Terminologies in Genetics and Plant Breeding Part -4

E. coli. The Escherichia coli; easily cultured prokaryotic organism. The bacterium is thusfar most studied and best understood.

Early generation test: Selection schemes in which poor recombinants are discarded already in F₂ and F₃ generations

Early Generation Testing. Also called early testing; the evaluation of breeding materialsfor specific characteristics during early segregating generations (F2, F3, and F4) basedon certain parameters. Early testing in maize refers to testing of inbred lines during I1,I2, and I3 (S1/S2/S3) generations. The objective is to enhance the possibility of findingsuperior inbred line by eliminating poor materials during early generations. It alsohelps save extra expenditure. When materials are visually selected, it is a goodexercise for isolating families of high combining ability. It has been criticised on theground that the performance of inbred lines may change with the degree ofhomozygosity attained by those inbreds. It is also not desirable when high combininglines are agronomically poor, and are likely to be eliminated during inbreeding.

Early selection: It is conducted on highly heterozygous individuals whichbecome the parents of the next screening generation

Ear-to-Row Selection. A form of selection in which desired ears are harvestedindividually and subsequently grown an ear-to-a row, and the cycle is repeated fromthe aggregate of seeds of selected rows. It differs from mass selection in basing theselection on the performance of progeny.

Ear-to-row selection: A separate growing of progenies (i.e. the separate sowingof lines or families

Ecdysone. A molting hormone in insects.

Ecological Combining Ability. The ability of a genotype to perform synergistically inassociation with other genotypes in mixed populations. Such genotypes are goodneighbours, and at the same time they are good competitors as well. In such mixedpopulations, natural selection may be operating for superior neighbourhood; however,in competition, it also appears to perpetuate many surviving genotypes with superiorpure-line performance.

Ecological Niche. The place occupied by a species in the community structure which it ispart of.

Ecological Regions. Specific areas where crop plants originated. Six such ecologicalregions have been documented by Harlan (1992); these are: (1) Mediterranean, (2)Savanna, (3) Tropical low lands/coastals, (4) Tropical highlands, (5) Tropical forests,and (6) Temperate woodlands. In these regions, wheat and barley, corn and rice, appleand grapes, potato, sugarcane and coconut, and apple and oranges, respectively aresupposed to be originated.

Ecology (Haeckel 1869). The study of pattern of relations between organisms and theirenvironment. It has been derived from Greek words: oikos and logos, meaninghousehold and study, respectively. Thus the study of the environmental houseincludes all the organisms in it and all of the functional processes that make the househabitable. Literally, then, ecology is the study of life at home with emphasis ontotality.

Economic heterosis: Superiority of F1 hybrids over the commercial variety of the crop.

Economic heterosisSuperiority of F1 hybrids over the best commercial variety of the crop.

Ecospecies. A group of ecotypes capable of interbreeding without any adverse effect onthe fitness of offspring.

Ecosphere. Also called biosphere; the largest and most nearly self-sufficient biologicalsystem. It includes all the earth’s living organisms interacting with the physicalenvironment as a whole to maintain a steady-state system intermediate in the flow ofenergy between the input of the sun and the thermal sink of space. Steady stateimplies a self-adjusting equilibrium or balanced condition relatively immune to atleast small-scale disturbances.

Ecosystem (Tansley 1935). Also called ecological system; the interaction between orfunctioning together of the community and the non-living environment.

EcoTILLING: A high throughput, low cost technique for rapid discovery ofpolymorphisms in natural populations of plants; it is similar to TILLING but itdiffers from TILLING in that natural polymorphisms are detected rather thanpolymorphisms induced through chemical mutagenesis; on the other hand, singlenucleotide polymorphisms (SNPs), small insertions and deletions, and variationsin microsatellite repeat number can be efficiently detected using the EcoTILLINGtechnique

Ecotypes. The locally adapted populations having optima and limits of tolerance(adjusted to local conditions) of species with wide geographical ranges. It may also bedefined as a local race with genotypes adapted to a particular restricted habitat as aresult of natural selection. Ecotypes may be the result of factor compensation.Compensation along gradients of temperature, light or other factors may involvegenetic races (with or without morphological manifestations) or physiologicalacclimation without a genetic change(s).

Ecovalence: This parameter is a quantitative measure for the evaluation ofecological adaptability

Effective Breeding Population. The number of breeding individuals of a population,contributing to the gene pool of the next generation.

