normally self-fertilizing plants and propagatingssuccessive generations of the segregating population in bulk in specificenvironments so that natural selection is the principal force acting to producegenetic change; artificial selection may also be imposed; the resulting populationis expected to have a continuously changing genetic makeup

Composite-Error Effect. The effects of uncontrolled factors during experimentalmeasurements of genotypic values. It includes effect of plot compared to others in thesame replication, error due to sampling among plants of the same family, errors ofmeasurement, and the like.

Composites. A mixture of genotypes from several sources, maintained by normalpollination in isolation. It is technically advance generation seed mixture fromintervarietal or intravarietal crosses. Dhawan (1963) outlined breeding methodologyfor developing commercial varieties in maize named as composites. Initially the usualprocedure was to make intervarietal crosses and evaluate them for inbreedingdepression during F2, F3,…., etc. generations. The final population is constituted fromcrosses showing least inbreeding depression. These days composites are developedeven through making full-sibs within a variety or population. The highest yieldingcomposites are obtained from S1 progenies followed by full-sib progenies.

Compound chromosome: Formed by the union of two separate chromosomes

Compound cross: A combination of desirable genes from more than two inbredlines, breeding strains, or varieties

Concatenated cDNA sequencingIt involves isolation and pooling of multiple cDNA clones, their enzymatic concatenation, followed by shotgun sequencing.

Conditional lethal genes: Genes that are expressed in response to a specificenvironmental stimulus such as a specific chemical; when expressed, they arelethal to the plant

Conditional mutation: A mutation that has the wild-type phenotype undercertain environmental conditions (temperature, age, nutrition) and a mutantphenotype under other conditions

Confidence Limits. The limits within which any given proportion of the sample means isexpected to lie under the condition of normal distribution of the means of samples.For example, if x is the sample mean, the limits x } 2σ/√n would contain thepopulation mean (μ) on an average in 95 out of 100 cases. In other words, we mayexpect the inequality {x-2σ/√n ≤ μ ≤ x + 2σ/√n} to hold good on the average in 95%of the samples. The two limits (on either sides) is called the confidence limits. (Alsosee level of significance).

Confirmation of marker–trait linkageEvaluation of the observed marker–trait linkage in another mapping population developed from the same cross or in the same mapping population by another worker.

Confirmation of QTLReplication studies conducted to ensure that the detected QTL is real and to verify its position and effect size.

Confounding. A technique of reducing the size of replication over a number of blocks atthe cost of loosing some impractical information on some effects. The device ofconfounding consists of sub-dividing the replicates into two or more equal sub-groupsof equal size following certain rules. This leads to loss of some information on certainhigher order interaction and allocation of the treatment combinations of any group toany block at random. If the same interaction is confounded in all replications, it iscalled total confounding. In the case of partial confounding, an interaction isconfounded in one replication, but not in others or the other combination isconfounded in other replication.

Conjugated Proteins. Proteins that are attached to a non-protein moiety, calledprosthetic group. To such a group belong the glycoproteins, lipoproteins,hemoglobins, etc.

Conjugation: A process whereby organisms of identical species, but oppositemating types, pair and exchange genetic material (DNA); in molecular biology, natural process of DNA transfer between bacteria in which the DNA is neverexposed

Consanguineous matings: Matings between two individuals who share acommon ancestor in the preceding two or three generations

Consensus accuracy (of reads)Accuracy of the sequence of a fragment obtained as consensus sequence of all the reads of the fragment.

Consensus linkage mapA linkage map created by merging two or more linkage maps for a given species. Syn., merged linkage map, integrated linkage map.

Consensus sequence: If a particular nucleotide sequence is always found withonly minor variations, then the usual form of that sequence is called consensussequence; the term is also used for genes that encode the same protein in differentorganisms

Conserved DNA-derived polymorphism markers
Markers based on conserved DNA regions of a selected set of well-characterized plant genes.

Conserved orthologous sequences: Orthologous sequences with almost similar sequence.

Conserved orthologous set of genes: A group of genes conserved in sequence and copy number during evolution.

