Terminologies in Genetics and Plant Breeding Part -16

Tag oligonucleotide In SNP genotyping, a unique oligonucleotide unrelated to the sequences of the locus to be genotyped; each tag oligo is attached to a known position on the microarray/chip.

Tagging. The use of a piece of foreign DNA or a transposon to label a gene so that aclone of that gene can be identified readily in a library.

tagSNPs (tSNPs):The subset of SNP loci that together enable a reliable deduction of genotypes at the remaining SNP loci of the haplotype block.

Taichung Native-1. A variety of rice introduced from Taiwan in 1966. It heralded thebeginning of cultivation of photoinsensitive rice in India. It was developed from across between Tsai-yuan-chung and Dee-geo-woo-gen.

Tandem Duplication. Adjacent identical chromosome segments (abcdbcdef). Whethertandem or reverse tandem, duplication supplies additional genetic material capable ofevolving new functions.

Tandem repeat sequences: Multiple copies of the same base sequence on achromosome; used as a marker in physical mapping.

Tandem repeat: A chromosomal mutation in which two identical chromosomesegments lie adjacent to each other, with the same gene order; the DNA, whichcodes for the rRNA, contains many tandem repeats

Tandem Selection. Successive selection of different types one after another through oneor more cycles. For example, screen a population intensively for resistance to pest Athrough one or more cycles of selection, then repeat the same for pest B, and then forpest C.

Tandem selection: In the case of successive multiple selection, the selectionconcerns other traits in the first few generations than in later generations

Taq polymerase: A DNA-dependent RNA polymerase from phage T7, whichrecognises a very specific promoter sequence; it is used in many expression vectors

Target region amplification polymorphism: A marker that detects polymorphism around the desired candidate genes; it uses a PCR primer based on the target EST, while the other primer targets either an intron or an exon.

Targeting-induced local lesions in genomes (TILLING): A technique to screen a population that has either been deliberately mutagenized or possesses naturalbiodiversity (EcoTILLING) to identify those plants with a change in a specificgene of interest; the technique uses high-throughput methods useful to plantbreeders, including a reverse molecular method that combines random chemicalmutagenesis with PCR-based screening of gene regions of interest; it provides arange of allele types, including mis-sense and knockout mutations; by comparingthe phenotypes of isogenic genotypes differing in single sequence motifs, TILLINGprovides direct proof of function of both induced and natural polymorphismswithout the use of transgenic modifications

TATA box: A canonic DNA sequence; part of a plant promoter; promotes thetranscription of DNA

Tautomeric Shift. The spontaneous isomerization of a nitrogen base to an alternativehydrogen-bonding structure/ condition, possibly resulting in a mutation.

Taxon. A group of similar individuals sharing a set of characters that are consideredsufficiently distinctive to be worthy of a formal name.

tBLASTn: It converts the submitted protein sequence into a nucleotide sequence and compares it with a nucleotide sequence database.

tBLASTx: It translates the submitted nucleotide sequence as well as the nucleotide database sequence into protein sequences and searches for homology between the two.

T-Chromosome. A monocentric chromosome whose terminal segments (T-ends) showneocentric activity at meiosis.

T-DNA. A part of the Ti plasmid that is inserted into the genome of the host plant cell.

Technology Mission. A technology oriented mission that was launched by theGovernment of India during 1986. Initially it included programmes pertaining toimprovement in production of oilseeds, availability of drinking water, and childimmunisation. Later on, several other programmes such as literacy,telecommunication, dairy development, and enhancement of pulses and sugar cane233production were also added to the TM. The mission ended by the end of ninth fiveyearplan.

Technology transfer: The process of converting scientific findings from researchlaboratories into useful products by the commercial sector.

Technology. The application of art and science to the welfare of mankind. In its broadestsense, it is the applied aspect of art and science collectively. As plant breeding isconcerned with the art and science of improving the heredity of crop plants in relationto their economic use, it is essentially a technology.

Telocentric (chromosome): Refers to the chromosomal centromere which liesat the end

Telocentric Chromosome. A chromosome having the centromere (placed) at one end.

Telomerase. An enzyme that acts from telomeric end; an enzyme that adds repetitiveunits to the ends of linear chromosomes to prevent shortening after replication, byusing a special small RNA as a template. By way of its action, it shortens the lengthof a chromosome. Cancerous cells do not have this enzyme.

Telomerase: A reverse transcriptase (hTERT) containing an RNA molecule(hTR) that functions as the template for the tandem repeat at the telomere; itsynthesizes the telomere to maintain its length after each cell division; it is activein young cells and gametes, inactive in differentiated somatic cells, and reactivatedin malignant cells; telomerase can add one base at a time to the telomeric end of achromosome; this maintenance work is required for cells to escape from replicativesenescence

Telomere. The tip (or end) of a chromosome. It consists of repetitive units of nucleotides,which possibly confer non-sticky property to the telomere.

