Terminologies in Genetics and Plant Breeding Part -14

Q banding: A chromosomal staining technique using the fluorescence dyequinacrin mustard; under UV light a characteristic light and dark banding isinduced

Q matrix: A Q value indicates the likelihood that an individual belongs to a given putative homogeneous cluster/group present in a population.

QPM. Quality Protein Maize.

QTL analysis: QTL detection, mapping, and fine mapping.

QTL confidence intervalThe genomic region in which the QTL is likely to be located. Syn., QTL support interval.

QTL fine mapping: Identification of markers located very close to (<1 cM) the concerned QTL.

QTL hotspot: A genomic region having QTLs involved in the control of different correlated traits.

QTL meta-analysisIntegration of findings from different QTL studies to determine the “actual” number of QTLs affecting a trait, estimate their “actual” positions in the genome, and reduce the QTL confidence intervals.

QTL validationConfirmation of the marker–QTL association and the QTL position in unrelated germplasm and assessment of the effect of genetic background on QTL expression.

QTL-environment interaction: The effect size estimates for the same QTL in the same mapping population vary from one environment to the other, and some QTLs may not even be detected in some of the environments.

QTL-NILAn NIL that contains a single segment of DP genome having, ideally, a single favorable QTL.

QTLs. Quantitative Trait Loci; several loci (or genes) affecting the phenotypic variationin continuously varying traits such as height, weight, yield, and the like.

QTL-Seq: An extension of BSA for QTL mapping by whole-genome resequencing of the two DNA bulks, i.e., the “high” and “low” trait phenotype bulks.

Qualitative Character. A character for which variation between genotypes is discrete,thus making easy classification into distinct categories. For this kind of trait, thereoccurs a one to one correspondence between genotype and phenotype. As aconsequence, each genotype (ignoring ephemeral effects of dominance) is capable ofproducing a unique phenotype; differences in environmental conditions haverelatively little effects on the expression of genotypes with respect to a particularlocus. Even characters conditioned by many a gene can show discrete variationprovided environmental effects are too small to permit each genotype to produce aunique phenotype associated with it (under unambiguous norm of reaction).

Qualitative character: A character in which variation is discontinuous

Qualitative inheritance: An inheritance of a character that differs markedly inits expression amongst individuals of a species; variation is discontinuous; suchcharacters are usually under the control of major genes

Qualitative Resistance. A general term to describe plant resistance in which thefrequency distribution of resistant and susceptible plants in a population isdiscontinuous. With this type of resistance, it is easy to classify plants either asresistant or as susceptible or into well-defined classes of disease reaction.

Qualitative trait A trait governed by one or few genes with large effects, the phenotypic expression of which is relatively little affected by the environment so that individuals can be readily classified into two or more distinct classes on the basis of their phenotype.

Qualitative trait: Traits that are easily classified into distinct phenotypiccategories. These phenotypes are under the genetic control of only one or a fewgenes with little or no environmental modification to obscure the genetic effects.

Quality. Physical, chemical, and nutritional characteristics of the product that affect itsutilisation by human beings directly or indirectly. Sellers may be interested in themarket quality, but the millers are primarily concerned with the milling quality,whereas the ultimate users may have primary concern for physical and nutritionalquality.

Quantitative Character. A character in which variation is continuous so thatclassification into discrete categories is not possible. Such characters cannot beanalysed by standard methods of classical genetics, but can be specified only in termsof metric system of measurements, and as such they are also called metrical traits. Forsuch characters, the norm of reaction is ambiguous, that is, one to manycorrespondences between genotype and phenotype is possible. Characters of this kindare usually governed by several genes, each usually with a small effect on thephenotype. However, multiple allelic series of a single gene can also produce a varietyof continuously varying phenotypes on the scale of measurement (but the presence ofall members of such a series is unlikely in any one population at a given point oftime). Expression of a quantitative character can be depicted as:Envirn. 1 Environ. 2 Envirn.3 Environ. nth↓ ↓ ↓ ↓Gene A -------› Precursor A--------›Precursors AB ---------›ABC -----------› Final product↑ ↑ ↑ ↓Gene B Gene C Gene nth a wide rangeof variationowing to effectsof environmentat each stepMost characters with which plant breeders work are unfortunately of this type, e.g.,protein content, cold or drought tolerance, etc. However, it must be understood thateven a one gene-two alleles system can result in a continuous distribution ofphenotypes if environment variation is large. Therefore, a quantitative trait is one forwhich phenotypic difference between genotypes is small as compared to differencebetween individuals within genotypes.

Quantitative character: A character in which variation is continuous so thatclassification into discrete categories is arbitrary

Quantitative Genetics. The genetics of quantitative traits or continuously varyingcharacters.

Quantitative genetics: A branch of genetics that deals with the inheritance ofquantitative traits; sometimes it is also called biometrical or statistical genetics

Quantitative genetics: A branch of genetics which deals with inheritance of quantitative or polygenic charcaters

Quantitative inheritance: An inheritance of a character that depends upon the cumulative action of many genes, each of which produces only a small effect; the character shows continuous variation (i.e. a graduation from one extreme to theother)

Quantitative Resistance. A class of resistance for which there occurs a continuousgradation between resistance and susceptibility within a population of plants.Therefore, no clear-cut distinction between resistant and susceptible plants isobserved, that is, they form a single spectrum consisting of different degrees ofresistance and susceptibility.

Quantitative trait A trait governed by several genes each having a small individual effect on the trait phenotype, which are, usually, cumulative. The phenotypic expression of such traits is markedly affected by the environment so that the individuals cannot be classified into distinct classes on the basis of trait phenotype.

Quantitative trait loci (QTL): Regions of the chromosome associated with theinheritance of polygenic traits

Quantitative trait locusThe genomic region associated with the expression of a quantitative trait; a QTL may contain one or more genes affecting the given trait.

Quantitative trait nucleotidesThe nucleotide changes that produce different alleles of a QTL.

Quantitative Variation. The existence of a range of phenotypes for a specific character,differing by degree rather than by distinct qualitative differences.

