F2. The second filial
generation obtained by self-fertilization or crossings inter se of
F1individuals.
F3. The third filial
generation progeny obtained by self-fertilizing F2 individuals.
Facilitated recurrent selection: A type of recurrent selection in which
geneticmale sterility is maintained in the population to maintain
heterozygosity andgenetic diversity and to permit the recombination and
shifting of gene frequencies
Factor. A genetic determinant
of a character. It is synonymously used for gene byclassical geneticists; same
as gene.
Factored spectrally transformed linear mixed modelIt reduces
computation time by using a low-rank relatedness matrix based on a few thousand
SNPs in place of all the SNPs used for AM.
Factorial Experiment. An experiment
in which the treatments consist of all possiblecombinations of given levels of
two or more factors. The term complete factorialexperiment is sometimes
used when the treatments include all possible combinationsof the selected
levels of the variable factors. In contrast, the term incomplete factorialexperiment
is used when only a fraction of all the combinations is tested. Note thatthe
term factorial describes a specific way in which the treatments are
formed anddoes not, in any way, refer to the experimental design used. For
instance, if a factorialexperiment is performed in a randomized complete block
design, then the correctdescription would be ‘a factorial experiment in a
randomized complete block design’.A factorial experiment provides valuable
information on interaction, and is moreinformative than a single factor
experiment. However, practical considerations likelarge size, complexity and
cost limit the use of factorial experiments.
Factorial. Multiplication
of the number by all integers down to 1. It is designated by thesymbol ‘!’. For
example, 5! = 5.4.3.2.1 = 120. It should be noted that 0! (zerofactorial)
equals 1, and any number raised to the zero power also equals 1 [e.g., (½)0 =1].
Facultative heterochromatin: Heterochromatin that is present in
only one of apair of homologues or not permanently present
False discovery rateThe expected
ratio of the wrongly rejected null hypotheses to the total number of H0
rejected in the experiment multiplied by the probability of making at least one
rejection of H0.
Familial Trait. A trait shared
by members of a family for whatever reasons (notnecessarily the genetic ones).
It should be carefully differentiated from a heritable traitfor which similarity
arises from shared genotypes.
Familial trait: Any trait that is more common in
relatives of an affectedindividual than in the general population; could be due
to genetic and/orenvironmental causes
Family mappingLinkage mapping
using populations created by crossing usually two homozygous lines.
Family Selection. A breeding
technique of selecting a pair on the basis of the averageperformance of their
progeny.
Family. A group of individuals
directly related by descent from a common ancestor.83
Family-Line Breeding. Also called mother-line
breeding; a method of breeding utilizedto develop Cercospora resistant
varieties in sugar beet. It is similar to half-sibselection procedure or
an ear-to-row method of breeding corn. In this method,superior mother
beets are identified from progeny performance. Remnants seeds frommother beets
with superior progeny performance may be bulked to begin a seedincrease.
Alternatively, roots from superior progenies may be harvested and bulked
tostart a seed increase. The seed increase may be utilized as a new variety or
it may beused as the source population to start the next selection cycle.
Farmer selection (syn participatory
plant breeding): An aspect of some
plantbreeding programs in which the farmers make the final selection of
cultivar; eachfarmer is given a different group of new clones or pure lines of
a crop, emergingfrom a breeding program
Farmer’s privilege: A clause in the plant breeder’s rights
legislation of mostcountries that permits a farmer to use some of their own
crop of a registeredcultivar for seed on their own farm
Farmer’s privilegeFarmers can save
a portion of their harvest of a protected variety and use it as seed for
planting their next crop, but they can neither sell nor exchange this produce.
Farmer’s rights: The recognition of farmers (past,
present, and future) as insitu agricultural innovators who collectively
conserve and develop agriculturalgenetic resources around the world; as such,
farmers are recognised as innovatorsentitled to intellectual integrity and to
compensation whenever their innovationsare commercialised
Farmers’ Right. A legal right
that entitles farmers to save, use, sow, resow, exchange,share or sell their
farm produce including seed of a variety protected under IPRs.However, farmers
are not entitled to sell branded seed of the variety protected underthe law.
