Terminologies in Genetics and Plant Breeding Part -9

 

Japonica Rice. The temperate ecotypes of rice, characterized by more leaves, fewertillers, relatively shattering resistance, and having broad and short grains with loweramylose content.

Javanica Rice. An intermediate (between indica and japonica types) type of rice selectedfrom tropical varieties in Indonesia. This type is characteristically tall, thick culmed,low tillering, resistant to shattering, and have broad stiff leaves, long awns and largebold grains. Also called bulu rice, it is of recent origin.

Karyogamy. The fusion of nuclei of male and female gametes. It is the ultimate event(culmination) of fertilization. The result of the karyogamy is the zygote.

Karyokinesis. The division of nucleus; the nuclear division (mitosis).

Karyolymph. The karyoplasm; nucleoplsm.

Karyotype. The whole group of characteristics that allow identification of a particularchromosome set, for example, the number, relative size, position of centromere,length of the arms, secondary constrictions, satellite, and the like. It is characteristicof an individual, species, genera, or a larger group.

Kilobase. 1000 nucleotide pairs.

Kinetochore. A complex of proteins to which a nuclear spindle fibre attaches. Cellbiologists use the term more frequently instead of centromere, which is synonymousto kinetochore.

Klinefelter Syndrome. An abnormal human male phenotype due to an extra Xchromosome (XXY).

Knobs. The darkly stained heterochromatic regions present in normal maizechromosomes. These are repeated sequences of nucleotides. The number of knobsvaries from variety to variety, and from plant to plant. Some have reported that theirstandard number may be 23. They are not randomly distributed; rather they occupyfixed positions on different chromosomes. Most of the knobs are intercalary.Terminal knobs are rare. They have been used as markers to establish phylogeneticrelationship between maize and its wild relatives.

Knockout. Inactivation of one specific gene; same as gene disruption.

Krebs Cycle. A common pathway for degradation of “fuel” molecules such ascarbohydrates, fatty acids, and amino acids. Also called tricaboxylic acid cycle orcitric acid cycle, it takes place in mitochondrial matrix. The fuel molecules are actedupon metabolically (in the cytoplasm through the process of glycolysis) to produceacetyl groups, which are taken into the Krebs cycle by acetyl coenzyme. It takes two130turns of the cycle to metabolise the two acetate molecules that are produced byglycolysis from one molecule of glucose.

Kurtosis. The excess or deficiency of frequencies in the centre and the two extremescompared to the flanks of a frequency curve. Higher kurtosis enhances value ofselection intensity; the reverse is true for low kurtic traits compared to normaldistribution. (Also see skewness).

Laggards. Chromosomes or pairing configurations that show slow movement or nomovement at all during nuclear division (anaphase). Such chromosomes may not beincluded in one of the daughter nuclei giving rise to aneuploidy.

Lagging Strand. The strand of the DNA double helix that is synthesized by the ligationof short fragments synthesized individually in the 5􀆍 to 3􀆍 direction during DNAreplication.

Lamarckism. An invalid concept of organic evolution, advocated by Lamarck. It statesthat adaptive changes induced by the environment within an individual is transmittedto its progeny. Also see inheritance of acquired characters.

Land Race. A line/strain/group of individuals evolved directly under influence of naturalselection; the earliest cultivated types; the old-established local stocks of a cropspecies; any distinctive race of a cultivated species that has become geneticallydifferentiated as a result of natural and/or human selection operating in ecologicallydifferent circumstances in various regions to which cultivated species have beenintroduced; a heterogeneous mixture of genotypes having mutually beneficialassociations with each other and with environmental conditions. One of the mostimportant uses of such land race is to provide genetic resources for improvement ofour present-day varieties. They are usually tolerant to any pests or diseases probablybecause they have had co-evolved at a given point of time. A series of local land racesis collectively called square heads.

Lateral Inhibition. The signal produced by one cell that prevents adjacent cells fromacquiring its fate.

Latin Square Design. An experimental design known for its capacity to handlesimultaneously two known sources of variation among experimental units. It makes it131possible to estimate variation among row-blocks as well as among column-blocks andto remove them from experimental error. However, this is possible only when thenumber of treatments is equal to the number of blocks (replication), and thus iscompletely a square. This enables the treatments to individually appear in each rowblockand in each column-block. This design becomes impractical if the number oftreatments increases. On the other hand, if the treatment number is small, the degreeof freedom associated with the experimental error becomes too small for the error tobe estimated reliably. This design is used for field trials in which the experimentalarea has two fertility gradients running perpendicular to each other or has aunidirectional fertility gradient but also has some residual effects from the previoustrials.

