P. A shorthand to designate parental
generations in crosses.
P1, P2, P3,……. First,
second, third, etc. generations from a parent; also used to designatedifferent
parents used in making a hybrid or series of hybrids. P1 also refers to
theimmediate parents of a first filial generation or F1.
Pachytene. The
four-strand stage of meiosis during which crossing over occurs
betweennon-sister chromatids of a pair of homologous chromosomes.
Paired-end sequencing: In NGS,
sequencing of both the ends of each DNA fragment.
Paleolithic Age. Cultural
period beginning with the earliest chipped stone tools(~750,000 years ago)
until the beginning of the Mesolithic Age, ca. 15,000 years ago.
Palindrome.Pangenesis Theory (Darwin, 1809-1882). An obsolete theory of evolution. According toit, pangenes (gemmules),
which are very small, exact, but invisible copy of each bodyorgan and
component, assemble in gametes and upon fertilization, they separate out
todifferent parts of the body during development to constitute a mixture of
maternal andpaternal organs and tissues. Although a disproved idea, however, it
suggested aphysical basis of heredity.
Palindrome: Adjacent inverted DNA repeats; the
identical base sequencesare on the opposite strands; long (>130 bp)
uninterrupted palindromes occur ineukaryotic DNA but are lethal in bacteria
Panmictic Index. A measure of
the relative amount of hetrozygosity that is reduced byinbreeding in a random
mating population of limited size. It is a complementaryparameter to inbreeding
index or coefficient. Mathematically, P = 1 – F; the initialvalue of this
parameter in a large population is taken as unity as F = 0 in such a case.The
loss of heterozygosity in a small sized population is equal to the factor
1/2N(where N = population size = number of diploid individuals).
Panmictic Population. A random
mating population.
Panmixia. Random mating
without restriction (usually extended to include randommating under the
restrictions of sex or incompatibility).
Panmixis: Random mating; a mode of sexual reproduction
in which male andfemale gametes encounter each other incidentally
Paracentric Inversion. An inversion
that excludes the centromere of the chromosome. Itdoes not change the
morphology of the chromosome. It is very difficult to detect, as itdoes not
change the arm ratio. There is selective recovery of parental type gametes
in170an inversion heterozygote for crossover types are always deletion products
for one ora few genes.
Paragenetic. Of chromosomal
changes that affect the expression but not the constitutionof the genes
concerned (position effect, for example). The term genetic is
concernedwith the constitution of any one of genes concerned).
Parallel mutation: A mutation
that causes similar phenotypes but in differentspecies or genotypes
Paralogous Genes. Two genes
within a species that have evolved by gene duplication.
Paralogous genes: Homologous genes that have arisen
through geneduplication and that have evolved in parallel with the same
organism; as opposedto orthologous genes
Paralogous genes: Two or more
genes present in the genome of the same species that originated from the same
ancestral gene and have the same function.
Parameter. A numerical
quantity that specifies a population in respect to somecharacteristics.
Parameter is to population, what a statistic is to sample.
Paramutable allele: An unstable allele where the
phenotypic consequences areenhanced by the
Paramutagenic allele: An allele possessing the ability to
cause paramutation
Paramutation. An epigenetic
phenomenon in plants wherein genetic activity of a normalallele (paramutable)
is heritably changed/ reduced in heterozygous condition by aspecial
“paramutagenic” allele. It was first noted in maize. The
paramutationalalterations persist, but show a tendency towards reversion to the
standard phenotypeover a number of generations. This may occur due to mutation
in the paramutagenicallele.
Paramutation: A mutation in which one allele in the
heterozygous conditionpermanently changes the partner allele
Parasexual. Of
reproductive systems that achieve genetic recombination by anymechanism other
than sexual one (meiosis). Parasexual cycle is observed in lowerplants such as
fungi.
Parasite. An organism
that lives upon or within another living organism at whoseexpense it obtains
some advantage without any compensation to the host.
Parasitic Epistasis (Sidhu, 1984). The effect of one parasite (pathogen) on thepathogenicity of another.
For instance, Sidhu and Webster (1979) have shown that anon-virulent strain of Fusarium
sp. blots out parasitic effect of Verticillium on tomatoplants known
to be separately resistant and susceptible to Fusarium and Verticillium,respectively.
Parasitism. A type of
interaction between two species in which one species (the parasite,which is
usually smaller) benefits at the cost of other (the host, usually larger).