Conserved orthologous set of markers: Markers based on conserved orthologous set of genes.

Conserved region amplification polymorphismMarkers based on one primer derived from an exon of a gene and the other primer targeting introns, similar to TRAP markers.

Conserved sequence: A base sequence in a DNA molecule (or an amino acidsequence in a protein) that has remained essentially unchanged throughoutevolution.

Conserved sequence: A base sequence in a DNA molecule (oran amino acid sequence in a protein) that has remainedessentially unchanged throughout evolution.

Constitutive heterochromatin: The material basis of chromosomes or segmentsthat exhibit heterochromatic properties under most conditions (e.g., centromericor telomeric heterochromatin)

Constitutive mutation: Causes genes that usually are regulated to beexpressed without regulation contain their own DNA which is separated fromthe cell’s nuclear DNA; in transplastomic plants, the DNA in the chloroplasts hasbeen genetically engineered; since only the nuclear DNA is inherited, the geneticmodification in the chloroplasts will not be passed on to the next generation; therefore, transplastomic plants may be a solution for ensuring biocontainment

Contig map: A map depicting the relative order of a linked library of smalloverlapping clones representing a complete chromosomal segment.

Contig: A set of overlapping clones that provide a physical map of a portion of a chromosome

ContigA series of clones containing overlapping DNA inserts covering a specific genomic region.

Contiguous map: The alignment of sequence data from large, adjacent regionsof the genome to produce a continuous nucleotide sequence across a chromosomalregion

Contingency Test. A statistical test for independence of the results of a given experimentobserved under different experimental conditions. For example, if one has advancedthe same F1 and grown the F2 in two environments, this test facilitates in decidingwhether there is an interaction between the results of a cross and its experimentalconditions by calculating contingency chi-square.

Continuous culture: An in vitro suspension culture continuously supplied withnutrients by the inflow of fresh medium; the culture volume is normally constant

Continuous Variation. Variation showing an unbroken range of phenotypic values.

ControlIn association mapping, individuals lacking the disease and unrelated to the cases.

Controlled Environment Agriculture. Also called Protected Agriculture; a high-leveltechnology to gain the maximum while maintaining quality of environment throughmanipulation of genetic potential of crops to the maximum under controlledconditions.

Controlling Element. A mobile genetic element capable of producing an unstablemutation through insertion in a target gene. Two types exist: the regulator and thereceptor elements.

Conventional breeding: The selection process used to try and improve thecharacteristics of a plant; genetically superior parents are selected for breeding ina cyclic process until the desired trait is received; the goal of breeding is to producegenetically improved populations

Convergence breeding: A breeding method involving the reciprocal additionto each of two inbred lines of the dominant favorable genes lacking in one line andpresent in the other; backcrossing and selection are performed in parallel, each ofthe original lines serving as the recurrent parent in one series

Convergence-divergence selection: A breeding scheme in which selection ofpromising genotypes is made in a bulk population at different locations followedby massing of selection and allowing mating among them in a pollination field; the harvested bulk seeds constitute the basis for the next propagation cycle

Convergent Cross. A cross attempted to accumulate in one genotype the desired genesscattered in two or more parents.A x B C x D E x F G x H↓ ↓ ↓ ↓F1 x F1 F1 x F1↓ ↓F1 x F1↓F1This multiple convergent cross (F1), according to Harlan et al. (1940), facilitatescontinued recombination through intercrossing of F1’s.

Convergent Improvement. A method of improving two inbred lines simultaneouslythrough backcrossing the single cross independently to both of its inbred parents, thatis, (A x B) x A and (A x B) x B.

Copy number variationVariation in the number of copies of a given genomic region in the genomes of different individuals/lines of a species.