Effective number of markers
It is that number of markers with which the standard deviation of the estimates is not significantly affected by reducing or increasing the number of loci/bands analyzed.

Efficient mixed-model association (EMMA)
Corrects AM for population structure and kinship; it uses an algorithm for deducing the phylogenetic kinship matrix from genome-wide markers and applies it to the linear mixed model.

Egg Mother Cell. A megasporocyte that gives rise to an egg cell after megasporogenesisin higher plants.

Egg. The female gamete or germ cell. It gives rise to the zygote after getting fertilisedwith a sperm.

Electron Microscope. An instrument that uses a focussed beam of electrons to producean enlarged image of an object.

Electrophoresis. A technique for separating the components of a mixture of molecules(proteins, DNAs or RNAa) through directional movement of charged particles in a gelplaced in an electrical field.

Electrophoresis: A method of separating large molecules (such as DNAfragments or proteins) from a mixture of similar molecules. An electric currentis passed through a medium containing the mixture, and each kind of moleculetravels through the medium at a different rate, depending on its electrical chargeand size. Separation is based on these differences. Agarose and acrylamide gels arethe media commonly used for electrophoresis of proteins and nucleic acids.

Electrophoresis: A method of separating substances, such asDNA fragments, by using an electric field to make themmove through a “gel” at rates that correspond to their electriccharge and size.

Elimination Coefficient. The frequency with which individuals carrying a specific genewith deleterious effect(s) gets genetically eliminated from the population. Forexample, suppose a certain gene has elimination coefficient of 5%; it implies that outof every 20 individuals, one will die before the gene concerned is transmitted to theoffspring.

Emasculation. Removal of immature anthers from a bisexual flower with little injury tothe ovary. It is one of the techniques to control pollination, and is essentially a firststep to artificial hybridization. Some techniques used for emasculation includeexposure of flowers to heat, cold or chemicals such as alcohol. These techniques arebased on the fact that pollen is usually more sensitive to unfavourable environmentalconditions than the stigma. Suction has successfully been used to emasculate smallfloweredlegumes. The timing of emasculation is also important. If the operation isdelayed, there is every possibility of anther bursting during emasculation. On theother hand, emasculation at too early stage (while the floral bud is immature andtender) will result in unnecessary mutilation of the pistil.

Emasculation: The removal of anthers from a flower before the pollen is shed.To produce F1 hybrid seed in a species bearing monoecious flowers, emasculationis necessary to remove any possibility of self-pollination

Embryo culture: A method of inducing the artificial growth of embryos byexcising the young embryos under septic conditions and placing them on suitablenutrient media; the method is often applied when postgamous incompatibilityexists (Eg. in wide crosses)

Embryo rescue: The removal and culture of an immatureembryo to produce a plant, often following a wide cross.

Embryo rescue: When cross-pollination is made or occurs between geneticallywidely different plants, the resulting embryo may be aborted because of parentalmutual incompatibility; such embryos may be excised during an early stage andgrown on a congenial medium such as nutrient

Embryo Sac. Typically, an eight nucleate female gametophyte; the maturemegagametophyte in higher plants. It arises from one of the megaspore by successivemitotic divisions.

Embryo. The rudimentary plant in a seed. The embryo arises from the zygote (2n). It canalso be defined as the young sporophyte arising from the union of female and malesex cells.

Embryogenesis. The origin, development, and the evolution of the embryo; also calledembryogeny.

EMS. Ethyl Methane Sulphonate. It is a chemical mutagen that causes GC to ATtransition. Although it can add ethyl groups to any unsaturated positions of nitrogenbases of the DNA, but mutagenicity is best described by the addition of alkyl groupespecially at O6 position of guanine.

Endocytosis. The processes of phagocytosis, pinocytosis, and micro-pinocytosis. It leadsto bulk ingestion of solid or fluid materials by the cell. Exocytosis is the reverseprocess, by which membrane-lined products are released at the plasma membrane.

Endogamy. See inbreeding.

Endomitosis. A form of somatic polyploidization, fairly common in differentiatedtissues. It takes place within an intact nuclear envelope, and duplication ofchromosomes (increase in DNA content) occurs without nuclear division in usualsense (endopolyploidy).

Endomitosis: A doubling of the chromosomes within a nucleus that does notdivide, thus producing a polyploid; the doubling may be repeated a number oftimes, which leads to endopolyploidy

Endonuclease. An enzyme that cleaves the phosphodiester bond within a nucleotidechain of a DNA molecule.

Endonuclease: An enzyme that cleaves the phosphodiester bond within anucleotide chain.