Law of Homologous Series in Variation. Characters found in one plant species mayalso be expected in similar species. Characters occurring in one collections made inone place may abound in those from other places within the species. Vavilov (1951)expressed this concept in genetic terms and used this principle as a clue to charactersremaining to be discovered. Also called law of parallel variation.

Law of independent Assortment. Mendel’s second law. During gametogenesis, thesegregation of one gene pair is independent of other gene pairs (or the inheritance ofone character is independent of the others). Notice that the phenomenon of genelinkage is an important exception to this law.

Law of Minimum (Liebig 1840). A law stating that the growth of a plant is proportionalto the foodstuff, which is available in minimum quantity; also called the law oflimiting factor. The two key points for its practicability are: steady-state conditionsand factor interaction. Steady state implies a balance between inflow and outflow ofenergy and materials. Factor interaction includes involvement of other condition withthe essential element. For instance, some plants have been shown to require less zincwhen growing in the shade than when growing in full sunlight; therefore, a lowconcentration of zinc in the soil would less likely be limiting to plants in the shadethan under the same conditions in sunlight.

Law of Segregation. The first law of Mendel. It states that the two dissimilar alleles of agene pair separate from each other during gametogenesis and distributed equally andrandomly into gametes. The law is true in all those organisms which utilize meiosis atleast in some part of its life cycle. It does not hold true if there is non-disjunctionduring meiosis.

LD50. The dose of a mutagen at which 50% of the mutagenized individuals die (beforereproduction). It is used as an important parameter for effectively inducing mutation.It varies with genotypes, plant species, and the like.

Leader Sequence. The sequence at the 5􀆍 end of an mRNA that is not translated intoprotein.

Leading Strand. The strand of the DNA double helix that is synthesized continuously inthe 5􀆍 to 3􀆍 direction during DNA replication.

Leaky Mutation. A mutation that still retains a low but detectable wild-type functionbesides displaying mutant phenotype.

Lesion. A damaged area in a gene (a mutant site), a chromosome or a protein.

Lethal. Of a gene (genotype) which, when expressed, is fatal to its carrier.

Lethal Gene. A gene whose expression results in the death of the carrier individual.

Leucoplast. A plastid containing no visible pigments. It is found in embryonic, germ,and fully differentiated cells. Leucoplasts are also found in meristematic cells and inthose regions of the plant not receiving light. Leucoplasts in certain differentiatedzones of the root produce starch granules, called amyloplasts. They do not havethylakoids and ribosomes.

Level of Significance. Also called confidence limit; the frequency at which chance errorsin performance are allowed to occur beyond which any variation is supposed to bereal one and hence significant. In other words, the probability chosen for deciding adeviation to be significant (or non-significant) is called level of significance.Conventionally, 1% or 5% (or in some genetical experiment, even 50%) error isallowed. Thus, 99% or 95% is the confidence limits, respectively. In other words, wecan assert with confidence that in 99% or 95% cases, variation observed amongtreatments is real (genetic) and not due to chance error. In all biological experiments,133the level of significance is arbitrarily chosen at 5%. It means a chance deviation isconsidered real one once in 20 times on an average. If we choose a more stringentprobability level, i.e., 1%, it implies a deviation arising from chance would beinterpreted as a real one once in 100 times. However, this level may let us miss somegood types when non-significant results are found. The less easily we reject ahypothesis, greater is the chance that what we have accepted as valid may be false andvice-versa. Thus as a compromise between the two extremes, a commonly acceptedlevel of significance for testing hypothesis is 5%.

Life Cycle. All the significant events that lead a particular life form to beget of its ownkind. It is species-specific and controlled by a particular genetic system. In higherplants, it involves a regular alternation of generations.

Ligase. An enzyme that can rejoin a broken phosphodiester bond in a nucleic acid.

Limits of Tolerance (Shelford 1913). A range in between ecological minimum andmaximum of organisms. It led to the birth of toleration ecology; and thus limits withinwhich various plants and animals can exist are known.

Line Breeding. The mating, usually in successive generations, of individuals having aknown common ancestor. It is also a system of breeding in which a group of progenylines is composited on the basis of desired traits. Since pollination is not controlled, itremains essentially a form of random mating with selection, and thus geneticcomposition of the population is subject to a very slow change for a quantitative traiteven when there is adequate genetic variability.

Lineage. A group of individuals descended from a common ancestor; descendants of anancestor.

Line x Tester Analysis (Kempthorne 1957). An extension of top-cross method. Itinvolves crossing a number of lines, each with the same set of testers and growing theresulting crosses in a suitably laid-out experimental design to provide for informationabout various genetic parameters such as general and specific combining ability, geneeffects, and the like. The number of tester must be greater than one (contrast it withtop cross method that involves crossing with a single broad-based tester).134Line. A group of individuals/plants with similar appearance and breeding behaviour. Thegroup is pure-breeding (or nearly so) and may be diploid or polyploid, and can bedistinguished from any other such group of the same species by some uniquephenotype and genotype. It is a more narrowly defined group than a strain or a variety.