Parental Generation. The generation
in which plants from two contrasting pure linesare crossed. It is usually
designated by the letter P.
Parental Imprinting. An epigenetic
phenomenon in which the activity of a gene isdependent upon whether it was
inherited from the father or the mother. Some genesare paternally imprinted,
others maternally.
Parent-offspring analysis: The linear regression of the
performance of offspringon that of the parents was proposed as a method of
estimating heritability
Parthenocarpy. The
development of fruits without seeds or without embryo in seeds. Itresults from
a failure of pollination, a failure in fertilization, or a failure in
embryodevelopment.
Parthenocarpy: Production of fruit without seeds, as
in bananas and somegrapes
Parthenogenesis. Development of
an organism from a sex cell, usually a female gamete,but without fertilization.
This occurs especially among some lower plants andanimals.
Parthenogenesis: The development of an individual from
an egg withoutfertilisation; it occurs in some plants
Partial Correlation Coefficient. A statistic that measures the association of twovariables after making
allowance for their association with the third one (as againsttotal correlation
coefficient). PCC between variables 1&2 = r12.3 = (r12 – r13 x
r23)/[(1-r213) (1-r223)]½. The variable whose influence is allowed for in the
calculation of PCCis spoken as the eliminated variable.
Partial correlation: Displays the numerical relationship
between a single Xiand Y in multiple correlation; in contrast to the simple
correlation, the partialcorrelation accounts for interaction between the Xi
variables and illustrates thetrue relationship between the Xi and Y
Partial Diallel (Kempthorne and Curnow 1961). A set of crosses resulting from crossinga given number of parents in
only restricted number of combinations (not in allpossible
combinations). In a normal diallel, each line is involved in n-1 crosses. Butin
partial diallel, only a random sample of crosses ‘s’ is made (where, s <
n-1).However, either s or n should be odd from analysis point of
view. Thus with n lines,the total number of crosses to be analysed in a
partial diallel is ns/2. Partial diallelanalysis provides information on
both general and specific combining ability;however, the precision of estimates
depends on the sample size s vis-à-vis n (total no.of lines).
Various workers have clearly shown that bias is more common when s <(n/2).
Partial Dominance. A condition in
which the heterozygote deviates from the midparentalvalue towards one of the
homozygotes [for example, AA (3), Aa (2.75), andaa (2)];
also called incomplete dominance.
Partial dominance: Incomplete dominance; the production
of an intermediatephenotype in individuals heterozygous for the gene concerned;
it is generallyconsidered to be a type of incomplete dominance, with the
heterozygote resemblingone homozygote more than the other
Partial self-incompatibility: Self-incompatibility in some species
results in alower percentage of seed set than occurs with cross-pollination
Partially balanced design: A design is partially balanced with
respect to anassociation scheme if the number of blocks containing two points
depends only onwhich class of the partition contains the given pair of points
Partially balanced incomplete block
design (PBIB): Refers
to an experimentaldesign where the residual variance of the difference between
the candidates mayadopt one out of only two different values
Participatory plant breeding: Approaches that involve close
collaborationbetween researchers and farmers, and potentially other
stakeholders, to bringabout plant genetic improvements within a species;
participatory plant breedingcovers the whole research and development cycle of
activities associated withplant genetic improvement, such as identifying
breeding objectives, generatinggenetic variability or diversity, selecting
within variable populations to developexperimental materials, evaluating these
materials, release of materials, diffusion,seed production, and distribution;
it also may include assessing existing policy orlegislative measures, or both,
and designing new ones where needed
Participatory variety selection: Selection of fixed lines (including
landraces) byfarmers in their target environments using their own selection
criteria; it consistsof four methodological steps: (a) situation analysis and
identification of farmer’svarietal needs, (b) search for suitable genetic
materials, (c) farmer’s experimentationwith new crop varieties in their own
fields and with their own crop-managementpractices, and (d) wider dissemination
of farmer-preferred crop varieties
Particulate Inheritance. An accepted
model of inheritance which states that the geneticinformation is transmitted
from one generation to the next in discrete units (particles)that maintain
their integrity in the resulting zygotes even after fusion of gametes(without
blending or mixing of units).