EndonucleasesEnzymes that produce internal cuts or cleavages in DNA molecules.

Endopolyploid: Diploid individuals whose cells contain 4C, 8C, 16C, 32C, etc.,amounts of DNA in their nuclei

Endopolyploidy. An increase in the number of chromosome sets caused by replicationwithout cell division.

Endoreduplication: Chromosome reduplication in the interphase of the mitoticcell cycle

Endosperm. A tissue specialised for nourishing the developing embryo of higher plants.It is typically a triploid tissue (3x), formed from the triple fusion of a sperm nucleuswith the two polar nuclei of the embryo sac. But it may also be diploid, tetraploid, oreven pentaploid depending on the species in question as it may also originate from thefusion of one female nucleus with one or more others or with a male nucleus or both.

Endosperm: In grasses, the reserve food material in the caryopsis lying outsidethe embryo; it is a starchy tissue that is formed during grain development; itprovides nourishment for the developing embryo and for the seedling aftergermination until it can establish itself

Enforced Outbreeding. Deliberate avoidance of mating between relatives.

Enhancement: The process of improving a germplasm accessionby breeding while retaining the important genetic contributionsof the accession.

Enhancer. A cis-regulatory sequence that can elevate levels of transcription from anadjacent promoter. Many tissue specific-enhancers can determine spatial patterns ofgene expression in higher eukaryotes.

Enthalpy. The total energy contained in chemical compounds of the cell. The energyexists as chemical energy primarily locked in high-energy bonds. The cell uses onlypart of the total energy at any given point of time.

Entropy. A measure of randomness or disorder. It also measures unavailable energyresulting from transformations. The law of entropy (the second law of76thermodynamics) states that every thing, whether living or non-living, tends todisorganise in order to attain the state of maximum stability (high entropy). Tomaintain a high state of internal order (a condition of low entropy), living bodiesrequire energy. Although entropy in technical sense relates to energy, the word is alsoused in a broader sense to refer to degradation of materials. Entropy is not allnegative. As the quantity of available energy declines, the quality of the remaindermay be enhanced greatly.

Enucleate Cell. A cell having no nucleus.

Environment. The sum total of factors/ conditions that affect survival and reproductionof an organism(s); also, the complex of physical and biotic factors within which anindividual organism or a population exists.

Environmental Variance. That portion of phenotypic variance caused by differences inenvironmental factors to which the individuals of a population were exposed.

Enzyme. A biochemical (usually protein) that functions as a catalyst. Most enzymescannot function alone; they are referred to as apoenzymes. The non-protein part thatmakes them functional is called cofactor (a metal or a prosthetic group in case ofconjugated proteins) or coenzyme (small molecules). The combination of protein andnon-protein parts (functional state) is called holoenzyme. There may be a group ofenzymes, which differ slightly in their molecular structure, and sometimes in theirregulation, are called isoenzymes (isozymes). Not all enzymes are proteins. SomerRNA and tRNA have been found to have catalytic activities.

Enzyme: A protein catalyst which is essential to the correct functioning ofbiochemical reactions.

Enzyme: A protein that acts as a catalyst, speeding the rate atwhich a biochemical reaction proceeds but not altering thedirection or nature of the reaction.

Enzyme-linked immunosorbent assay (ELISA): A technique using antibodiesfor detecting specific proteins. Used to test for the presence of a particulargenetically engineered organism.

Epigenesis: The concept that an organism develops by the new appearance ofstructure and functions, as opposed to the hypothesis that an organism developsby the unfolding and growth

Epigenetic changesChanges involving DNA methylation, RNA interference, and histone modification (acetylation, methylation, phosphorylation, and ubiquitination).

Epigenetic Inheritance. Processes by which heritable modifications in gene functionoccur but are not due to changes in the base sequence of the DNA of the organism(e.g., paramutation, X-chromosome inactivation, parental imprinting, and the like).

Epigenetic marksEpigenetic changes.

Epigenetic recombinant inbred linesRILs with the same genotype, but differing from each other in terms of epigenetic modifications.

Epigenetic regulation: Regulation of gene activity mediated by a reversiblechange in DNA modification or chromatin structure

Epigenetic: Heritable variation caused by differences in the chemistry ofeither the DNA (methylation) or the proteins associated with the DNA (histoneacetylation), rather than in the DNA sequence itself

Epigenetics: Study of a change in gene function without any change in the gene base sequence.