Telomere: The ends of chromosomes. These specialized structures are involvedin the replication and stability of linear DNA molecules.

Telophase. The last stage in cell division during which daughter chromosomes reachtowards respective poles and daughter nuclei re-form.

Telotrisomic: In allopolyploids, such as hexaploid wheat, a cell or individualwith one missing chromosome but having a telocentric and an isochromosome forthe same arm of the missing one

Telotrisomics. An otherwise diploid individual carrying a telocentric chromosome as theextra one (2n + telocentric chromosome). The total number of telotrisomics amountsto 2n.

Temperate Phage. A phage that can become a prophage.

Temperature-sensitive Mutation. A conditional mutation that produces the mutantphenotype in one temperature range and the wild-type phenotype in anothertemperature range.

Temperature-sensitive mutation: A class of conditional mutations; the mutantphenotype is observed in one temperature range and the wild-type phenotype isobserved in another temperature range.

Template strand: The strand of the DNA double helix that is copied by basepair complementarity to make an RNA. The other, non-template strand of theDNA duplex has a sequence that is identical to the synthesized RNA (except inRNA, U replaces T).

Template switching: During production of cDNA, reverse transcriptase uses one RNA molecule as template for some distance and then uses another RNA molecule as template; as a result, the cDNA molecule is made up of the 30 region of the first RNA template and the 50 region of the second RNA template.

Template. A molecular mold that shapes the structure or sequence of another molecule.For instance, the nucleotide sequence of DNA acts as a template to control thenucleotide sequence of RNA during transcription.

Template: The DNA single strand, complementary to a nascent RNA or DNAstrand, which serves to specify the nucleotide sequence of the nascent strand.

Tentative ESTs: Contigs obtained by de novo assembly of RNA-Seq sequence data.

Teosinte Theory (Beadle 1939). An accepted theory for evolution of maize. Accordingto it, modern maize was derived directly by human selection from teosinte (Zeamexicana L.). Several scientists and findings in the course of time have substantiatedthis old theory.

Teratogen. An agent that interferes with normal development.

Terminalisation: A progressive shift of chiasmata from their sites of origin tomore terminal positions.

Terminalization. A process by which chiasma move towards either end of the pairedhomologues.

Termination codon: Stop codon.

Terminator Codon. A chain terminating stop codon.

Terminator genes: A set of transgenes designed to arrest the final stages of seeddevelopment in a crop plant; the resulting trait is the production of seeds that willnot germinate; it is also called the technology protection system.

Terminator Technology. A technology that ensures that the plants grown fromgenetically engineered seeds will produce only sterile seeds of their own. This isachieved by selectively programming a plant’s DNA to kill its own embryo. That thepatent that was initially granted to Delta and Pine Land Company (DPL), which waslater on owned by Monsanto, is innocuously titled “Control of Plant GeneExpression”. However, it has been globally derided as the Terminator Technology.[The term has actually been coined by Rural Advancement Foundation International(RAFI), which has been spearheading an international campaign against it]. TT isbiotechnology at its sophisticated best. It uses three constructs of DNA that ensurethat the transgenic plants become terminators that abort their own embryos. The threeconstructs are something akin to promotor, inducer and repressor. The technology hasseveral drawbacks: (1) it breaks plant-to-seed-to-plant to seed cycle, the cycle thatsupports most life on the earth, (2) it gives multinational companies an unprecedentedand extremely dangerous capacity to control world’s food supply, (3) the terminatorgene could be transmitted to other cultivated species for some extent of outcrossingtakes place in almost all species, (4) the planting of such strains owing to theirseeming superiority may wipe out biodiversity, (5) the monoculture of such strainswill enhance their vulnerability to insect pests, (6) the ecologists fear that the use ofthree gene constructs will adversely affect soil microflora and fauna, (7) thenutritional aspects of such seeds are also likely to be affected, and (8) the fallout ofthe technology will directly affect 90% of the farmers who operate in the traditionalstyle. Because of these and other limitations, the technology has been banned.

Terminator technology: Plants are genetically engineered so when the cropsare harvested, all new seeds produced from these crops are sterile.

Tertiary Gene Pool. Genetic resources of a crop species that includes distantly-relatedwild species compared to secondary gene pool. Hybrids tend to be sterile or lethal dueto abnormality in development of embryo. Successful hybrid embryos can beproduced through techniques of embryo culture, tissue culture and chromosomedoubling or bridge species.

Tertiary gene pool: Gene transfer from a species of the tertiary gene pool to thecultivated species, since the primary gene pool usually requires special crossingand embryo rescue techniques in order to get viable hybrids.

Tertiary Structure (of protein). The folding or coiling of the secondary structure to forma globular molecule.

Tertiary Trisomics. Trisomics carrying an extra tertiary or translocated chromosome.Considerable number of tertiary trisomics was developed by Ramage and coworkers(1961) in barley. Total number of TTs may be infinite.