Particulate inheritance: The model proposing that genetic
information istransmitted from one generation to the next in discrete units
(particles) so that thecharacter of the offspring is not a smooth blend of
factors from the parents
Passive Resistance. The resistance
mechanisms which may already be present in the hostbefore the attack by any
kind of pathogens. For instance, resistance to a fungalpathogen may be
attributable to thick cuticle, thick hairs, wax, etc., which preventinfection
or impede sporulation of the fungus, or to a preformed antibiotic
compound(gossypol in adult cotton plants).
Patent. The legal right, which
provides protection to the interests of the experimenter.Indian patent act was
enacted for the first time by the British in 1859, which was laterrevised, and
modified Indian Patent Act came in force in 1971. It excluded patentingof inventions
like atomic energy, agriculture and horticulture. Under the act, onlyprocess
patent was granted for seven years. However, in 1994, the patent act wasagain
modified keeping in view of GATT agreement. It included agriculture
andhorticulture while safeguarding the interests of experimenters and farmers.
But itpermitted patents of products also.
Path Coefficient Analysis. An analysis of
direct and indirect effects of various causalfactors on the dependent variable
through diagrammatic representation. Pathcoefficient analysis is simply a
standardized partial regression coefficient that breaksthe correlation
coefficient into measures of direct and indirect effects. The effect of acausal
factor (e.g., seed weight, x1) on the dependent variable (e.g., yield) via thesecond
causal factor (x2) is called indirect effect of that factor. Thus
indirect effect ofx1 on y through x2 will be the product
of path coefficient of (x2) and rx1.x2. Pathcoefficient analysis also
includes effect of undefined variables (not included in thestudy) on the
dependent variable (yield, y); it is called residual effect,
which can becalculated by the formula: R = {1-Pi.
Path Coefficient. The ratio of
the standard deviation due to a given cause (on the effect)to the total
standard deviation of the effect. For example, if y is the effect and x1
is oneof the causes, the path coefficient for the path from the cause x1
to the effect y will be(x1y). This path coefficient due to a
particular cause is referred to as the directeffect of that cause on yield
(effect).
Path-coefficient analysis: A method for analysing regular and
irregularbreeding systems; the path coefficient is a measure of the importance
of a givenpath of influence from cause to effect; it is the ratio of the
standard deviation of theeffect to the total standard deviation
Pathogen. A parasite
that causes a disease in the host plants; an organism causingdisease in another
organism.
Pathogen: A simple organism which damages a crop
plant. The mostimportant crop pathogens are fungi, bacteria and viruses. Larger
pathogens, suchas nematodes, insects, rats, birds etc. are usually referred to
as pests rather thanas pathogens
Pathogen: A specific biological causative
agent of disease inplants or animals.
Pathogenesis. The chain of
events that lead to the development of a disease in the host.For example, at
first a pathogen (bacterium, for example) establishes contact with thehost.
Thereafter, it multiplies and grows into a mass at the cost of nutrients and
otherfood materials of the host. These proliferating mass also block
transporting tissues ofthe host and thence symptoms of disease appear on the
plants. This sequence ofevents, that is, from infection to appearance of
disease symptoms, is calledpathogenesis.
Pathogenicity. The ability of
a pathogen to cause a disease.
Patroclinous Inheritance. A type of
inheritance in which all offspring have the nucleusbasedphenotype of the
father.
Pattern of Evolution. Different
designs or models of evolution of plant species. Thesedifferent models are not
mutually exclusive, that is, two or more methods may beinterwoven in a slow and
gradual change eventually leading to formation of a newspecies.
PCR Cycle. The
Photosynthetic Carbon-Reduction Cycle; also called Calvin cycle. Inthis cycle,
the fixation of CO2 in form of hexose (carbohydrate) occurs in the stromaof
chloroplasts with the aid of several enzymes and energy provided by ATP
andNADPH (produced during light reaction).
PCR. Polymerase Chain Reaction. A method for amplifying specific DNA segmentsthat exploits certain
features of DNA replication.
PCR. Polymerase Chain Reaction. A technique to amplify a sample of DNA aided byprimers and Taq
polymerase (obtained from a bacterium called Thermus aquaticus)through
regulating temperature changes. Entire exercise is done in a machine calledPCR
machine. Taq polymerase can withstand the denaturing temperatures. More thanone
million and one billion copies of a given DNA sample can be produced in 20
and30 cycles, respectively. Some PCR machines can process 96 samples at a time.
PCRhas been used to create DNA fingerprints by amplifying microsatellite DNA.