Epigenetics: The study of the mechanisms by which genes bring about their phenotypic effects

Epigenomics: A genome-wide study of epigenetic marks.

Epimutation: A heritable change in gene activity that is not due to a change inbase sequence; generally applied to an abnormal change in gene activity (Eg. in atumor or a cell culture

EpimutationHeritable genetic variation generated by epigenetic changes.

Epiphytotic. An unarrested spread of a plant disease. Under conditions of favourableenvironment and monocropping of a susceptible variety over a wide geographicalarea, it has been often observed that the disease occurs in devastating form and soonoccupies the entire area even after the efforts have been made for its control. It is thussaid that the disease has appeared in an epiphytotic form (e.g., brown spot disease ofrice in W.B. during 1940s).

Epistasis hypothesisHeterosis results from epistatic gene interactions.

Epistasis. The masking effect of one gene over a non-allelic gene; the expressed gene iscalled epistatic, and the suppressed one is known as hypostatic. The term has acquireda more general meaning in quantitative and population genetics where it is usedsynonymously to include any kind of gene interaction. It should be carefullycontrasted with dominance (which refers to the masking effect of one allele over theother at the same locus) that is necessarily associated with heterozygosity, and is onlymomentary or short-lived in autogamous species. With epistasis, one can hope for aworthwhile type to appear owing to step-by-step completion of a biochemicalpathway.

Epistasis: The interaction of genes at different loci; the situationin which one gene affects the expression of another.

Epistasis: The nonreciprocal interaction of non-allelic genes; the situation inwhich one gene makes the expression of another; more specifically, gene interactionin which one gene interferes with the phenotypic expression of another non-allelicgene so that the phenotype is determined effectively by the former; the latter isdescribed as hypostatic

EpistasisInteraction between two and more different genes; the expression of a gene is modified due to the influence of other interacting genes.

Epistatic Gene Action. A kind of interloci interaction. The final outcome (phenotypegoverned by two or more genes) gets changed according to the presence or absence ofa particular allele of the genes in question.

Epistatic QTLsThese QTLs interact with the main effect QTLs to influence the trait phenotype.

Epistatic selectionSelection for a phenotype produced by interaction between two and more genes.

Epistatic Variance. That portion of genetic variance, which results from an interaction ofgenes at different loci. It is of three types: (a) additive x additive, (b) dominance x dominance, and (c) additive x dominance. If a trait is governed by two gene pairs, all the three types of variances, viz., additive, dominance, and epistatic will be present.So far as epistatic or interaction variance is concerned, only additive x additivecomponent can be exploited through selective breeding.

eQTL hotspotA genomic region containing eQTLs affecting the expression of many different genes located in the same genomic region.

Equational Division. A nuclear division that maintains the same ploidy level of the cell.

Equational division: The division of each chromosome during the metaphaseof mitosis or meiosis into two equal longitudinal halves (i.e. sister chromatids),which are distributed to the two cell poles, and then incorporated into separatedaughter nuclei

Equatorial Plane. The plane midway between the two daughter nuclei of a dividing cell.

Equatorial Plate. The metaphase plate.

Equilibrium Population. A population in a state of genetic equilibrium; also see Hardy-Weinberg equilibrium.

Error Variance. Also called environmental variance.

Error variance: Variance arising from unrecognised or uncontrolled factors inan experiment with which the variance of recognised factors is compared in testsof significance

Erucic acid. A fatty acid containing long hydrocarbon (C22) chain. Its proportion inrapeseed - mustard oil is very high which is undesirable nutritionally. A reduction inerucic acid through breeding results in proportional increase in oleic and linoleic acids(low carbon containing unsaturated fatty acids with two double bonds). The presenceof erucic acid is controlled by two alleles at the same locus. However, its expressivityappears to be enhanced by two additive genes in rapeseed.

Escape (Drought). A mechanism of pseudo-resistance to drought, often achieved byrapid phenological development or by developmental plasticity. The rapidphenological development is closely related to the earliness of maturity in the cropplants. This helps the plants complete their life cycle before the very occurrence ofmoisture deficit in the soil. It is perhaps most dramatic in the ephemeral plants of thedesert regions which complete life cycles in as few as four to six weeks.Developmental plasticity is considerable in determinate annuals such as wheat. Wheatcommonly produces more tillers than are required; the number, which survives toproduce spikes, is reduced by water deficits between floral initiation and spikeemergence. Excessive tillering would of course be wasteful of soil moisture in themoisture-restricted environments. Screening and selection for drought escape throughmaturity or developmental plasticity is relatively simple compared to screening andselection for some other drought resistance characteristics. However, in areas wherethe length of the growing season is clearly defined by cold temperatures, there is littleopportunity for manipulation of maturity.