Test Cross. A cross of an F1 hybrid to its corresponding recessive (homozygous) parentto test for homozygosity or linkage. In plant breeding, it is the cross of an individualof unknown genotype to an individual known to carry only recessive alleles of loci inquestion for the purpose of determining the genotype of the unknown parent. Theterm is also extended (in plant breeding) to include a cross of an individual or aninbred line with an appropriate tester to evaluate combining ability of that individualor inbred line.

Test cross: A cross between a heterozygote of unknown genotype and anindividual homozygous for the recessive genes.

Test of Significance. A statistical test designed to distinguish differences due to samplingerror from differences due to discrepancy between observation and hypothesis. Thetest of significance is necessary in case of biological experiments because these areaffected by considerable amount of uncontrollable variation. But in sciences likephysics and chemistry, uncontrolled variation is so small compared to the magnitudeof the observation that the mean of two or three repetitions of an observation comes tothe real one.

Tester. An inbred line, single cross, three-way cross, double cross or an open-pollinatedvariety used to test combining ability. A desirable tester is one, which providesmaximum information about the performance of the line(s) likely to be used in hybridbreeding. It should also be that is simple to use. The choice of tester is decidedaccording to the desired objectives; if the object is to determine general combiningability, an open-pollinated variety is obvious choice. However, if the objective is tofind a replacement for an existing inbred line in a single cross, the most appropriatetester will be the second inbred line of that single cross. In genetics, an individualhomozygous for one or more recessive alleles that is used in a testcross is called atester.

Tetrad Analysis. The use of tetrad (products of meiosis) to study the behaviour ofchromosomes and genes in meiosis.

Tetrad analysis: The use of tetrads to study the behavior of chromosomes andgenes in crossingover during meiosis; particularly used in studies of fungi.

Tetrad. A group of four. It may be four homologous chromatids in a bundle visibleduring meiotic prophase and metaphase. It may also be the four haploid product cellsof a single meiosis. Dyad and octad mean a group of two and eight cells orchromosomes, respectively.

Tetramer. A protein consisting of four polypeptide subunits, for example, haemoglobin.

Tetraploid. A cell with four basic (x) sets of chromosomes. An organism composed ofsuch cells is also referred to as a tetraploid. If all the sets are identical, the individualis said to be an autotetraploid (AAAA). Allotetraploids (AABB) have dissimilargenomes or sets of chromosomes. They are also sometimes called amphidiploids.

Tetraploid: Having four sets of chromosomes in the nucleus.

Tetraploidisation: The mitotic or meiotic procedure which produces tetraploids

Tetrasomic. An otherwise diploid cell having a particular chromosome present fourtimes, thus having 2n+2 chromosomes; also the organism composed of such cells.Tetrasomics often behave more regularly than the other aneuploids with oddchromosome number. The pairing possibilities among the four homologs and gameticoutput are almost similar to those of tetraploids (4x).

Tetrazolium test: A quick test to determine seed viability; tetrazolium is a classof chemicals that have the ability to accept hydrogen atoms from dehydrogenaseenzymes during the respiration process in viable seeds; this ability is the basis ofthe test during which the tetrazolium chemical undergoes a color change, usuallyfrom colorless to red (formazan).

Textbook. A book giving a systematic presentation of the principles and vocabulary of aparticular subject.

Third-generation DNA sequencing methods: These methods sequence single large DNA molecules.

Three-endonuclease AFLP: A modification of AFLP, in which three restriction enzymes are used to digest the sample DNA.

Three-line System. A widely used system for producing hybrid varieties involving A, B,and R lines.

Three-point test cross: Cross involving one parent with three heterozygousgene pairs and another (tester) with three homozygous recessive gene pairs.

Three-point Testcross. A testcross in which the tester parent has three homozygous genepairs, for example a cross between AaBbCc × aabbcc.

Three-way Cross. A cross between a single cross and an inbred line [(A × B) × C]. Thenumber of possible three-way hybrids involving n inbreds will be [n. (n-1). (n-2) / 2].

Three-way cross: A first generation hybrid between a single-cross and aninbred line or pure line.

Threshold characters: Such characters require a specific environment, i.e., a threshold environment, for their expression.

Threshold Effect. A term usually applied to traits with a polygenic basis that developwhen the dosage of contributory alleles exceed a critical value in particularenvironments (sometimes used to explain all-or-none phenomena based onpolygenically inherited characters such as resistance vs. susceptibility to somediseases); the environmental condition which obscures expression of a trait. It allowscharacter expression below/above a particular environmental condition. It is discernedthat a character develops through a series of physico-chemical reactions, which in turnis dependent upon genetically controlled threshold - the point at which a stimulus(gene) produces a response (character), e.g., temperature sensitive albinism.

Throughput: The number of assays, e.g., SNP genotyping, carried out by an assay system in a unit time.

Thymidine. The nucleoside having thymine as its base.

Thymine (T): A nitrogenous base, one member of the base pair A-T (adeninethymine).