Copy-choice hypothesis: The interpretation of intrachromosomal geneticrecombination that is not regarded as a physical exchange of preformed geneticstrands

Core Collection. A subset of accessions from the entire collection representing most ofavailable diversity of the species. The core subset thus formed can be evaluatedextensively to derive information that could be used as guiding criterion for moreefficient utilization of the entire collection. The reduced collection size will alsofacilitate in reducing expenses required to manage the gene bank. First, arepresentative core collection (10%) is developed from the entire collection, usinginformation on origin, geographical distribution, and characterization and evaluationdata. The core collection is then assessed for various qualitative and quantitativecharacters, and ultimately, a subset of 10% accessions from the core subset (that is,1% of the entire collection) that captures most of the useful variation in the crop isformed. At both stages, standard clustering procedures are used to separate groups ofsimilar accessions, and various statistical tests are used to assess representatives of thecore and mini core collections. Mini-core collections of chickpea, groundnut, and afew other crops are available at ICRISAT.

Core collection: The basic sample of a germplasm collection; it is designed torepresent the wide range of diversity in terms of morphology, geographic range or genes

Core markerA highly polymorphic marker that is expected to be polymorphic in most, if not all, mapping populations of the given species. Syn., anchor or framework marker.

Corepressor: A metabolite that in conjugation with a repressor moleculebinds to the operator gene present in an operon and prevents the synthesis of arepressible enzyme

Correct reading frameThe longest reading frame in a given DNA sequence that is uninterrupted by a stop or termination codon.

Correlated Response. The change in mean value of a trait brought about through directselection for an otherwise associated character. For example, if x and y are associatedwith each other, one can predict correlated response in y while selection is directlypracticed for x. Thus CRy = ix.hx.hy.rg.σpy, where, ix is a constant value dependingupon selection intensity for x, hx& hy are square-roots of the heritability of concernedtraits, rg is the genetic correlation between the two traits, and σpy is the phenotypicstandard deviation of y.

Correlation Coefficient. A statistic that measures the precision of relationship betweentwo variables. It is also called simple correlation coefficient, simple linear correlationcoefficient or product moment correlation coefficient. It is usually designated by r,which is a ratio of the covariance between the two variables and product of theirstandard deviations [r = σxy / σxσy]. It is alternatively defined as geometric mean ofthe two regression coefficients. The value of r lies between +1 to –1. The extremevalue indicates the perfect association between the two variables. If the two variableschange in the same direction, the correlation is positive. However, when a + change inone character is accompanied by a – change in the other, there is negative association.An r value of zero indicates either (a) absence of association whatsoever between thetwo variables, or (b) presence of non-linear association. Sometimes, the numericalvalue of genetic correlation coefficient may exceed the extreme limit (} 1). As it isnot directly measured, larger experimental error could inflate the numerical estimate.The r is a pure number, and is thus independent of units of measurement of the twovariables and a change of origin and scale. The calculated value of r is compared withthe table value at (n – 2) degree of freedom and 5% (usually) probability level, wheren is the number of paired observations from which computed r value is obtained.

Correlation. The association between two variables based on the amount of variability inone character that can be explained by a linear function of the other. The associationmay be bi-directional, that is, both in positive and negative direction. Positive andnegative correlations arise in reponse to coupling and repulsion phase linkages,respectively. Correlation may also stem from pleiotropy called developmentalcorrelation. The same gene is controlling two traits (and thereby differences) throughinfluencing the same developmental or metabolic pathway. Linkage disequilibriummay also cause transient genetic correlation. No correlation indicates that the twogenes in question are either on different chromosomes or if on the same, both are farapart (>400 cM) to permit 50% recombination. It is emphasized here that the natureof correlation can often be altered by selection and hybridisation. Some times, it isobserved that two variables are found associated for no valid reason, that is, the twoare correlated purely by chance; this is called spurious correlation (the correlationbetween population and agricultural growth after independence, for instance).

Correlation: The degree to which statistical variables vary together; measuredby the correlation coefficient, which has a value from zero (no correlation) to –1 or+1 (perfect negative or positive correlation)

Cosegregation. Parallel inheritance of two genes due to their close linkage on achromosome.

Cosmid. A cloning vector that can replicate autonomously like a plasmid and can bepacked into a phage.

Cosmid: Artificially constructed cloning vector containing the cos gene ofphage lambda. Cosmids can be packaged in lambda phage particles for infectioninto E. coli; this permits cloning of larger DNA fragments (up to 45 kb) than can beintroduced into bacterial hosts in plasmid vectors.