Escape. A mechanism of functional resistance in which a plant with certaincharacteristics escapes attacks of pests. For example, an early maturing variety mayescape the attack of a pest whose population build-up occurs late in the growingseason.

Essentially derived varietyA variety predominantly derived from the initial variety so that it retains the expression of essential characteristics from the genotype or combination of genotypes of the initial variety.

EST. Expressed Sequence Tag; a sequence-tagged site derived from a cDNA clone andused to position and identify genes in genomic analysis.

EST: Expressed sequence tag.

Estimate. The numerical value of the estimator.

Estimation error: The amount by which an estimate differs from a true value;this error includes the error from all sources (Eg. sampling error and measurementerror)

Estimator. Any statistic used for estimating the parameter (e.g., mean & variance).

Ethidium Bromide. A molecule that can intercalate into DNA double helices when thehelix is under torsional stress.

Eucentric: A chromosomal interchange by which the translocated segmentdoes not change the relative position to the centromere

Euchromatin. A chromosomal region that stains normally. It is thought to containnormal functioning genes.

Euchromatin: Chromatin that shows the staining behaviour of the majorityof the chromosome complement; it is uncoiled during interphase and condensesduring mitosis, reaching a maximum density at metaphase

Euchromatization: The induced or spontaneous change of heterochromatininto euchromatin

Euchromosome: A chromosome showing the typical features of the standardcomplement of a given species

Eugenic: Favourable to the genetic quality of a population, as opposed todysgenic

Eugenics. Controlled human breeding in an attempt to improve future generations, basedon notions of desirable and undesirable genotypes. During early part of twentiethcentury, it became quite fashionable to propose that persons having genetic disordersshould be prevented from having any offspring (a programme called negativeeugenics). Most deleterious alleles are rare, and mostly occur in heterozygotes.Assuming frequency of 0.01 of a deleterious allele, it takes about 100 generations toreduce its frequency to half, that is, 0.005 {qn = 1/(n+1/q0)}, if all the homozygoteswere prevented from producing offspring. Clearly, it was a futile exercise.

Euhaploid: A haploid genome showing no deviating number of chromosomescompared with the standard genome of the species

Eukaryon: The highly organised nucleus of a eukaryote

Eukaryote. A cell having true nucleus. The cell has cytoplasm separated by a distinctnuclear membrane.

Eukaryote: An organism whose cells have a distinct nucleus

Eukaryote: Cell or organism with a membrane-bound, structurallydiscrete nucleus and other well-developed subcellularcompartments.

Euploid: Having the “correct” chromosome composition. Cells containing onlycomplete sets of chromosomes.

Euploidy. A situation wherein an organism has any number (one, two or more) ofcomplete chromosome sets; such an individual is called euploid. It covers situationssuch as monoploidy, diploidy, and polyploidy.

Euthenics. Improvement in conditions for people to live in.

Ever Green Revolution. Achievement of sustainable productivity advances, rooted inthe principles of ecology, economics, social and gender equity, and employmentgeneration. It is a concept that applies to improvement in crop productivity inperpetuity without ecological harm.

Evolution Pressure. The combined action of mutation, migration, hybridisation, andselection in changing the genetic structure of a population, and thereby contributing to evolution.

Evolution. Gradual change usually with a directional component. Biological evolution isbest defined as the gradual change in the diversity and adaptation of populations oforganisms. It involves change in gene frequencies, which results from (a) selectionpressure from the environment and interacting species, (b) recurrent mutation, (c)genetic drift, and (d) migration. The process of evolution has two dimensions:Phyletic evolution and speciation. Phyletic evolution is the gradual changes that occurwith time in a single lineage of descent; as a rule, these changes result in greateradaptation to the environment and often reflect environmental changes. Speciationoccurs when a lineage of descent splits into two or more new lineages and is theprocess that accounts for the greater diversity of the living world. Biological evolutionis quite distinct from cultural evolution that is a unique human process and is a rapidprocess compared to the biological evolution. Human beings may evolve culturally80through transmission from generation to generation of learned information includingmoral and immoral values (inheritance of acquired characters).

Evolutionary Breeding (Suneson 1949). A breeding procedure in which the variety isdeveloped from an unselected progeny of a cross, or multiple crosses, that haveundergone evolutionary changes. Only natural selection operates in such populations.A variety of barley ‘Harland’ was produced by this procedure.