Thymine Dimer. A pair of chemically bonded adjacent thymine bases in DNA. Ifpresent, this lesion is repaired by cellular processes. However, errors may be leftduring DNA repair that ultimately results in mutation.

Thymine. A pyrimidine base that pairs with adenine in a DNA double helix. It has asingle ring structure compared to its pairing partner, which has two.

Ti Plasmid. Tumour Inducing Plasmid; a vector for gene transfer to plant cells. It is acircular plasmid that enables the bacterium to infect plant cells. It is contained outsidegenome of Agrobacterium tumefaciens and causes crown gall of plants. It has a virregion (responsible for virulence towards the host) and a T-DNA region that istransferred to the host along with the gene intended to be transferred. It has selectablemarker genes that help in selecting transformed cells.

Ti plasmid: Established tumors in plants contain only a part of the total plasmid

Tift 23A (Burton 1965). A cytoplasmic male sterile line containing A1 cytoplasm. Themale-sterile condition was found due to homozygous recessive alleles of a nucleargene pair ‘ms1ms1’, besides sterile cytoplasm. It was used previously as a femaleparent to develop hybrid bajra (HB series). Its use stopped after 1970 when it gaveway to downy mildew.

Tissue Culture. In vitro culture of cells, tissues, organs, etc on an artificial mediumunder aseptic condition.

Tissue culture: Growing cells, tissues, or tissue fragments (from complex, multicellular organisms) on a nutrientmedium in a dish, test tube, or flask.

Tissue Specific Expression. The expression of a gene in a higher eukaryote in a specificand reproducible subset of tissues and cells during development.

Tissue. A mass of cells woven together with their intercellular substances.

Tolerance (Disease). An inherent or acquired ability of the host to endure a disease orparasite. However, Virologists use the term to imply lack of symptom expression.Tolerant cultivars show few or no disease symptoms although the virus is present.Tolerance, like avoidance or resistance, helps the host to cope with the parasite. Itenables the host to suffer low biological damage compared to susceptible ones. Toevaluate tolerance, it is imperative to compare the damage inflicted by equal amountsof parasite at the same developmental stage of each host genotypes. However, it isdifficult to measure because it is confounded with partial resistance and diseaseescape (because of early maturity). A tolerant genotype should be biologically moreefficient and productive. When the quality of product depends on the absence ofdisease symptoms, tolerance would be of little worth. For example, tolerance to smutpathogens in cereals is of no value because they attack kernels.

Tolerance (Insect Pests). The ability of the host to grow and reproduce or to repair insectinjury to a marked degree in spite of supporting an insect population nearly equal tothat damaging a susceptible host. Tolerance, which is measured through yielddepression being minor, is polygenically determined. A tolerant and non-tolerantcultivar would be indistinguishable when rated for the number of insects present, butthey would less affect the tolerant one. Tolerance differs from non-preference andantibiosis in its mechanism. The latter two require an active insect response or lack ofresponse. However, the former (tolerance) response requires a thoroughunderstanding of the ways in which plants are injured by insects as well as the ways inwhich plants may repair the damage. Tolerance is more subject to variation as resultof environmental fluctuations more than non-preference and antibiosis. The age orsize of the plant and size of the insect population strongly influence the degree oftolerance. Since tolerance does not involve prevention of insect infestation or injury tothe plant, some researchers prefer not to include it as a type of resistance.

Tonoplast. A unit membrane bordering the vacuole of plant cells. It has characteristicssimilar to those of plasma membrane excepting greater permeability barrier.

Top Cross (Davis 1927). In corn, an inbred-variety cross; a cross between a selection,line, clone, etc., and a common pollen parent which may be a variety, single cross, ora number of elite inbred line. The common pollen parent is called the top cross ortester parent. It is used to test general combining ability of inbreds or selections. Topcrosses to an open-pollinated variety, do in fact, reduce the burdensome labour ofmaking [n.(n-1)/2] single crosses and their evaluation for estimating GCA. However,single crosses are more efficient than top crosses in estimating GCA, and estimates ofadditive effects of GCA should be based on as many single cross combinations aspossible.

Top cross hybrid: The first generation of a cross between an inbred line and anopen pollinated variety.

Top Cross Test. A test for GCA of selected individuals/inbred lines or clones byevaluating their progenies derived from crossing them with a single tester variety(usually an open-pollinated variety).

Top cross: A cross between a selection, line, clone, etc., and a common pollenparent, which may be a variety, inbred line, single cross, etc.; the common pollenparent is called the “topcross” or “tester” parent; in maize, a topcross is commonlycalled an “inbred-variety cross”; usually, it is used in order to test the “general combining ability”.

Topography (of a gene). The differences in the properties of the sub-elements of a gene.

Topoisomerase. An enzyme that can cut and reform polynucleotide backbones in DNAto allow it to assume a more relaxed configuration.

Topoisomerase: Enzyme that catalyses the reduction of supercoiling of DNA;it is important during DNA replication to relieve the negative supercoiling thatoccurs when the two strands of the DNA double helix are separated.