Cosuppression: Silencing of a gene by addition of transgenic DNA copies orinfection by a virus; this term, which can refer to silencing at the post transcriptional (PTGS) or transcriptional

Covariance analysis: An analysis of the mean of the product of the deviationof two variates from their individual means; it measures the interrelationshipbetween variables

Covariance. A statistical measure of the interrelation between variables. The variationoccurring simultaneously in two variables or characters is called covariance.Numerically, it is the mean of the product of the deviation of two variables from theirindividual means. It is an important statistical parameter as it enters the computationof several analyses such as correlation and regression coefficients, D2-statistic,stability analysis, and the like. Further, covariance between relatives is translated intogenetic variance or its components in biometrical analyses.

Coverage of sequencing: The sequencing depth for the whole-genome, e.g., 10x, 20x, 30x, etc., coverage or depth.

cpDNA. Chloroplast DNA. DNA found in the chloroplast. It is more complex thanmtDNA with respect to size, genes encoded, and in the structural organization.

CpG island: Repetitive CpG doublets creating a region of DNA greater than200 bp in length with a G+C content of more than 0.5 and an observed/expectedpresence of CpG more than 0.6; usually associated with transcription-initiationregions of (housekeeping) genes transcribed at low rates that do not contain aTATA box; the CpG-rich stretch of 20–50 nucleotides occurs within the first 100–200 bases upstream of the start site region; a transacting transcription factor calledSP1 recognizes the CpG islands

Crisscross Inheritance. Transmission of a gene from male parent to female child to malegrandchild (X-linked inheritance, for example).

Criss-cross inheritance: The transmission of a gene from mother to son orfather to daughter

Critical Difference. Also called least significant difference. It is a value beyond whichdifference between means of two treatments is significant. After performing analysisof variance, it is calculated as: CD = [2 x σ2e / r ]1/2 x t, whereas, σ2e = errorvariance, r = number of replication, and t = table value of t at error degree of freedomand 5% probability level.

cRNA. Also called complementary RNA. Synthetic RNA produced by transcription froma specific DNA single-stranded template.

Crop Simulation Model. A model used to study the interactive response of variousgrowth factors on crop yields. It is perceived as a black box in which we feed aminimum number of data set relating to crop, soil, weather and other variables. Themodel will then utilize this input data set in calculating various growth processesusing established quantitative relationships and give us the required informationregarding the daily growth and development of the crop, etc. and the simulated finalyield of the crop. In this endeavour, of course, computer plays an important role. Inthe past, statistical regression type technique to forecast crop yield has been used onthe basis of only a limited number of independent variables. However, in reality, 100or even more variables are involved. On the other hand, simulation models are basedon more variables and more physiological processes and could be universallyapplicable. Such models have already been developed for wheat, rice, maize, and thelike.

Cross Classification. A system of arrangement of various treatments in relation to oneanother. If all the levels of one factor are common to each level of the other, it iscalled cross classification (for example, testing v varieties in r replications).

Cross Inoculation Group. Host specificity of a Rhizobium strain. A particularRhizobium species has a particular legume host(s). For example, Rhizobium phaseoliinfects mung bean, whereas Rhizobium meliloti infects Melilotus alba.

Cross Pollination. Pollination effected through transfer of pollens from one plant to thefloral stigma of the other with a different genetic constitution. Also calledoutcrossing.

Cross. A process of bringing together genetic materials from different individuals(genotypes) to provide for genetic recombination. Also the result of the process.

Cross: The deliberate mating of selected parents based on particular genetictraits desired in the offspring.

Cross-fertilisation: The fusion of male and female gametes from differentgenotypes or individuals of the same species, as base of genetic recombination

Cross-hybridisation: In biotechnology, the hydrogen bonding of a singlestrandedDNA sequence that is partially but not entirely complementary to asingle-stranded substrate; often, this involves hybridising a DNA probe for aspecific DNA sequence to the homologous sequences of different specie

Crossing Over. The exchange of corresponding segments between any two non-sisterchromatids of a pair of homologous chromosomes during meiotic prophase. Itsgenetic consequence is the recombination of linked genes, that is, crossing over is thecause and recombination is the effect.