Quarantine: The official confinement of plants subject to phytosanitaryregulations for observation and research or for further inspection and/or testing; more general, a legal ban on the export or import of certain noxious weeds orinsects that may be attached to the plants

Quasidiploid. A cell with diploid chromosome number but aneuploid chromosome sets,trisomic-monosomic (2n + 1 – 1), for example.

Quasiqualitative Character. An otherwise quantitative character which pretends to bequalitative one, e.g., kernel colour in corn. Such traits show continuous distributionson the phenotypic scale; however, their inheritance is oligogenic like that ofqualitative traits. But so many minor genes regulate it. Continuous distribution maybe ascribed to the presence of several modifiers and regulatory genes affectingexpression of those oligogenes.

Quaternary Structure (of Protein). The multimeric constitution of the protein.

R Plasmid. A plasmid containing one or several transposons that bear resistance genes.

Race. A population or aggregate of populations with characteristic gene frequencies thatdistinguishes it from any other such groups within formally recognizable subspeciesor species. It is essentially an intraspecific category. Differences between races areonly relative and not absolute. Any race is able to interbreed freely with any other raceof the same species. There may be geographical races (subspecies occupying ageographical subdivision of the range of a species), ecological races (ecotypes),physiological races (differences are physiological rather than morphological), etc.

Races (pathological). Pathogens of the same species with or without identical/similarmorphology but are characterized by differing pathogenic capabilities. This impliesthat the two races may have the same genetic complements except for theirpathogenic capacity. Zadoks (1966) defined a race as a “taxon” within a pathogenspecies characterized by a specific combination of virulence genes. Differential seriesof cultivars used to identify races, in fact, characterize particular virulence genes. Inolder classification, races were used to be subdivided into biotypes. However, inmodern classification, the two terms are used interchangeably; but the term, biotype,is used more frequently by entomologists than by plant pathologists. Terms likepathotype, physiological race, and strain are also used as synonyms for the race.

RAD tag Short genomic sequences flanking the restriction site for the concerned restriction enzyme.

RAD. Radiation Absorbed Dose; a measure of radiation dose. It can be defined as theabsorbed dose of 100 ergs of energy per gram of tissue. The Roentgen (R), an olderunit which, strictly speaking, is to be used only for γ and χ-rays. One Roentgen unitprovides 93 ergs of energy per gram of tissue.

Random amplified polymorphic DNA (RAPD) technique: A comparativestudy (among individuals, populations, or species) of the DNA fragment lengthproduced in controlled DNA synthesis reactions started with short sequencesof DNA (primers); as a genetic mapping methodology, it utilises as its basis thefact that specific DNA sequences (polymorphic DNA) are repeated (i.e., appearin sequence) with a gene of interest; thus, the polymorphic DNA sequencesare linked to that specific gene; their linked presence serves to facilitate geneticmapping within a genome

Random Chromatid Assortment (Haldane 1930). A type of partition and segregation(or assortment) of chromatids wherein sister chromatids at a given locus may end upin the same gamete (in a higher order even polyploids). For example, in anautotetraploid, when quadrivalent form and crossing over takes place betwixtkinetochore and the locus in question, sister chromatids at this locus can end upattached to different kinetochores. Consequently, sister alleles may be included in thesame gamete. If quadrivalent formation is complete and crossing over results in 50%recombination, we have to think in terms of chromatids (instead of chromosomes) topredict gametic output. For instance, in a simplex (Aaaa), there are 2A chromatids and6a chromatids. Three types of gametes are possible: AA, Aa and aa. The probability ofpicking two A chromatids (out of AAaaaaaa) is 2/8×1/7 = 1/28AA. Similarly, theprobability for Aa is 2/8×6/7 + 6/8×2/7 = 12/28Aa. Obviously, the probability for aais 15/28. Thus the gametic output in a simplex will be in a ratio of 1AA: 12Aa: 15aa.Similarly, gametic output in the duplex (3AA: 8Aa: 3aa) and triplex (15AA: 12Aa:1aa) can be predicted under such conditions.

Random Chromosome Assortment (Muller 1914). A type of partition of chromatids inwhich sister chromatids always go to different products of meiosis in anautotetraploid (or in any higher order even polyploids). It happens if bivalents formregularly during meiosis. This type of segregation also occurs, when quadrivalentsalways form and the locus in question is inseparably linked to the centromere. Theeffect of linkage is to cause the locus to separate reductionally at the first anaphaseand equationally at second anaphase, exactly as happens in case of bivalent formation.In an autotetraploid, five genotypes namely AAAA, AAAa, AAaa, Aaaa and aaaa arepossible. Gametes produced by the first and the last will be AA and aa, respectively.Gametic output in triplex (AAAa) and simplex (Aaaa) will be 1AA: 1Aa and 1Aa: 1aa,respectively. Duplex (AAaa) produces three types of gametes in the ratio of 1AA: 4Aa:1aa.

Random DNA markersDNA markers derived from polymorphic sequences located at random sites in the genome.

Random Fixation. The fixation (100% allelic frequency) of one of two alleles in apopulation by chance events (e.g., genetic drift). Random fixation depends on anumber of factors such as selective value of the allele(s), mutation pressure, geneflow, the degree of genetic relationship between the number of breeding individuals.

Random Genetic Drift. Random changes in allelic and genotypic frequencies in a smallrandom mating population owing to sampling errors. The genetic effect is similar tothat of inbreeding, that is, there is gradual loss of heterozygosity. The rate of this lossis 1/2N, where N is the number of diploid individuals in the population. Thus, Ht ≅H0e-t/2N, whereas, Ht and H0 are proportions of heterozygotes in the tth and originalgenerations, respectively. Which one of the original alleles (A or a) becomes fixed ateach locus is a chance matter.

Random genetic drift: Variation in gene frequency from one generation toanother due to chance fluctuations.

Random Inbreeding. Mating between relatives occurring by chance owing to spatialproximity, synchrony in flowering time, etc. in a random mating population.However, there is no continuity of such inbreeding because of random distribution ofinbred and outbred progeny in the next generation. The genetic consequence is similarto Hardy-Weinberg equilibrium but with more homozygotes.