Topology (of a gene). The manner in which the component parts of a gene areinterconnected.

Totipotency. The ability of a cell or a tissue to develop into a complete adult individualafter proceeding through all the stages of development.

Totipotency: The potential ability of a cell to express all its genetic informationunder appropriate conditions and to proceed through all the stages of developmentto produce a fully differentiated adult; A. Hansen first postulated in 1879 thatplants are totipotent, referring to the power of regeneration of Begonia that candevelop new plantules of leaf cuttings, a feature still used by gardeners today;Hansen ’s statement was generalised by G. Haberland.

Totipotent. A cell having the property of totipotency. It is also the state of a cell lineagethat is able to give rise to all possible cell fates found within a given organism.

Totipotent: A cell that is capable of regenerating an entireadult organism by itself.

TPS Technology. A technology related to the production of botanical seeds throughsexual reproduction in cultivated potatoes. The technology offers low cost on seed,ease in storage and transportation and lower incidence of disease and insect pests. It isan alternative technology for crop production in areas where quality seed tuberscannot be produced due to unfavourable agroclimate and transportation of seedpotatoes from distant places is very expensive. It is especially suited to small andmarginal farmers of Bihar, Orissa, Maharashtra, Karnataka, and North-Eastern States.Thus far three TPS hybrids have been released (TSS C-3, HPS I/13 and 92 PT-27) forgeneral cultivation. In a clonally propagated crop like potato, F1 generation itself is asegregating one, individuals of such hybrids are heterogeneous.

Traditional breeding: Modification of plants and animals through selectivebreeding. Practices used in traditional plant breeding may include aspects ofbiotechnology such as tissue culture and mutational breeding.

Training population: In case of GS, the population used for training the GS model and for obtaining estimates of the marker-associated effects.

Trait ontology: It lists the details of evaluation procedure and the environments, in which a specific trait of a given species was assayed.

Trait: A recognisable, measurable character in a plant, which is under some genetic control

Trans configuration: The configuration of two sites refers to their presence ontwo different molecules of DNA (chromosomes).

trans Conformation. A conformation of having the arrangement a1+/+a2 in aheterozygote with two mutant sites within a gene or gene cluster.

trans-acting Factor. A diffusible regulatory molecule (almost always a protein) thatbinds to a specific cis-acting element.

Transcription Factor. A protein that binds to a cis-regulatory element (for example, anenhancer) and thereby, directly or indirectly, affects the initiation of transcription.

Transcription factors: Proteins that are directly involved in regulation oftranscription initiation by binding to the control elements and allowing RNApolymerase to act; there are ubiquitous transcription factors as well as cell- andtissue-specific ones; several families have been identified including helix-loophelixproteins, helix-turn-helix proteins, leucine zipper proteins and zinc fingerproteins

Transcription unit: The distance between sites of initiation and termination byRNA polymerase; may include more than one gene.

Transcription. The synthesis of a RNA molecule using one of the two strands of DNA asa template.

Transcription: The polymerisation of ribonucleotides into a strand of RNA ina sequence complementary to that of a single strand of DNA; by this means, thegenetic information contained in the latter is faithfully matched in the former; theprocess is mediated by a DNA-dependent RNA polymerase

Transcription: The transfer of information from specificsequences in a DNA molecule to produce new strands ofmessenger RNA, which then carry this information from thenucleus to the cytoplasm (where the messenger RNA istranslated into protein).

Transcriptome: DNA sequences of the expressed genome.

Transcriptome: The full complement of RNA molecules, including their quantities, produced by a cell during a specific developmental stage and under a given environment.

Transcriptomics: Cataloguing of all the species of RNA transcripts expressed in a tissue/organ, their expression levels, splicing patterns, etc. and the effects of developmental stages and environmental conditions on their expression.

Transcriptomics: The study of global gene expression and changes caused bygenetics, environmental effects, drugs or chemicals, or tissue location; it is theapplication of micro- or macroarrays and sequence-based methods to conductexpression profiling to determine gene expression at a global (genome wide) level

Transduction. A mechanism of unidirectional recombination in bacteria. It refers to themovement of genes from a bacterial donor to a bacterial recipient with the use of aphage as the vector.

Transfection of eukaryotic cells: The acquisition of new genetic markers byincorporation of added DNA.

Transfection. The process by which exogenous DNA in solution is introduced intocultured cells.

Transfer RNA (tRNA): A class of RNA having structures with triplet nucleotidesequences that are complementary to the triplet nucleotide coding sequences ofmRNA. The role of tRNAs in protein synthesis is to bond with amino acids andtransfer them to the ribosomes, where proteins are assembled according to thegenetic code carried by mRNA.

Transferability of SSR markers: Primers for SSR markers developed in one species can be used in some other species.

Transformation A process by which the genetic material carried by anindividual cell is altered by incorporation of exogenous DNA into its genome.