Farmers’ exemption in terms of farmers’ right has been done owing to thepast,
present and future contributions of farmers in conserving, improving and
makingavailable plant genetic resources (PGRs), particularly those in the
centres oforigin/diversity. FAO Commission recognized PBRs and Farmers’ rights
in 1989 tosupport developing countries to build their capabilities and required
infrastructuresespecially gene banks for conserving available genetic
resources.
Fatty Acids. Organic acids
having large hydrocarbon chains with the general formulaCH3-(CH2)n-COOH. Fatty
acids have always an even number of carbons because theyare synthesized by
joining two-carbon acetyl units, e.g., palmitic acid (16 carbons),stearic acid
(18 carbons). Sometimes, hydrocarbons have double bonds (-C=C-), andin such
cases, the fatty acid is said to be unsaturated (e.g., oleic acid).
Unsaturatedfatty acids are desirable because the double bonds present in them
increase theflexibility of the hydrocarbon chain, and thereby fluidity of
biological membranes.
Fatuoid. A mutant commonly
occurring in cultivated oats, and which resembles wild oats(Avena fatua).84
FeatureIn case of SFP, the 25 nt long oligonucleotides
used to construct the microarrays.
Fecundity. The
reproductive potential as measured by the quantity of gametes,particularly eggs
produced. In higher plants, this potential may be measured in termsof number of
pods/plant, seeds/pod, seeds/plant, etc. Also see fertility.
Feedback Inhibition. The inhibition
of an initial enzyme in a biosynthetic pathway bythe end product of that
pathway. This is a control mechanism in which the endproduct of a metabolic
pathway acts as an inhibitor of the first enzyme of themetabolic chain. Thus,
when enough product is synthesized, the entire chain can beshut off, and
useless accumulation of metabolites is avoided.
Feedback. A system in
which a deviation from a certain value induces control factors,which counteract
(negative feedback) or increase (positive feedback) the deviation.
Female Sterility. A situation of
occurrence of non-functional female gametes in plants(as in cassava). It is
less commonly encountered in nature compared to male sterilityprobably owing to
the nurturing effects of cytoplasm.
Fertile Crescent. Also called Levant;
areas comprising Jordan, Israel, Lebanon, Syria,Turkey, Iraq and Iran. It is so
called because most of the important cultivated speciesoriginated in these
regions.
Fertilisation: The union of two gametes to produce a
zygote that occurs duringsexual reproduction
Fertility. Ability to
produce biologically fit offspring.
Fertility-Restoring Genes. Nuclear genes
that act to restore fertility in plants with malesterilecytoplasm.
Fertilization. The fusion of
nuclei of male and female gametes.
FF1. The first generation
of a cross between genetically unrelated parents. It is also calledfirst
filial generation.
Field resistance: Synonymous with general resistance; it
is under polygeniccontrol (i.e. controlled by many genes with minor individual
effects); in general, field resistance is longer lasting than race-specific
resistance; field resistance slowsdown the rate at which disease increases in
the field
Field trial: A test of a new technique or variety,
including biotech-derivedvarieties, done outside the laboratory but with
specific requirements on location, plot size, methodology, etc.
Filial Generation. Any generation
following the parental one (P). The progenygeneration from a cross between two
contrasting parents is called first filialgeneration, and is designated
by F1. The selfing or intercrossing of F1 individualsleads to the F2, or second
filial generation. Progeny of F2 individuals derived throughselfing makes
the F3, or third filial generation. Method of propagation is
normallyspecified in the description of filial generation.
Fine mappingAnalysis of very large
populations using a sufficiently large number of markers to identify markers
located very close to a gene known to be linked to a marker. Syn.,
high-resolution mapping.
Fingerprint. The
characteristic spot pattern produced by electrophoresis of thepolypeptide
fragments obtained through denaturation of a particular protein with
aproteolytic enzyme.