Crossing over: The breaking during meiosis of one maternaland one paternal chromosome, the exchange of correspondingsections of DNA, and the rejoining of thechromosomes.

Crossing overA physical exchange of ordinarily strictly homologous segments between homologous chromosomes.

Crossing-over: The reciprocal exchange of material between homologouschromosomes during meiosis, which is responsible for genetic recombination. The process involves the natural breaking of chromosomes, the exchange ofchromosome pieces, and the reuniting of DNA molecules

Crossover Modifier. Any gene or chromosomal structural change increasing ordecreasing the crossing-over frequency. Reduction in crossing-over frequency isobserved more frequently than its enhancement. With rare exceptions, all structuralheterozygotes have lower crossing-over value for regions included in or immediatelyadjacent to the structural change. The decrease is often offset in those segmentsfarther removed from the aberration.

Crossover Suppressor. An inversion (usually complex) that makes pairing and crossingoverimpossible.

Cross-pollination: The transfer of pollen from the stamen of a flower to thestigma of a flower of a different genotype but usually of the same species, withsubsequent growth of the pollen tube

Cross-protection: Plant protection conferred on a host by infection with onestrain of, for example, a virus that prevents infection by a closely related strain

Cross-sterility. The failure of fertilisation because of genetic or cytoplasmicincompatibility in crosses between pairs of individuals despite formation of normaland functional gametes.

Cry1A protein: Derived from the bacterium Bacillus thuringiensis that is toxicto some insects when ingested; this bacterium occurs widely in nature and hasbeen used for decades as an insecticide although it constitutes less than 2% of theoverall insecticides used

Cryptic Species. Phenotypically very similar species, which do not hybridise undernormal conditions.

Cryptic Structural Hybridity. A kind of chromosomal sterility due to heterozygosity forchromosomal differences too small to affect meiotic pairing appreciably. Suchstructurally heterozygous individuals (cryptic structural hybrids) are not identifiableon the basis of pairing configurations of chromosomes at meiosis.

Crystallography: The study of, for example, a protein structure by crystallisingthe protein and examining the crystals using X-rays; the diffraction angles of theX-rays are used to compute the relative positions of components of the protein and thus its structure.

Cultivar. An international equivalent of cultivated variety. It is a distinctiveagriculturally derived cultivated variety of plants produced through selectivebreeding. (Also see variety).

Cultivar: A product of plant breeding that is released foraccess to producers.

Culture. Tissue or cells multiplying by asexual division, grown for experimentation.

Cumulative Selection (Rickey, 1945). A method of obtaining superior inbred lines frompromising crosses between better performing families (based on their top crossperformance) derived from original population following any scheme of inbreeding.In essence, it represents a philosophy for accumulation of desirable genes in eachcycle of inbreeding and thus increasing the chance of obtaining superior inbred lines.

Curie. The basic unit of the quantity of a radioactive substance. It can be defined as theamount of material in which 3.7 x 1010 atoms disintegrate each second [or 2.2 x 1012disintegration per minute (dpm)].

Cuticle. A lipophilic layer on the outer wall of epidermal cells; a waxlike covering of theexterior surface. It protects outer surface of the plants from desiccation in the air.

C-value. Characteristic DNA content of the cells of a given species.

Cybrid: The hybrid formed from the fusion of a cytoplast and a whole cell; thecytoplast may transmit cytoplasmic components independently of the cell genome

Cybrids. Cytoplasmic hybrids having cytoplasms from two unrelated types but nucleusfrom only one. Cybrids are produced through somatic cell hybridisation.

Cyclical Selection. Selection favouring different phenotypes alternatively because ofshift in environmental condition between generations/seasons. Such shifts may resultin selection in one direction, and selection in the opposite direction for the next. Italso maintains genetic differences in a population, since different traits will beadvantageous at different times.