Random Mating. A form of mating system in which each individual has an equal chanceof mating with any other individuals of the same population. (In case of self-fruitfulcross-pollinated species such as maize, random mating also includes self-mating, thatis, each male gamete has an equal opportunity to fertilize each female gamete). In aninfinitely large population, it leads to constancy of gene frequency, genotypicfrequencies, amount of heterozygosity and genetic variability, and genetic relationshipbetween individuals in succeeding generations in the absence of forces enumeratedunder genetic equilibrium. Random mating of individuals is equivalent to randomcombination or matching of male and female gametes during fertilization.

Random mating: For a given population, where an individual of one sex has an equal probability.

Random Sample. A random collection from a population such that all items of thepopulation are likely to be represented equally in the collection.

Random Sampling. The process of selecting a sample completely on the basis of chance.Although a chance event cannot be individually predicted, the results of a largenumber of such trials can be anticipated with considerable accuracy and confidence.Its main advantage lies in the elimination of human biases and attainment of ultimateprecision. Another property is that the “mean” of the means derived from randomsamples approaches the population value as the number of sample means averagedincreases.

Random. Arrived at by chance.

Randomisation: The process of making assignments at random; in field trials, randomization of entries is required to obtain a valid estimate of experimentalerror; each entry must have an equal chance of being assigned to any plot in areplication and an independent randomization is required for each replication.

Randomised block design: A randomised block analysis of variance design (eg.one-way blocked ANOVA) is created by first grouping the experimental subjectsinto blocks; the subjects in each block are as similar as possible (eg. littermates);there are as many subjects in each block as there are levels of the factor of interest;randomly assigning a different level of the factor to each member of the block,such that each level occurs once and only once per block; the blocks are assumednot to interact with the factor

Randomised Complete Block Design (RCBD). An experimental design characterizedby the presence of blocks of equal size each of which contains all the treatments ofthe experiment. It is one of the most widely used designs in plant breeding trials. Thedesign is especially suited for field experiments where the number of treatments is notlarge (40) and the experimental area has a predictable productivity gradient.However, if becomes necessary, larger number of treatments can be included at thecost of reducing plot size for each entry within the blocks.

Randomization. Random assignment of treatments to experimental plots. It ensures thateach entry or treatment will have an equal chance of being assigned to anyexperimental plot, and consequently of being grown in any particular environmentexisting in the experimental site. In essence, it is a technique to obtain an unbiasedestimate of experimental error.

Randomly amplified microsatellite polymorphismMarkers generated by using a 50 anchored SSR primer in combination with a RAPD primer.

Randomly amplified polymorphic DNAsA dominant marker system; uses a single, typically, 10 nt long primers with an arbitrary base sequence for amplification of sequences from genomic DNAs of test individuals.

Range. The simplest measure of dispersion. It is the difference between the largest (L)and the smallest (S) of observations and provides, at least, some idea of the amount ofvariability present. It is affected by fluctuations of sampling and is completelyunrelated to any type of frequency distribution. It is unit-dependent and expressed inthe unit of scale of measurement. Thus it cannot be used to compare variability of twodifferent traits. To make it comparable, a similar statistic called Range Coefficient[(L-S)/(L+S)] is used.

RAPD. Randomly Amplified Polymorphic DNA; a set of several genomic fragmentsamplified by single PCR primer. It is somewhat variable from individual toindividual. Heterozygotes (+ / -) for individual fragments can act as markers ingenome mapping.

Raphanobrassica (Karpechenko 1928). The classical allopolyploid synthesized bymaking a cross between Brassica and Raphanus spp. The objective was to combinethe leaves of cabbage (Brassica) and the roots of radish (Raphanus). However, theresult came out to be just reverse. This clearly showed difficulty in predicting theprecise combination of parental characteristics that would appear in ensuing alloploid.

Reaction Norm. The range of phenotypic reactions of a genotype as manifested by thevariety of phenotypes that the specific genotype is able to produce in response toenvironmental influences.

Read accuracy: Accuracy of the sequence of a single read.

Read alignment: Aligning the short sequence reads onto a reference genome sequence.

Read length: The length of the sequence generated from one DNA fragment.

Reading Frame. The codon sequence that is determined by reading nucleotides in groupsof three from some specific start codon.

Reading frame:  The arrangement of sets of three bases, each representing a codon, beginning at a specific nucleotide in a DNA sequence.

Reading frame: A sequence of sense codons such that each suceeding tripletgenerates the correct order of amino acids resulting in a polypeptide chain.

Realised genetic gain: Refers to the observed difference between the meanphenotypic value of the offspring of the selected parents and the phenotypic valueof the parental generation before selection

Realised Heritability. The ratio of the single-generation progress of selection to theselection differential of the parents. Numerically, it is tantamount to narrow-senseheritability (h2).

Realised heritability: Refers to heritability measured by a response to selection; it is the ratio of the single-generation progress of selection to the selectiondifferential of the parents

Reannealing. Spontaneous realignment of two single strands to reform a DNA doublehelix that had been denatured.

Recalcitrant seed: Seed that does not survive drying and freezing; in particular, seed that cannot withstand either drying or temperatures of less than +10°C and, therefore, cannot be stored for long periods, as compared to orthodox seeds

Recapitulation Theory. A theory stating that ontogeny recapitulates phylogeny (thedevelopmental history of organisms repeats their evolutionary history).

Receptor Element. A controlling element that can insert into a gene (making it a mutant)and can also excise (thus making the mutation unstable). However, both of thesefunctions are non-autonomous, being under the influence of the regulator element.

Recessive Allele. An allele whose phenotypic effect is not expressed in a heterozygote.

Recessive gene: A gene whose phenotype is expressed only when it is presentas two copies of both alleles (eg. aa).

Recessive Phenotype. The parental phenotype that is not expressed in the hybrid(heterozygote/cross/F1 offspring) between two parents (homozygotes). It is thephenotype of a homozygote for the recessive allele (dwarf strain of Mendel’s peas, forexample).

Recessive: A phenotype that is expressed in organisms only ifit is homozygous for the corresponding allele.

Recessivity. The failure of one allele to express itself phenotypically in heterozygousstate (heterozygote).