Transformation. The directed modification of a genome by the external application ofDNA from a cell of different genotype. It may also be the conversion of normal highereukaryotic cells in tissue culture into a cancer-like state of uncontrolled division.Griffitth (1928) initially discovered this mechanism in Diplococcus pneumoniae andas such called it Griffith effect. In his experiment, transfer of genetic material fromone bacterium to another occurred without involving any other intermediate organism(unlike transduction). A bacterial cell incorporating in itself genetic material frommedium is also referred to as transformation. Now-a-day, the term is extended toinclude collectively introduction, integration, and expression of foreign genes in thehost.

Transformation: Introduction of an exogenous DNA moleculeinto a cell, causing it to acquire a new phenotype (trait).

Transformational Theory. An obsolete and disproved theory to account for the processof evolution. The proponents including Jean-Baptiste Lamarck (1744-1829)postulated the same transformation of quality for each individual organism within aspecies, much as every individual in its lifetime changes from an infant to an adult.According to this view, these individual changes are passed on to the offspring.

Transgene. A gene that has been modified by externally applied recombinant DNAtechniques and reintroduced into the genome by germ-line transformation.

Transgene: A modified native gene or a gene from another species that isinserted into plants to bring about a desired change or introduce a trait not nativeto the natural genome of that species.

Transgenic organism: An organism resulting from the insertion of geneticmaterial from another organism using recombinant DNA techniques.

Transgenic Plants. Plants that carry additional stably integrated and expressed foreigngene(s) usually transformed from unrelated organisms. The whole process ofintroduction, integration and expression of foreign gene(s) in the host is referred to astransformation.

Transgenic: An organism that has been transformed with aforeign DNA sequence.

Transgressive Segregation. Appearance in segregating generations (F2, or F1 in case of across between clones) of individuals falling outside the parental range with respect tosome characters. For instance, if we cross aaBB and AAbb, we are likely to get AABBand aabb in F2 generations. These genotypes may have enhanced or retardedphenotypic expressions compared to their parents.

Transgressive segregation: The segregation of individuals in the F₂ or a latergeneration of a cross that shows a more extreme development of a character thaneither parent

Transient Diploid. The stage in the life cycle of predominantly haploid fungi (and algae)during which meiosis occurs.

Transition. A type of nucleotide-pair substitution involving the replacement of a purinewith another purine (adenine with guanine or vice-versa) or of a pyrimidine withanother pyrimidine (cytosine with thymine or vice-versa). This substitution may occurdue to a spontaneous error or mispairing between base pairs under the influence of aphysical or chemical mutagen. It ultimately results in mutation (GC→ AT transition,for example).

Translation The process in which the genetic code carried by mRNA directs thesynthesis of proteins from amino acids

Translation. The ribosome-mediated production of a polypeptide whose amino acidsequence is derived from the codon sequence of an mRNA molecule.

Translation: Synthesis of protein using information contained in a messenger RNA molecule.

Translocation. The change in the position of a segment of a chromosome to anotherlocation in the same or a different chromosome; the relocation of chromosomesegment in a different position in the genome. If in the same chromosome, it is calledsimple translocation.

Translocation: A change in the arrangement of genetic material, altering thelocation of a chromosome segment; the most common forms of translocation arereciprocal, involving the exchange of chromosome segments between two nonhomologouschromosomes

Transmission Genetics. The study of the mechanisms involved in the passage of a gene(and thus a trait) from one generation to the next.

Transpiration Efficiency. The ratio of growth (net production) and water transpiredusually expressed as grams of dry matter produced per 1000 grams of watertranspired. Most species of agricultural crops have transpiration efficiency of 2 orless. However, drought resistant crops, such as sorghum/ millets may haveefficiencies of 4.

Transplastomic plants: Plants with genetic modifications in the DNA oftheir chloroplasts; plant cells contain chloroplasts, cell organelles responsible forphotosynthesis; these chloroplasts

Transposable element: A chromosomal locus that may be transposed from onespot to another within and among the chromosomes of the genome; it happensthrough breakage on either side of these loci and their subsequent insertion into anew position either on the same or a different chromosome

Transposable elements Mobile DNA sequences.

Transposable Genetic Element. A general term for any genetic unit that can insert into achromosome, exit, and relocate. It includes insertion sequences, transposons, somephages, and controlling elements.

Transposition. The transfer of a chromosome segment to another position owing tointra- or interchromosome structural changes. See translocation/ shift.

Transposition: In molecular biology, the process of moving a transposon orother inserts from one position to another within a genome

Transposon tagging: The blocking activity of functional genes by insertion of foreign DNA

Transposon. A segment of genetic material that is capable of changing its location in thegenome, especially when it contains genetic material controlling functions other thanthose needed for its insertion. It is a mobile piece of DNA that is flanked by terminalrepeat sequences and typically bears genes coding for transposition functions.