First division restitution (FDR): Results from an abnormal orientation
of thespindles right before meiotic anaphase II; non-sister chromatids end up
in thesame nucleolus; it was found in several crop species, such as potato,
rye, etc.
First Division. The first of
the two meiotic divisions. Also called reductional division.
First-generation DNA sequencingSequencing
methods based on in vivo cloning and chemical or enzymatic sequencing
procedures.
FIS. International Seed
Trade Federation. It was formed
in 1924 with well definedobjectives such as: (a) to formulate and deliberate
opinion of all concerned in the seedtrade, (b) to carry out continued action
for the improvement of seed trade conditionsbetween various countries, and to
find solutions to problem that affects internationalseed trade, and (c) to
facilitate settlement of international disputes in seed trade. Infact, FIS is
the prime international organization of the seedsmen of the world. India isalso
a full member of FIS since 1968.
FISH (fluorescence in situ hybridisation):
A physical
mapping approachthat uses fluorescein tags to detect hybridization of probes
with metaphasechromosomes and with the less-condensed somatic interphase
chromatin.
FISH. Fluorescence In Situ Hybridisation. It is in situ hybridisation using a probecoupled to a
fluorescent molecule. This is a technique to characterize ‘alien’
genes(introduced) in our crop plants. It can also be used in the study of
nuclear architectureand chromatin packaging, and the fundamental principles of
biology such as DNAreplication, RNA processing, gene amplification, gene
integration and chromatinelimination.
Fisher’s Theorem. A theorem
pertaining to natural selection. “The greater the geneticvariability upon
which selection for fitness may act, the greater will be the
expectedimprovement in fitness”. In mathematical terms, increase in fitness
of a populationshould be proportional to the genetic variability or genetic
differences in fitnesspresent in the population.
Fitness. The relative
probability of survival and rate of reproduction of a phenotype orgenotype. It
is therefore the ability of alleles, multigenic combinations of
alleles,individuals, or populations to survive and transmit their genotype to
followinggenerations. A population is said to have maximum fitness if its
members haveoptimum phenotypes for most ‘fitness’ traits. Although we
loosely speak of fitness ofan individual, the concept really applies to classes
of individuals, and is statementabout the average survival and reproduction of
the individuals in that class. It isdistinct from physical fitness, which may
be related to the survival. But a bettersurviving individual cannot be called
fit, if it is sterile. Fitness is a consequence of therelation between the
phenotype of the organism and the environment in which it lives,so the same
genotype will have different fitnesses in different environments. No86genotype
is unconditionally superior to all others in all environments. Fitness of
apopulation derived from an F1 between two or more parents is often low in
earlygenerations (F2 to F6) owing to the production of many unbalanced
genotypes.Elimination of inferior genotypes, however, leads to rapid
improvement in meanfitness. Thus gain in fitness (adaptedness) is achieved
through loss in adaptability ashomozygosity increases (or heterozygosity
decreases). At later stage (after F6),genotypes that cooperate in giving the
population a coordinated and cohesivestructure will remain in the population.
Such genotypes although slightly differentgenetically may be uniform for
characteristics such as height, flowering time, maturityperiod, etc. Also
called Darwinian fitness or biological fitness.
Fitness: The relative ability of a plant to
survive and transmit its genes to thenext generation
Fixed Allele. An allele for
which all members of the population under study arehomozygous, so that no other
alleles for this locus exist in the population.
Fixity of Species (Linnaeus 1707-1798). Organisms of one species giving rise toorganisms of the same type.
Flag Leaf. The last leaf
of a cereal plant. It is also referred to as boenting leaf in sugarcane.
Flanking markersOne marker
located on either side of the target gene/QTL.
Flat-file database The earliest
and the simplest database type suitable for storing small amounts of data.
Flexibility. The ability of
an individual, genotype or population to vary and adapt tochanging conditions
so as to survive. It stems from the cryptic or potential variability.Owing to
such variability, an individual may remain functional in a whole series
ofvariable environmental conditions. This phenotypic flexibility is also
referred to asplasticity by plant physiologists. It is of two types: (a)
developmental, and (b)behavioural. The former is the ability of an individual
to adapt reversibly to localcondition. However, the latter refers to faculty of
an individual to adapt itselfreversibly to local or time associated factors.