Reciprocal cross: One of a pair of crosses in which the two opposite matingtypes are each coupled with each of two different genotypes and mated with thereciprocal combination

Reciprocal Crosses. Crosses in which sources of male and female gametes are reversed;that is, A×B and B×A.

Reciprocal full-sib selection: A method of interpopulation improvement forspecies in which the commercial product is hybrid seed; a cycle of selection iscompleted in the fewest number of seasons by use of plants from which bothselfed and hybrid seed can be obtained

Reciprocal Recurrent Selection. A procedure for simultaneous improvement of twogenetically unrelated populations for both GCA and SCA. The procedure is verysimilar to R.S. for GCA except that the two populations serve as the tester for eachother.

Reciprocal recurrent selection: A breeding method used to achieve anaccumulation of genes that are valuable for specific traits but also for combiningability; in practice, two populations form the basis of selection; reciprocally,one population serves as a tester for the investigation of the selections derivingfrom the other population; from the first population, usually a greater numberof plants is selfed and at the same time crossed with several plants of the second population; the same procedure is realised with the second population; during thesecond year, the progenies of the test-crosses are subjected to performance trials;the progenies of the cross of one female parent, derived from population 1, arecombined with several male parents from population 2; based on the performancetesting, progenies from selfed seed, produced by the best plants, are grown duringthe third year; in the same year, the best progenies of selfings are crossed in manycombinations; seeds obtained from those crosses form the improved populationsfor growing during the fourth year; within such populations, individual plantsmay be selfed again and crossed for utilisation in a new cycle

Reciprocal Translocation. A translocation in which part of one chromosome isexchanged with a part of a nonhomologous chromosome.

Reciprocal translocation: A translocation that involves an exchange ofchromosomes segments between two non-homologous chromosomes

Recognition sequences: The sequences recognized by restriction enzymes. Syn., recognition sites, restriction sites.

Recombinant DNA technologies: Procedures used to jointogether DNA segments in a cell-free system (an environmentoutside a cell or organism). Under appropriate conditions, a recombinant DNA molecule can enter a cell andreplicate there, either autonomously or after it has becomeintegrated into a cellular chromosome.

Recombinant DNA technology: Procedures used to join together DNAsegments in a cell-free system (eg. in a test tube outside living cells or organisms).Under appropriate conditions, a recombinant DNA molecule can be introducedinto a cell and copy itself (replicate), either as an independent entity (autonomously)or as an integral part of a cellular chromosome.

Recombinant DNA. A novel DNA sequence formed by ligating together the pieces oftwo nonhomologous DNA molecules with the use of restriction endonucleases. Thetwo DNA molecules may be from two separate species within a genus, family, andkingdom or even from different kingdoms.

Recombinant DNA: A hybrid DNA molecule produced inthe laboratory by joining pieces of DNA from differentsources.

Recombinant Frequency. A ratio of the number of recombinant cells (individuals) to thetotal number of cells (individuals). The mean recombination frequency never exceedsthe limit of 50 per cent (0.5) as only two chromatids out of four take part in crossingover at any one point of time.

Recombinant Inbred Lines (RIL). A set of inbred lines, each derived independently,usually by selfing single plants within lines during a number of filial generations. Inplant breeding, individual RIL are often derived by single seed descent from abackcross of the F2 to one or the other parent. Each RIL is ultimately expected to havea different pattern of alternative alleles of multiple loci within an otherwise uniquehomozygous genetic background, allowing effects of individual alleles (orcombinations of alleles) to be evaluated in an otherwise homozygous background).

Recombinant inbred lines (RILs): A population of fully homozygousindividuals that is obtained through the repeated selfing of an F1 hybrid, and thatcomprises 50% of each parental genome in different combinations; they derivefrom multiple inbred strains (either by selfing or by full-sib mating) and canserve as a powerful resource for the genetic dissection of complex traits; however, the use of such multiple-strain requires a detailed knowledge of the haplotypestructure in such lines

Recombinant selection: Marker-assisted selection against the DP genomic regions flanking the target gene/QTL.

Recombinant. A cell or an individual with a genotype produced through recombination.

Recombinant: The individual having a new combination of linked genes.

Recombination frequency: The number of recombinants divided by the totalnumber of progeny, expressed as a percentage or fraction; such frequenciesindicate relative distances between loci on a genetic map

Recombination Gene. Any gene (allele) that controls the frequency of geneticrecombination. Such genes may be concerned with the structure of an enzyme or thestructure of a regulatory substance that influences genetic recombination.

Recombination. Formation of new combinations of genes as a result of segregation incrosses between genetically different parents;.also the rearrangement of linked genesdue to crossing over.

Recombination: Production of new combinations of linked genes.

Recombination: The process by which progeny derive a combinationof genes different from that of either parent. Inhigher organisms, this can occur by crossing over. The formation of a new combination of alleles throughindependent assortment or crossing-over.

Recombinational Repair. A mechanism for the repair of a DNA lesion through aprocess, similar to recombination, which uses recombination enzymes.

Recombined Triticales. See Triticales.

Recon. A region of a gene within which there can be no crossing-over (recombination),now known to be a nucleotide pair.

Recurrent full-sib selection: A method of intra population improvement thatinvolves the testing of paired-plant crosses; it is the only method of recurrentselection in which the seeds from two individuals, rather than one, are used fortesting and to form the new population

Recurrent half-sib selection: A method of intra population improvement thatincludes the evaluation of individuals through the use of their half-sib progeny; the general procedure for a cycle of selection is (1) to cross the plants beingevaluated to a common tester, (2) evaluate the half-sib progeny from each plant,and (3) intercross the elected individuals to form a new population

Recurrent mass selection: A breeding method designed to increase the levelsof desirable qualities, which are quantitative variables, by changing the frequencyof polygenes; in each screening generation, the best individuals are selected, andthey become the parents of the next screening generation; the process is repeatedfor as many generations as necessary, but the rate of progress declines dramaticallyafter a few generations recurrent parent is used as the selection criterion

Recurrent Parent. The parent to which successive backcrosses are made in the backcross breeding. It is usually an agronomically sound variety under cultivation. It isusually composed of a number of closely related pure lines (putative isogenic lines)that interact synergistically to give the recurrent parent its agricultural characteristics.However, it is deficient in one or a few characters.