Linkage Disequilibrium. A state of population in which there is a difference betweenrepulsion and coupling phase gametes, that is, (Ab) x (aB) – (AB) x (ab) 􀂏 0.However, under the condition of random mating, the difference (± d) is reduced toone-half each generation so that after 4-5 generations, only 10% or even less of thedisequilibrium value remains in the population.

Linkage Drag. The transfer of undesirable genes along with useful gene(s) because oftheir close association on the whole (or a segment of) chromosome. The problem oflinkage drag is often encountered in wide/distant hybrids, which largely restricts itsapplication in crop improvement.

Linkage Equilibrium. A state of population in which the difference between repulsionand coupling phase gametes is zero, that is, (Ab) x (aB) – (AB) x (ab) = 0. Consider apopulation in which frequencies of both A & B are 0.6 each and of both a & b are 0.4each, then (0.6 x 0.4) (0.4 x 0.6) – (0.6 x 0.6) (0.4 x 0.4) = 0 (that is, population is inequilibrium). This state of population will conserve the existing proportion ofgenotype frequency generation after generation of random mating in absence of otherdisturbing forces.

Linkage Group. A group of genes known to be linked. As linkage occurs in twoconformations (either in coupling or in repulsion phase), the number of linkage groupalways equals the haploid number of chromosomes of the given species.

Linkage Map. A map showing position of genes on chromosomes as determined byrecombination relationships.

Linkage Value. Recombination fraction expressing the proportion of crossovers versusparental types in a progeny; also called the recombination value. It varies from zero toone half. The reason for this upper limit is that at a time only two out of four (½ =50%) chromatids are involved in a crossing over.

Linkage. A situation of coexistence of two or more genes on the same chromosomeowing to their proximity to each other. If the genes are contiguous, there is a completelinkage that is a rare phenomenon. On the other hand, there is frequent occurrence ofpartial or incomplete linkage, which is often broken down by crossing over. Its maineffect relates to an increase of in the proportion of parental gametes and acorresponding diminution in recombinant gametes, eventually leading to deviationfrom Mendelian expectancy. If linked traits are desirable, it is an aid to plant breeders;if however, desirable characters are negatively correlated, then undesirable linkageneeds to be broken. For example, gene for rust resistance in wheat is closely linked tothat for late maturity, which can be broken. However, such opportunity is precluded inthe case of pleiotropy.

Linked. Of two genes showing a recombination value of less than 0.5. Linked genes tendto be transmitted together.

Lint. Long fibres of cotton separated from the seed after ginning.

Linters. The short fibres of cotton that generally remain attached to the seed in ginning;also called fuzz.

Lipids. A large group of different compounds characterized by their relative insolubilityin water and solubility in organic solvents. There are simple lipids (alcohol esters offatty acids), steroids (cholesterol), and conjugated lipids (glycolipids). Phospholipidsare the main components of biological membranes. They have a hydrophilic(phosphate containing region) and two hydrophobic (fatty acid) tails.

LMOs. Living Modified Organisms; see transgenics.

Local Control. The principle of reducing experimental error. The principle comprisesrandomisation and replication.Locus. The position occupied by a gene on a chromosome.

Lodging. The bending or breaking-over of a plant before harvest. It causes yield losses insmall grain crops, soybeans, cereals, and other crops. Unlike measurement of yield,the evaluation of lodging resistance is almost entirely a visual appraisal. Genotypicdifferences for lodging resistance have been noted within several crop species.136Lodging resistance may be directly related to the strength of the main stem, number ofnodes, height of the plant, and other traits.

Lodicule. One of two scale-like structures at the base of the ovary in a grass flower.

Low Productivity Environment. A crop production environment characterized by harshand erratically unpredictable climatic conditions with the high risk of crop failure.Such environments are prone to large errors, less differentiation between genotypes,and less repeatability across years. Various components of such environments arehighly unpredictable and intractable. (Also see subsistence agriculture).

Ludwig Theorem. A theory which states that new genotypes can be added to apopulation if they are able to utilize new components of the environment, even ifthese are inferior to the ancestral niche. The phenomenon is also called annidation.

Luxuriance. An accidental condition produced by complementary gene action in the F1hybrid between species, and varieties or strains of both self- as well as crosspollinatedspecies. The excessive size and vigour is not connected in any way with theadaptive superiority of such hybrids compared to their parents.

Lysis. The rupture and death of a bacterial cell on the release of phage