Cytochromes. A class of proteins, found in mitochondrial membranes, whose mainfunction is oxidative phosphorylation of ADP to form ATP.

Cytogamy: The fusion or conjugation of cells

Cytogenetic breeding: Breeding techniques that involve the manipulation oralteration of genetic material in cells (E.g. exposure to radiation or application ofchemicals such as colchicine)

Cytogenetic map: A map showing the locations of genes on a chromosome(i.e. the visual appearance of a chromosome when stained and examined under amicroscope)

Cytogenetic mapA genetic map depicting the locations of various genes in the chromosomes of a species relative to specific microscopically observable landmarks in the chromosomes.

Cytogenetics. The cytological approach to genetics, mainly consisting of microscopicstudies of chromosomes. The chromosome theory of inheritance led birth to thisbranch of genetics. In essence, it is a correlated study of cytology and genetics.

Cytogenetics: Scientific discipline that combines cytology with genetics; itincludes (a) the organisation of chromosomes in the nucleus with the requirementsof gene expression in different developmental and environmental contexts; (b)the behaviour of chromosomes with transmission of phenotypes to progeny;(c) changes in chromosomal structure and number with speciation; and (d) theevolution of the genome with the evolution of the species

Cytokinesis. The process of segmentation of the cytoplasmic portion of a cell along withthe segregation of daughter nuclei to separate cells (as distinct from karyokinesis).During this process, the cytoplasmic components are distributed to the daughter cells.

Cytokinesis: During the division of a cell, the division of the constituents of thecytoplasm; it usually begins in early telophase with the formation of a cell plate.

Cytoplasm. The protoplasm of a cell excluding nucleus and cell wall. It is the materialbetween the nuclear and cell membranes. It includes fluid, organelles and variousmembranes.

Cytoplasm: The part of a cell that is enclosed by the plasma membrane, butexcluding the nucleus

Cytoplasmic Genetic Male Sterility. Male sterility governed by a particularcombination of cytoplasmic factor and nuclear gene(s). Plants carrying this kind ofmale sterility is designated as A line. Maintenance of such lines is very easy whenplants with fertile cytoplasm (with recessive nuclear genes) called B-line is used aspollinators. In hybrid seed production, A line is crossed with a special line (R line)which restores pollen-producing ability in the F1 hybrid.

Cytoplasmic Inheritance. See extranuclear/cytoplastic inheritance.

Cytoplasmic inheritance: A non-Mendelian (extra-chromosomal) inheritancevia genes in cytoplasmic organelles (mitochondria, plastids)

Cytoplasmic male sterility (CMS): Pollen abortion due to cytoplasmic factors, which are maternally transmitted, but which act only in the absence of pollenrestoringgenes; this type of sterility can also be transmitted by grafting

Cytoplasmic Male Sterility. A kind of male sterility caused by cytoplasmic factorscarried on mitochondria (mt DNA). The cytoplasm is designated as ‘sterile’.However, such male sterile plants may produce seed if suitable pollinators (linecarrying ‘fertile’ cytoplasm) are available. The maintenance of male-sterile line isvery easy, since the progeny of such sterile individuals are all sterile. This happensbecause cytoplasm of the progeny is derived almost exclusively from female (malesterile) plants. It is unsuitable for production of hybrids in seed-propagated cropsbecause F1’s are all sterile.

Cytoplasmic Matrix. That portion of the cell cytoplasm not contained within theendomembrane system.

Cytoplastic Inheritance. The transmission of hereditary traits through the cytoplasm asopposed from transmission by genes carried on chromosomes. The geneticdeterminants of such characters are contained on cytoplasmic organelles likemitochondria and plastids. This type of inheritance is detected by differingcontribution of male and female parents in reciprocal crosses, and thus is opposed toMendelian inheritance. Also called cytoplasmic, extranuclear or maternalinheritance.

Cytosine (C): A nitrogenous base, one member of the base pair G-C (guanineand cytosine).

Cytosol. The fluid part of the cytoplasm, outside the organelles.

Cytosterility. Cytoplasmic male-sterility with maternal inheritance.