Recurrent parent: A homozygous line to which the F1 plants and subsequent generations are backcrossed.

Recurrent parent: The parent to which a hybrid is crossed in a backcross; itreplaces the dragged alleles step-by-step with the alleles of the original variety

Recurrent reciprocal selection: A recurrent selection breeding system inwhich genetically different groups are maintained and, in each selection cycle, individuals are mated from the different groups to test for combining ability

Recurrent Selection (for GCA). A form of recurrent selection in which a number ofdesirable plants on the basis of performance of their testcrosses with a heterozygoustester are propagated from the selfed seed and intercrossed in all combinations toestablish a population for the next cycle of selection. The population so improved canbe used as a source population for extraction of superior inbred lines.

Recurrent Selection (for SCA). A system of breeding in which a number of S1 linesbased on the testcross performance with a homozygous tester (inbred line) of originalselections (S0) are selected and crossed in all combinations to form the newpopulation for the next round of selection. The inbred derived from such improvedpopulation must be crossed with the homozygous tester for effective exploitation ofnon-additive gene action.

Recurrent selection backcross populationA population developed by backcrossing the F1 from a cross between lines having high (DP) and low (RP) values for a quantitative trait and the subsequent generations to the RP; in each backcross generation, a predetermined number of individuals with the top phenotypic values, i.e., values close to the DP phenotype, for the trait are selected for backcrossing.

Recurrent Selection. A cyclical scheme of plant selection designed to increasesystematically the frequency of desirable genes in a population primarily forquantitatively inherited traits. The method involves repeated selection in eachgeneration among the progeny produced by intercrossing in all possible combinationsof the selected individuals (or their selfed progeny) of the previous generation. Sinceintercrosses are made in each cycle of selection, appreciable heterozygosity (andhence, genetic variability) is maintained. Thus opportunity for continuous selection isenhanced because new recombinants are continually generated. Inbreeding depressionalso remains within limits.

Recurrent selection: A method designed to concentrate favourable genesscattered among a number of individuals; it is performed by repeated selection ineach generation among the progeny produced by matings inter se of the selectedindividuals of the previous generation

Rediscoverers of Mendel’s Principles. Carl Correns (of Germany), Hugo de Vries (ofNetherlands), and Tschermak (of Austria). However, some scientists credit principallyCarl Correns as the rediscoverer of Mendelian principles of heredity.

Reduced representation librariesLibraries constructed by fully digesting the genomic DNA with a frequent cutting restriction enzyme and selecting fragments of ~300 bp or so for cloning/sequencing; ~1–10 % of the genome is represented in a RRL.

Reduced representation sequencing: Only a subset of the genomic fragments is sequenced in each individual for marker discovery.

Reduction Division. The first nuclear division during meiosis that produces daughternuclei each having one-half as many centromeres as the parental nucleus.

Reduction division: The two nuclear divisions in meiosis that produce daughternuclei, each of which has half as many chromosomes as the parental nucleus

Redundant DNA. Also called repetitive DNA; the DNA sequences that are present inmany copies per chromosome set.

Redundant DNA: DNA that does not appear to be genetically active and henceis not translated or transcribed; it often consists of repeated sequences

Redundant gene: A gene that is present in many functional copies, so that onecopy can complement the loss of another copy

Reduplication: Doubling of the genetic matter of a haploid chromosome set

Regeneration: The embryonic development of shoots and roots from callus tissue, producing a plantlet.

Registered Seed. The progeny of foundation seed normally grown to produce certifiedseed. This class of seed is not produced in India.

Regression analysis: The process of fitting a regression equation to a set of databy using the method of least squares; it includes the various statistical tests andestimates associated with the use of the fitted equation

Regression Coefficient. A numerical measure of the rate of change of the dependent onthe independent variable. It measures the magnitude of change in a dependent variablefor a unit change in independent variable. It is mathematically the slope of the straightline that most closely relates two correlated variables. It is statistically designated by‘r’ and its numerical values range from +∝ to -∝. It is expressed as a ratio ofcovariance of the two variables and variance of the independent variable [by/x=σxy/σ2x]. It is a unit dependent measurement and is expressed in the unit of thedependent variable. Further it is independent of change of origin, but is dependentupon change of scale.

Regression coefficient: The rate change of the dependent variable with respectto the independent variable

Regression. A statistical description of functional relationship between a dependent andindependent variables. It describes the effect of one or more characters (designated asindependent variables) on a single character (designated as the dependent variable) byexpressing the latter as a function of the former. It can be classified according to thenumber of independent variables or the kind of functional relationship between thedependent and the independent variables. Thus we may have simple or multiplelinear/non-linear regressions. It is a term originally coined by Galton for the tendencyof the quantitative traits of offspring to be closer to population mean than are theirparents’ traits. It arises from dominance, gene interaction, and nongenetic influenceson traits.

Regulator gene: In the operon theory of gene regulation, a gene that is involvedin switching on or off the transcription of structural genes; when transcribed, theregulator gene produces a repressor protein, which switches off an operator geneand hence the operon that this controls; the regulator gene is not part of the operonand may even be on a different chromosome

Regulatory Genes. Genes that are involved in turning on or off the transcription ofstructural genes.

Regulatory Region. Upstream (5’) end of a gene to which bind various proteins thatcause transcription of the gene at the right time and place.

Regulatory regions or sequences: A DNA base sequence that controls geneexpression.

Regulon. A group of separately transcribed genes having operators with the samespecificity.

Relational databaseA database constructed using the SQL and organized in tables; the columns of tables are indexed according to common features.

Remote Sensing. The process of sensing, identifying, and delineating various objects andground features from a distance without coming in direct contact (physical) withthem. The term was at first used by US navy in 1961, when a naval project on a studyof aerial photography was renamed remote sensing. Electromagnetic radiation is themedium by which an object is sensored. The data gathered by remote-sensingsatellites can be utilised for agricultural crops, acreage and yield estimation, droughtand flood monitoring and assessment, flood control, land use, land cover, andmapping for agro-climatic zone planning.

Renaturation. The return to the native configuration of a denatured macromolecule (suchas DNA or protein). In case of DNA, annealing is the process, which brings back thedenatured DNA to its original state.