For a mobile individual, it is the abilityto seek out that environment to which
it is best adapted.
Floret. A small flower from an
inflorescence (as in a grass panicle).
Flow cytometry: Analysis of biological material by
detection of the light absorbingor fluorescing properties of cells or
subcellular fractions (i.e., chromosomes) passing in a narrow stream through a
laser beam. An absorbance orfluorescence profile of the sample is produced.
Automated sorting devices, used tofractionate samples, sort successive droplets
of the analysed stream into differentfractions depending on the fluorescence
emitted by each droplet.
Flow karyotyping: Use of flow cytometry to analyse
and/or separatechromosomes on the basis of their DNA content.
Fluctuation Test. A test used in
microbes to establish the random nature of mutation orto measure mutation
rates.Fluff. True botanical seeds of sugar cane. Seeds also contain long
silken hairs present atthe base of the spikelets; the term, fuzz also
applies to seeds of sugar cane.
FluorescenceA molecule absorbs light of a
given wavelength and emits light of a longer wavelength.
FluorometerMonitoring the level of
fluorescence following illumination with light of the appropriate wavelength.
FluorophoreA molecule that generates
fluorescence.
Footprinting: A method used to determine the length
of nucleotide chains thatare close to a protein (which bind to DNA); for
example, certain types of drugs actby binding tightly to certain DNA molecules
in specific locations
Foreground selectionMarker-assisted
selection for the target gene/QTL.
Foreign DNA. DNA from
another organism.
Foreign DNA: DNA that is not found in the normal
genome concerned; usuallyit is directly or indirectly introduced into a
recipient cell by several experimentalmeans
Formylmethionine (fMet). A specialized amino acid that is the very first oneincorporated into the
polypeptide chain in the synthesis of proteins.
Forward Mutation. A mutation
that converts a wild-type allele into a mutant allele. Theterm is
purely descriptive.
Forward mutation: A mutation that alters (usually
inactivates) a wild-typeallele of a gene
Forward phenomicsUse of
high-throughput methods for screening germplasm collections for valuable
traits.
Forward selection: Choosing good individuals out of a
progeny test for possibleuse in seed orchards and/or subsequent generations of
breeding
Fossil. A remanent or an
impression of an organism preserved from a past geologic age.
Foundation Seed. Seed stock
produced from the breeder seed by or under the directcontrol of an agricultural
experiment station. It is the source of certified seed.
Foundation seed: Seed stocks increased from breeder
seed, i.e. the progenyof breeder, select, or foundation seed; handled as to
closely maintain the geneticidentity and purity of the variety; it is a sort of
certified seed, either directly orthrough registered seed
Founder Effect. An acute
genetic drift that occurs when a small group breaks off from alarger population
to found a new colony. This drifts results from a single generationof sampling,
followed by several generations during which the population remainssmall (with
no alteration from mutation and migration). Founder effect may beresponsible
for absence of an allele in such a population.
Founder effect: Genetic drift due to the founding of a
population by a smallnumber of individuals
Founder parentsIn case of NAM,
several individuals/lines that are crossed with each of one to few nested
parents.
Founder population: The first generation of a breeding
population, e.g., inforest tree breeding often the initial plus trees; this is
usually the starting point ofcalculations
Founder populationThe group of
individuals that initiated the population under consideration.
Fragile Site: A site on a chromosome vulnerable to
mutation to breakage.
Frame shift mutation: A mutation that is caused by a shift
of the reading frameof the mRNA (usually by the insertion of a nucleotide)
synthesized from thealtered DNA template
Frame-shift Mutation. The insertion
or deletion of a nucleotide pair/pairs, causing adisruption of the
translational reading frame.
Framework mapA map constructed using a large
mapping population for precisely mapping a set of framework markers selected on
the basis of their even distribution throughout the genome.