Ex situ conservation: A conservation method that entails the removal of seed, pollen, sperm, or individual organisms from their original habitat, keeping theseresources of biodiversity alive outside of their natural environment; the storage ofplant genetic resources as seeds in genebanks at subzero temperatures is the mostwidely applied method

Ex situ germplasm conservation: Maintenance of germplasm accessions as seed samples, in the field as growing plants, as slow-growth shoot cultures, or as tissues/organs frozen in liquid nitrogen in gene banks located away from their natural habitats.

Ex situ: Out of place or not in the original environment (E.g. seeds stored in agenebank)

Excision Repair. The repair of a DNA lesion by removal of the faulty DNA segment andits replacement with a wild-type segment.

Exogamy. Cross-fertilisation or outbreeding leading to an increased incidence ofheterozygosity in the population.

Exogenous DNA: DNA originating outside an organism.

Exon. Sequence of base pairs in a gene that participates in the coding of amino acids of apolypeptide. It is non-intron portion of the coding sequence of a gene. Exonsconstitute mRNA, and are translated into protein.

Exon: Any segment of an interrupted gene that is represented in the matureRNA product. The protein-coding sequences of a gene.

Exonuclease An enzyme that cleaves nucleotides one at a time from an end ofa polynucleotide chain.

Exonuclease. An enzyme that cleaves nucleotides one at a time from an end of apolynucleotide chain.

Experimental design: The planning of a process of data collection; also usedto refer to the information necessary to describe the interrelationships within a setof data; it involves considerations, such as number of cases, sampling methods, identification of variables and their scale-types, identification of repeatedmeasures, and replications

Experimental Error. The difference among experimental plots treated alike. Forinstance, if the same variety is planted to two different plots, there may be differencein yield between these two plots. The difference may be owing to differences in soilfertility,soil-moisture, water holding capacity, and various other biotic factors. Thissort of difference is called experimental error. This error is the primary basis fordeciding whether an observed difference between two treatments is real or just due tochance. Clearly, every experiment must be designed to have a measure of theexperimental error. However, it is emphasized that experimental error cannot beeliminated totally; since two plots will not perform exactly the same no matter howcarefully these are treated alike.

Explant. An excised fragment of a tissue or organ used to initiate an in vitro culture.

Expressed SSRsSSR markers derived from ESTs.

Expression level polymorphismVariation in the expression levels of genes.

Expression proteomicsA comparative quantitative analysis of the patterns of protein expression between samples differing for some variable.

Expression QTLs: QTLs concerned with regulation of expression levels of the genes.

Expressivity. The extent of manifestation of a genetic character. It is the degree to whicha particular genotype is expressed in the phenotype. For instance, some leaves of limabeans show partial chlorophyll content, while others may show only at the margins,still others develop it only at the tip of the leaves, thus exhibiting variable expressivityfor this trait. Therefore, a gene may have variable penetrance and variableexpressivity.

Extrachromosomal inheritance: Inheritance that is not controlled bychromosomal determinants but by cytoplasmic components.

Extranuclear Genes. Genes located outside the cell nucleus, that is, on cytoplasmicorganelles (mitochondria, chloroplast, etc). Inheritance of such genes is calledextranuclear inheritance. The inheritance pattern is quite different from those of thenuclear genes (Mendelian genes). Reciprocal differences (as observed for sex-linkedgenes and genes conditioning sporophytic incompatibility) are encountered in theextranuclear inheritance. Interactions among loci of nuclear and the chloroplastgenomes have been reported in various wild species. Therefore, intergenomicinteractions should also be considered as the rational approach while conductingbreeding operations.

Extranuclear Mutation. A heritable change occurring in the extranuclear genes. It isalso referred to as cytoplasmic mutation because it is carried in the cytoplasmicorganelles like chloroplast and mitochondria.

Extranuclear. Of structures or processes, which are located outside the nucleus incontrast to intranuclear structures or processes.

Eye Ball Index. The visual judgement of plant breeders based on their experience andknowledge of plant traits. This constitutes the art of plant breeding. It is used forevaluation and selection of plants, plant progenies, or even families in earlysegregating generations (F2/F3/F4).

ezRAD-SeqA simplified RAD-Seq technique; it uses the standard Illumina TruSeq library preparation kits and sequencing by the NGS technology. Complexity is reduced by size selection (400–500 bp).