Renaturation: The reassociation of denatured complementary single strands ofa DNA double helix.

Renner Effect. Competition among the four genetically different megaspores (formed bymeiosis) as to which one will form the embryo.

Repair. Restoration of the original structure (biological activity) of damaged DNA byany one of the recovery mechanisms. Repair includes both reversion and replacementof an induced lesion.

Replicase. An enzyme catalysing the process of replication of nucleic acids.

Replication Fork. The point at which the two strands of DNA are separated to allowreplication of each strand.

Replication studiesSubsequent studies conducted to confirm and validate the results from primary studies.

Replication. In statistics, the process of repeating the same treatment to different plots. Itis essential for estimation of experimental error. In this process, the same treatment orthe same replica is planted twice, thrice or even four times. The process of replicationis something that amounts to sampling. In genetics, replication implies DNA synthesisthrough which a new replica (copy) of the original DNA is produced.

Replicon. A chromosomal region under the influence of one adjacent replicationinitiationlocus. It is a unit of replication, represented by a sequentially replicatinglinear or circular DNA structure.

Reporter Gene. A gene whose phenotypic expression is used to study tissue-specificpromoter and enhancer activities in transgenes. In essence, it reports the presence ofother gene or genes.

Reporter gene: A gene sequence that is easily observed whenit is expressed in a given tissue or at a certain stage ofdevelopment.

Reporter oligoThe oligo complementary to the 50 side of the SNP locus and lacking the polymorphic nucleotide.

Repressor Protein. A molecule that binds to the operator and prevents transcription of anoperon.

Repressor. A protein that binds to a cis-acting element such as an operator or a silencer,thereby preventing transcription from an adjacent promoter.

Reproduction. The propagation of an organism, a cell, or an organelle by one like itself.Reproduction may occur by sexual means (sexual reproduction) or by asexual means(asexual reproduction).

Reproductive Cell. Any of the germ cells (usually gametes) and their immediatepredecessors from which they arise by division.

Reproductive Isolation. Isolation by various genetically controlled mechanisms, whichprevent gene exchange between two populations and preserve differences in the genepools of populations previously attained by selection and other evolutionary factors.

Reproductive Potential. An organism’s ability to produce surviving offspring (up to thestage of sexual maturity).

Reproductive System. Several variables (organs) of an individual orchestrated toperform reproduction.

Repulsion Conformation. A type of linkage conformation in which one dominant andone recessive gene are linked on one chromosome and their counterparts occur inother homologous chromosome (Ab/aB).

Resistance Breeding. A system of breeding that involves selection of desired resistanttypes from a genetically variable population under artificial epiphytotic condition inthe breeding nursery. It has assumed a very important position in plant breedingbecause: (a) it plays a significant role in increasing and stabilizing supplies of food,fibre, vegetable oils, etc., (b) it adds little or nothing to the cost of production, (c) itdoes not create environmental or health hazards, and (d) it is an initial factor inintegrated disease management. Resistance breeding differs from any otherconventional methods for two reasons: (a) resistance can be assayed only by diseasingplants, i.e., employing another living and variable organism, and (b) resistance mayappear elusive, that is, the resistance may break down.

Resistance Erosion. The gradual loss of resistance of the host against a particularpathogen or pest. A variety may lose the resistance gene either due to mutation,segregation or natural out crossing with a susceptible variety. It is interesting to notethat environment also plays an important role in the expression of resistance gene(s).The same genotype that shows resistance to a particular race of the pathogen in oneseason succumbs to the same race in other season. For instance, tomato varietiescarrying cf1 gene show resistance to Cladosporium fulvum in summer but becomesusceptible in winter.

Resistance gene analog markersMarkers based on primers derived from conserved regions of disease resistance genes of plants.

Resistance Mosaics. A strategy of resistance management that involves the use of anumber of cultivars, each carrying a different resistance gene, simultaneously or insuccession (that is, in space and time) in a production area. It can provide a diverseenvironment to pathogens that would decrease the erosion of host resistance. It maybe fruitful if resistance genes are known, the racial composition of the pathogenpopulation is monitored closely and the mosaic pattern of cultivar use is controlled. Inabsence of the orchestrated pattern of cultivar use, the strategy is certain to fail.

Resistance. A heritable property of a host plant that lessens the effects of parasitism. Itimplies that some degree of host-pathogen interaction is always evoked. Therefore, aresistant plant may resist the establishment of a pathogen by reducing the amount ofinitial inoculum or may interfere the growth and reproduction of the establishedpathogen. Thus some symptoms of disease always appear contrary to immunitywherein no symptoms develop at all.

Resolution: Degree of molecular detail on a physical map of DNA, rangingfrom low to high.

Resolving Power. The ability to discriminate between two points. The human eye cannotresolve two points separated by less than 100􀈝m. The light microscope introduces a500-fold increase in resolution over the eye, and the electron microscope provides a500-fold increase over the light microscope.

Resource Conservation Technology. A technology aiming at conserving availableresources to maximize the output and profit in a cropping system. It includes zero-till(no-till), raised bed furrow system, laser levelling, innovative cropping systems andmanagement of crop residues. The technology is scale-neutral and can be used withadvantage by all farmers. It lowers production costs through omitting tillageoperations and saving one or two irrigations. It has potential to maintain and sustainproductivity. Scientists have asserted that conservation agriculture can raise cropyields by 20 to 50 per cent.

Restitution Nucleus. A single nucleus with unreduced chromosome number (producedas a consequence of failure of the first or second meiotic division) or with doubledchromosome number (owing to failure of mitosis).Restoration. Mitigating the effects induced by any physical or chemical agent to abiological system. The terms like recovery, reactivation are frequently used assynonyms for restoration.

Restorer Gene. A gene that brings back the changes brought about by the cytoplasmicmale sterility.

Restorer line (R line): A pollen parent line; it contains the restorer gene orgenes, which restore cytoplasmic male sterile plants to pollen fertility; it is crossedwith an A line in the production of hybrid seeds

Restorer Line. A line which restores pollen-producing ability in the hybrid after crossingwith A line by providing a copy of restorer gene; also called R line.