Freeze Preservation. Conditioning
and preservation of plant cells, tissues, or organs atextremely low
temperatures, usually in liquid nitrogen.
Freezing Injury. The damage to
plants caused by formation of ice-crystals within planttissues. Crops such as
red gram, field peas, etc encounter freezing injury during winterseason. Genetic
differences for resistance/tolerance to this injury have been noted inthese
crops. (Also see winter injury).
Frego-Bract. A bract type
mutant in cotton in which the bracts curl outward, exposingflower buds and
bolls.
Frequency Dependent Fitness. Fitness differences whose intensity change with changesin the relative
frequency of genotypes in the population.
Frequency Dependent Selection. Selection that depends on frequency-dependent fitness.
Frequency distribution: A specification of the way in which the
frequencies of members of a population are distributed according to the values
they exhibit
Frequency Histogram. A graph
representing the frequencies of various arbitrarilybounded classes.
Frequency Independent Fitness. Fitness that is not dependent on interactions with otherindividuals of
the same species.
Frequency Independent Selection. Selection in which the fitnesses of genotypes areindependent of their
relative frequency in the population.
Frequency-dependent selection: Selection where the fitness of a type
varieswith its frequency (i.e. whereby a genotype is at an advantage when rare
and ata disadvantage when common) from application of pollen produced on the
sameplant
Fruiting Body. In fungi, the
organ in which meiosis takes place and sexual spores areproduced.
F-Test. Also called Fisher’s
test after the name of a great statistician Ronald A. Fisher. Itis a
statistical test to indicate whether differences in mean performance of a
number oftreatments are significant. However, it does not identify the specific
pair or groups oftreatments that differed. To answer the question, one has to
apply another statisticcalled critical difference (least significant
difference). From the standpoint ofcomparison of mean performance of
treatments, it is considered more powerful than tor z tests. It
has wider application in that it also provides an overall test of
severaldifferences whereas the t-test provides a test of single difference.
Function. Any
relationship between one variable entity and another.
Functional AMThe phenotype of a dynamic trait
may be measured at several different time points during the development and
used for AM either independently or jointly to enable the identification of
different genes/QTLs that are expressed at specific developmental stages of
such traits.
Functional Complementation. The use of a cloned fragment of wild-type DNA totransform a mutant into wild
type. It is also used in identifying a clone containing onespecific gene.
Functional genomics The study of
gene expression patterns and the functioning of metabolic pathways.
Functional Genomics. Studying
pattern of gene expression and interaction in the genomeas a whole.
Functional genomics: The field of study that attempts
todetermine the function of all genes (and gene products), largely based on
knowing the entire DNA sequence of anorganism.
Functional genomics: The science of how the genes in
organisms interact toexpress complex traits - that is, the field of research
that aims to determine thefunction of newly discovered genes; attempts to
convert the molecular informationrepresented by DNA into an understanding of
gene functions and effects;functional genomics also entails research on the
protein function (proteomics) or,even more broadly, the whole metabolism (metabolics)
of an organism
Functional mapA special
category of linkage maps depicts locations of different genes of the given
species prepared by using gene-based markers, or the gene sequences themselves
are used as markers.
Functional markersMarkers derived from
such polymorphic sites within genes that have a causal relationship with
specific phenotypes of the concerned trait.
Functional proteomicsAnalysis of the
characteristics of molecular protein networks involved in a living cell.
Functional Resistance. Also called pseudo-resistance.
It results from some temporaryshifts in the environmental conditions favourable
to an otherwise susceptible hostplant. This mechanism is not necessary based on
heritable traits. These mechanismsare (a) host evasion, (B) induced resistance,
and (c) escape.
Fusion Nucleus. The product of
fusion of polar nuclei in the embryo sac of higher plants.The fusion nucleus
can be called the parent of the endosperm.
Fuzz. The dried florets with
pappus hair and seeds (as in sugar cane). In cotton, theremaining fibre (after
ginning) along with seed is called fuzz.
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