Transposon: Chromosomal loci capable of being transposed from one spot toanother within and among the chromosomes of a complement

Transverison: A mutation in which a purine is replaced with a pyrimidine orvice versa

Transversion. A type of nucleotide-pair substitution in which a pyrimidine replaces apurine or vice versa (thymine for guanine or adenine for cytosine), GC → TAtransversion, for example.

Treatments. The objects of comparison in an agricultural trial. Also called entries.

Triallel Analysis (Rawlings and Cockerham 1962). An analysis of triallels or three-waycrosses. In addition to information provided by the diallel analysis, it gives outinformation regarding epistatic component of variances and order effects.

Triallel. A cross product of three parents, (A × B) × C; also called three-way cross. Thenumber of three-way crosses or triallels possible among n inbred lines is given by aformula: (½) × n (n-1)(n-2).

Trihybrid: Progeny resulting from a cross of parents differing in three genes

Triisosomic: In allopolyploids, such as hexaploid wheat, when a cell orindividual lacks one chromosome pair while three homologous isosomes for thesame arm are present

Trioecious. Of plants having male, female, and hermaphroditic flowers on differentindividuals.

Tripartite Hypothesis (Mangelsdorf and Reeves 1939). A hypothesis proposed toaccount for evolution of maize. According to this hypothesis: (a) wild maize was aform of pod corn native to the low lands of South America, (b) teosinte originatedfrom a cross between cultivated maize and tripsacum, and (c) modern varieties ofmaize arose from crosses between maize and tripsacum or teosinte. However, recentadvances in modern genetics and cytogenetics do not substantiate any of these points.

Triple Test Cross Design (Kearsey and Jinks 1968). A mating design that involvescrossing of randomly selected each F2 individual to the F1 individual in addition to itsinbred parents. Thus it is an extension of NCD-III, which excludes crossing with theF1’s. It is the most informative mating design for the random mating population. Itgives a test of significance for the presence of epistasis (that cannot be obtained withNCD-III).

Triplet. The three-nucleotide (base) pairs that constitute a codon.

Triploid fusion nucleus: The result of the fusion of one male gamete (pollen)with two haploid female nuclei (polar cells) in the second polar event; this nucleusdivides to form the cells of the endosperm

Triploid. A cell having three chromosome sets (3x) or an organism composed of suchcells. Triploids are usually autopolyploids. They are characteristically sterile due topairing irregularities during meiosis. Although trivalent can form, bivalents usuallyoccur leaving one homologue of the third set unpaired. The asynaptic chromosomecan randomly go to either of the poles. This happens for every chromosomethreesome; thus probability of obtaining functional gametes (2x, x) gets highlyreduced as the number of chromosomes in the basic set increases. The probability thata triploid will produce functional gametes (2x, x) is: (½)x-1, where x is the no. ofchromosomes in basic set. For example, the triploid banana contains 11 chromosomesin a basic set; hence, the probability of formation of formation of functional gametesis: (½)10. Thus the probability that a triploid will form a viable seed is the product ofprobabilities of functional male and female gametes, that is, (½) 11-1 × (½) 11-1 =(½)20 = 0.0001%. Seedlessness of triploidy has also been exploited in watermelons.

Triploidy: A state in which three chromosome sets are present

Tripping. A mechanism of pollen dispersal by an explosive action usually effected bybees as in alfalfa. In the lucerne flowers, stamens and stigma are enclosed and heldunder considerable tension by keel. When this tension is released by mechanicalpressure supplied by honeybees, pollen is dispersed. Lucerne flowers are usuallytripped by bees, although automatic tripping by wind, rain or heat may occuroccasionally. A flower may be tripped artificially through application of light pressureon keel by the point of a pencil.

Trisomic analysis: A method for mapping gene loci on individual chromosomesby comparing disomic and trisomic segregation patterns of a series of individuals

Trisomic. An organism diploid except for one kind of chromosome which is present intriplicate, hence, having 2n + 1 chromosomes. The cell of the organism may becharacterized by the presence of a trivalent during meiotic prophase I. Trisomics tendto be somewhat more stable genetically than monosomics (see aneuploids).Nonetheless, the possibility that the unpaired chromosome (which may be the case)may lag at meiotic anaphase cannot be ruled out. The gametic output of a trisomicunder the conditions of various pairing possibilities can be predicted just like triploids(3x).