Restriction Endonucleases. Enzymes that recognise and cut specific nucleotidesequences in DNA. Type II restriction endonucleases are used in the construction ofrecombinant DNA molecules. These enzymes provide powerful tool for analysis ofDNA organization, gene structure and gene regulation.

Restriction enzyme cutting site: A specific nucleotide sequence of DNA atwhich a particular restriction enzyme cuts the DNA. Some sites occur frequentlyin DNA (E.g. every several hundred base pairs), others much less frequently (rarecutter; e.g., every 10,000 base pairs).

Restriction enzyme, endonuclease: A protein that recognises specific, shortnucleotide sequences and cuts DNA at those sites. Bacteria contain over 400 suchenzymes that recognise and cut over 100 different DNA sequences.

Restriction Enzyme. An endonuclease that recognises specific target nucleotidesequences in DNA and breaks the DNA chain at those points. A variety of suchenzymes is now known, and is used extensively in genetic engineering.

Restriction enzyme: An enzyme that functions in a bacterial modificationrestrictionsystem and recognises specific nucleotide sequences and breaks theDNA chain at these sites; there is a great number of them, each with differentrecognition and/or cutting sites; they are intensively used as a tool in moleculargenetics and also in producing chromosomal banding patterns in cytogenetics

Restriction enzyme: An enzyme that recognizes a specificnucleotide base sequence (usually four to six base pairs inlength) in a double-stranded DNA molecule and cuts bothstrands of the DNA molecule at every place where thissequence occurs.

Restriction enzymeAn endonucleases that cleaves DNA only within or near a site that has a specific base sequence.

Restriction Fragment Length Polymorphism (RFLP). Variations occurring within aspecies in the length of DNA fragments generated by a specific endonuclease. RFLPsare useful as molecular markers.

Restriction fragment length polymorphism (RFLP): Thepresence of two or more variants in the size of DNA fragmentsproduced by a restriction enzyme. These differentsized fragments result from an inherited variation in thepresence of a restriction enzyme’s target sequence. RFLPsare used for gene mapping and DNA profiling.

Restriction fragment length polymorphism (RFLP): Variation betweenindividuals in DNA fragment sizes cut by specific restriction enzymes; polymorphicsequences that result in RFLPs are used as markers on both physical maps andgenetic linkage maps. RFLPs are usually caused by mutation at a cutting site. Seemarker.

Restriction fragment length polymorphismA single restriction enzyme produces fragments of different lengths from the same genomic regions of different individuals/ strains/lines.

Restriction Fragment. A fragment of DNA created by cleavage at specific sites by arestriction endonuclease.

Restriction Map. A map of a chromosomal region showing the positions of target sitesof one or more restriction enzymes.

Restriction map: Representation of DNA with the position of restriction sitesindicated

Restriction site: A certain nucleotide sequence within the double-strandedDNA; it is recognised by a restriction endonuclease; the enzyme cuts the doublestrand within the recognition sequence; the restriction sites are usually composedof four to six base pairs and are bilaterally symmetric; both strands are cut eitheron exactly opposite positions (blunt ends) or alternated ones (sticky ends); thetype of cutting depends on the enzyme used

Restriction-site-associated DNA markers
Polymorphisms in the recognition sites for the restriction enzyme used for preparation of the assay sample.

Restriction-site-associated DNA sequencingShort regions surrounding all recognition sites present in the genome for the selected restriction enzyme are sequenced, derived from the RAD tag marker technique.

Restrictive Conditions. Environmental conditions under which a conditional mutantshows the mutant phenotype.

Retrotransposon. A transposable element that utilises reverse transcriptase to transposethrough an RNA intermediate.

Retrotransposon: Retrotransposons are a ubiquitous and major componentof plant genomes; those with long terminal DNA repeats (LTRs, Ty1-copia-likefamily) are widely distributed over the chromosomes of many plant species

Retrotransposon-based insertion polymorphism Detects retrotransposon insertions at specific sites using PCR amplification; one primer derived from the concerned retrotransposon and a pair of primers derived from the sequence flanking the insertion site.

Retrotransposons These sequences transpose via RNA intermediates; Syn., Group I transposons.

Retrovirus. An RNA virus that replicates by first being converted into double-strandedDNA.

Reverse Genetics. The study of genetics that begins with a segment of DNA (genotype)or a protein sequence to investigate its function (phenotype). It also determines how amutation at a particular site in a gene affects the phenotype. It is so called as it directlydeals with and changes in the DNA unlike Classical/ Mendelian genetics, which usesa phenotype to trace the genotype. (Mendelian genetics is called forward genetics).

Reverse genetics: Using linkage analysis and polymorphic markers to isolatea disease gene in the absence of a known metabolic defect, then using the DNAsequence of the cloned gene to predict the amino acid sequence of its encodedprotein; in general, a technology aiming at isolating mutants of a given sequence;it is also applied for identification of gene function.

Reverse Mutation. A heritable change in a mutant gene that restores its originalconstitution (nucleotide sequence).

Reverse mutation: The production, by further mutation, of a premutation genefrom a mutant gene; it restores the ability of the gene to produce a functionalprotein; strictly, reversion is the correction of a mutation (i.e. it occurs at the samesite).

Reverse phenomics Detailed analysis of a trait to unravel the various physiological, biochemical, and biophysical processes and the genes involved in control of the trait.

Reverse Transcriptase. An enzyme that catalyses the synthesis of a DNA strand usingRNA as its template.

Reverse transcriptase: An enzyme from retroviruses for the synthesis of aDNA complementary to a RNA molecule (i.e., cDNA); it is used for (1) filling-inreactions, (2) for DNA sequencing, and (3) for cDNA synthesis

Reversion. The production of a wild-type gene (phenotype) from a mutant one(phenotype) by either genetic or non-genetic mechanisms.

RFLP Mapping. A technique in which DNA restriction fragment length polymorphismsare used as reference loci for mapping known genes or other RFLP loci.

Rhizobium. A bacterium that resides insides the root nodules of legumes as a symbiont.It is highly sensitive to higher O2 concentration. Legume plants provide it shelter; inreturn, it provides them high quality growth protein through fixing atmosphericnitrogen.

Rho. A protein factor required to recognise certain transcription termination signals in E.coli.

Ribonucleic Acid (RNA): A chemical substance made up of nucleotidescompound of sugars, phosphates, and derivatives of the four bases adenine (A), guanine (G), cytosine (C), and uracil (U). RNAs function in cells as messengers ofinformation from DNA that are translated into protein or as molecules that havecertain structural or catalytic functions in the synthesis of proteins. RNA is also thecarrier of genetic information for certain viruses. RNAs may be single or doublestranded.

Ribonucleic acid (RNA): A molecule that translates theinstructions encoded in DNA to build proteins.

Ribonucleotide. A nucleotide having ribose sugar.

Ribosomal RNA (rRNA): A class of RNA found in the ribosomes of cells.

Ribosome. A complex organelle that catalyses the translation of genetic message ofmRNA into an amino acid sequence of a polypeptide. It is composed of proteins andrRNA.

Ribosomes Small cellular components composed of specialised ribosomalRNA and protein; site of protein synthesis.

Ribosomes: Small cellular components composed of specializedribosomal RNA and protein; site of protein synthesis.

Ribozymes. RNA molecules having catalytic activities, the self-splicing RNA moleculesin Tetrahymena, for instance.

Ridge regressionIn this model, all the marker effects are considered to belong to a normal distribution with mean zero and variance σg 2; it shrinks all marker effects toward zero.

Ring Formation: Occurs where the ends of a chromosome bend over and fusetogether with a loss of genetic material.

RNA interference (RNAi): The use of double stranded RNA to interferewith gene expression; RNAi is usually mediated by approximately 21-nt smallinterfering RNAs

RNA Polymerase. An enzyme that catalyses the synthesis of an RNA strand from a DNAtemplate. In eukaryotes, there are several classes of RNA polymerase; structural genesfor proteins are transcribed by RNA polymerase II. However, in prokaryotes, a singleclass of RNA performs all the necessary functions.

RNA polymerase: An enzyme that transcribes an RNA molecule from thetemplate strand of a DNA molecule; it adds to the 3′ end of the growing RNAmolecule one nucleotide at a time using ribonucleotide triphosphates (rNTPs) assubstrates; RNA polymerase I is dedicated to the synthesis of only one type of RNAmolecule (pre-rRNA); RNA polymerase II is required for general transcriptionreactions; RNA polymerase III produces small RNAs such as tRNAs and 5S rRNA

RNA transcriptase: The enzyme responsible for transcribing the informationencoded in DNA into RNA; it is also called transcriptase or RNA polymerase

RNA. Ribonucleic Acid; a constituent of all living cells, consisting of a long chain ofnucleotides with ribose (as a pentose sugar) and uracil (as a distinguishing pyrimidineN-base). It sometimes takes double-stranded structure while performing proteinsynthesis. It is mainly of three kinds: mRNA, rRNA and tRNA. The base sequence ofrnRNA determines the amino-acid sequence of polypeptide. The rRNA is the majorconstituent of ribosomes, which act as sites of protein synthesis. The last one, tRNA,identifies and carries a specific amino acid to the site of protein synthesis in responseto the codons of mRNA. Some RNAs also act as enzymes, called ribozymes. Innature, it evolved prior to DNA due perhaps to its simple structure. RNA replicasemust have been the first simplest living molecule that catalysed its own replication. Itcontained ribose sugar because it is more readily synthesized than deoxyribose ofDNA.

RNA-SeqSequencing of the complete transcriptome using a NGS technology.

Robertsonian Translocation. A translocation that involves breakage at centromeres oftwo non-homologous acrocentric chromosomes and rejoining of the larger parts of thetwo to form a metacentric chromosome. The smaller chromosomal segments aresubsequently lost. Robertsonian translocation, which is also called centric fusion, hasbeen important in the phylogeny of many species in reducing chromosome number(Drosophila melanogaster L., for example).

Robertsonian translocation: A chromosomal mutation due to centric fusionor centric fission (i.e., a reciprocal translocation with breakpoints within thecentromeric regions); in wheat, Robertsonian translocations arise from centricmisdivision of univalents at anaphase/ telophase I, followed by segregation of thederived telocentric chromosomes to the same nucleus, and fusion of the brokenends during the ensuing interkinesis root disease in certain plants

Rogue. A variation from the standard type of a variety or strain.

Roguing. The removal of undesirable individuals to purify the seed stock of a variety.

Round robin mating schemeEach member of a set of lines is mated as male to a defined number of lines and as female to an equal number of other lines.

rRNA. Ribosomal RNA; a class of RNA molecules, coded in the nucleolar organiser,which have an integral role in ribosome structure and function. However, its role inribosome structure and function is not fully understood at present.

Rule of Thumb. A principle of broad application which is not so much (100%) preciseand accurate. However, it is easily learned and easily applied procedure for findingsome value or making some determination with closer approximation. For instance,given the probability of an infrequent desired event is p, the no. of individuals to besampled to give 95% chance of at least one occurrence of this event will be ~ 3/p.Thus, if the probability of an event (aa in F2 generation from an F1 hybrid, Aa) is ¼, itcan be shown that the actual number of individuals to be sampled is 11.9, whereas3/p=3×4=12, a very close approximation.

S Phase. The part of interphase of the cell cycle in which DNA synthesis occurs.

S. Svedberg unit; a unit of sedimentation velocity that is commonly used to describemolecular units of various sizes as sedimentation velocity is proportional to the size.

S0. Symbol used to designate the original selfed plant.

S1, S2, S3… Symbols used to designate first, second, etc. generations after selfing anancestral plant (S0t).

S-allele. Any allele of those genes which control incompatibility in plants. The variousalleles of the incompatibility may be represented by S1, S2, S3, etc. SF-alleles belongto the same allelic series but which control self-fertility.

Sample. A finite series of observations taken from a population. Since it is not feasible tostudy all the individuals of a population owing to its large size and hypotheticalnature, samples are almost always taken to represent the entire population.

Sampling Distribution. A process through which different sample values are puttogether for further study.

Sampling Error. Deviation of a sample value from the true value owing to the limitedsize of sample.