Trisomic: A genome that is diploid but that contains an extra chromosome, homologous with one of the existing pairs, so that one kind of chromosome ispresent in triplicate

Triticale (Rimpau 1888). A new crop (man-made cereal) that was obtained by combiningthe genomes of wheat and rye (Secale cereale). The principal objective insynthesising triticale (X Triticosecale Wittmack) was to combine the quality of wheatand ruggedness of rye. The hexaploid triticale (obtained from tetraploid wheat, T.turgidum)) has better agronomic traits than the octaploid form (obtained from breadwheat, T. aestivum) and is generally favoured for this reason. Tetraploid forms(synthesised from diploid wheat, T. monococcum) are more of a botanical curiosityand have not been considered as agronomic crops. Plants of triticale are similar tothose of wheat, except for having large spikes and kernels, and greater vigour orgrowth. Low fertility and shrivelled grains are some objectionable features. It is moredrought tolerant than wheat. Primary triticales are obtained directly from wheat-ryecross. Unstable aneuploid forms characterize hexaploid and octaploid triticales,necessitating selection among themselves for genetic stability. Recombined triticalesare obtained by crossing primary triticales among themselves accompanied byselection for a superior type. Secondary triticales are obtained by crossing primarytriticales with hexaploid wheat or octaploid triticales followed by selection forsuperior segregates in the ensuing generations. Earlier it was reported that grain oftriticale contained a higher protein percentage than wheat, but as yield and kernelquality of the triticales were improved through hybridisation with wheat and amongthemselves accompanied by selection, the differences in protein content betweentriticale and wheat were diminished. A natural cross of wheat and triticale atCIMMYT produced a superior genetic combination, which was named Armadillo. InArmadillo, 2D from hexaploid wheat had been substituted for the 2R of the rye.Additional substitutions of R chromosomes may be performed, however, as thenumber of wheat chromosomes replacing rye chromosomes increase, the triticalestrains become more like wheats. The triticale characteristics are mainly due to 3Rand 5R rye chromosomes. Secondary triticales are released as triticale cultivars indifferent parts of the world (such as TL 419, IL 2129, and the like).

Tritium. A radioactive isotope of hydrogen.

Tritordeum. A synthetic cereal obtained by crossing Triticum aestivum and Hordeumchilense.

Trivalent. A multivalent consisting of three meiotically paired chromosomes. Trivalentsmay be seen by performing meiotic analysis in trisomics, triploids, or any otherpolyploids.

tRNA. transfer Ribonucleic Acid. A class of small RNA molecules that bring specificamino acids to the site of protein synthesis (ribosome). The specificity of amino acidis determined by matching of the anticodon of tRNA with the codon of the mRNAbeing translated.

True Breeding. Of genotypes which do not segregate because they are homozygous atthe locus (loci) in question.

True breeding: A situation in which a group of identical individuals alwaysproduce offspring of the same phenotype when intercrossed; a true-breedingplant is that when self-fertilized, only produces offspring with the same traits; thealleles for this type of plants are homozygous

True SNP:  In case of polyploid species, allelic variation between homologous loci of the same genome present in the same or different polyploid species.

Truncated Selection. A form of selection in which plants or lines performing above orbelow a certain value (truncation point) are retained as parents for the next generation.The rest are eliminated from breeder’s population. The phenotypic value (truncationpoint) may be a fixed value over successive generations, that is, selection is byconstant truncation. In this case, selection intensity decreases with time, as more andmore of the population exceeds the fixed truncation point. However, an usual practiceis to alter the truncation point in each generation of selection – that is – selection is byproportional truncation. In this case, selection intensity is constant, but the truncationpoint moves upward as the population distribution moves.

t-Test. A statistical test designed to test significance of difference between two samplemeans (of small size). It is only an approximate test, influenced by errors inestimation of the population standard deviation due to small size.

Tube Nucleus. The nucleus of the pollen tube which controls the growth and behaviourof the pollen tube in higher plants.

Twin Species. Two species which are phenotypically very similar but separated fromeach other by reproductive isolation.

Twin Spot. A pair of mutant sectors within wild-type tissue, produced by a mitoticcrossover in an individual of appropriate heterozygous genotype.

Twins: May be genetically identical (monozygous) when they arise from asingle fertilised egg or non-identical (dizygous) when they arise from two separateeggs.

Two Stage Testing (Hanson and Brim 1963). A scheme for evaluation of advancegeneration homozygous lines (F6/F7) which involves testing of all lines in one or twoenvironments and selecting better performing lines for retesting in a number ofenvironments. The two stage-testing programme is more efficient than testing all thelines in one or two environments. The use of two locations for the first stage testprovides an insurance against abnormal conditions or seasonal hazards.

Two-factor Cross. A genetic recombination experiment involving two genetic markers(a+b+/ab).

Two-factor Experiments. Biological experiments that deal with two variables whilekeeping constant all other factors. Thus when response to the factor of interest isexpected to differ under different levels of the other factors, factorial experiments aredesigned to handle simultaneously two or more factors.

Two-line System. A system for producing hybrid rice involving only two lines (A and Rlines). Since male-sterility of A line is mediated by photoperiod (or temperature), itcan be maintained easily under antagonistic condition. (Also see PSGMS).

Type I error: The probability of null hypothesis, e.g., lack of marker–trait association, being wrongly rejected, i.e., being rejected even when it is correct.

Type Number. The most frequently occurring chromosome number in a particulartaxonomic group (modal number). The term is often used with the implication of itsbeing the ancestral number of the group in question. Other numbers are then assumedto be derived from the type number.