PCRamplification can be done without restriction cutting. It gives the results
directly uponelectrophoresis. It is now a routine tool in the laboratory of
molecular geneticists whouse it to amplify rapidly DNA regions of interest for
research purposes.
PCR-based markers: Markers based on
DNA sequence polymorphisms detected by PCR amplification of sample DNAs. Often
called second-generation molecular markers.
PDR. Pathogen derived
resistance in plants.
Pedigree Breeding. A system of
breeding in which individual plants are selected in thesegregating generations
from a cross on the basis of their desirability judgedindividually and on the
basis of a pedigree record. It has been a widely used method inbreeding
self-pollinated crops.
Pedigree breeding: A system of breeding in which
individual plants are selectedin the segregating generations from a cross on
the basis of their desirability judgedindividually and on the basis of a
pedigree record; the advantages are (1) if selection is effective, inferior
genotypes may be discarded before lines are further evaluated;(2) selection in
generation involves a different environment, which provides goodgenetic
variability; and (3) the genetic relationship of lines is estimated and can
beused to maximise genetic variability
Pedigree. A record of
ancestry of an individual, family, or a strain. In pedigree methodof handling
segregating generations, it makes it possible for the elimination of allexcept
one member of the closely related families at the final stage. It is
usefulprimarily in avoiding selection of closely related lines whose probable
worth is nearlyidentical. However, it does not establish retraceable route that
can be followed indeveloping the same variety by repeating the same cross.
Pedigree: The record of the ancestry of an
individual, genetic line or variety
PEG. Polyethylene glycol. A
chemical that acts as fusogenic agent for the fusion ofprotoplasts. It is
non-specific in that it induces fusion between protoplasts of the sameas well
as of different species. The fused product is a somatic hybrid
(amphidiploid).
Penetrance. The frequency
with which an allele of a single locus or alleles of several lociare manifested
on the phenotype of the carriers. Its value ranges from zero to hundredper
cent. Suppose, a gene is expressed in 10 individuals out of 100. This implies a
10per cent penetrance of the gene in question. Thus penetrance is also defined
as theproportion of individuals with a particular genotype expressing a
phenotypeassociated with that specific genotype. Penetrance of a gene depends
upon theposition of other genes in the genome, the presence of modifiers and
the externalenvironment. Incomplete penetrance complicates the task of breeders
working withthe specific gene.
Penetrance: The proportion of individuals with a
specific genotype whomanifest that genotype at the phenotype level.
Peptide Bond. A bond joining
two amino acids.
Peptide. An amino acid.
Perfect Population Size. The minimum
size of a population that permits expression ofeach genotype expected in an F2
population from a cross differing at one, two, etc.loci. It is represented by
4n, where ‘n’ is the number of segregating loci in a hybrid.According to
Comstock and Robinson (1940), the number of individuals in an F2population for
a monogenic trait should be at least 40. However, according to Allard(1999), it
should be 12.
Pericentric Inversion. An inversion
that involves centromere of the chromosome. Itgreatly alters the morphology
(and hence, arm ratio) of the chromosome. The changedarm ratio facilitates its
easy detection. Like paracentric inversion, crossover types arenot recovered
but for a different reason. Recombinants are simultaneously duplicated(for one
part) and deleted (for the other) products. Thus there is selective recovery
ofparental types in an inversion heterozygote.
Pericentric inversion: The inversion of a chromosome segment
containing ablock of genes that involves the centromere
Periclinal chimera: A plant made up of two genetically
different tissues, onesurrounding the other
Permissive Conditions. Those
environmental conditions under which a conditionalmutant shows the wild-type
phenotype.
Pest-resistant crops: Plants with the ability to withstand,
deter or repel pestsand thereby prevent them from damaging the plants. Plant
pests may includeinsects, nematodes, fungi, viruses, bacteria, weeds, and
other.
Ph Gene (Pairing homoeologous gene). The gene(s) that suppresses homeologouspairing and thus ensures
homologous pairing in bread wheat. It results in diploid-likegenetics
for this basically hexaploid species. The gene is situated on the long arm of5B
chromosome. Two such genes are known: Ph1 and Ph2. However, Ph1
is thegenetic system that determines exclusive homologous pairing in modern
wheat.
ph Mutant (Wall et al. 1971). A mutant that carries a mutation in the Ph gene, and thuspermits
homeologous pairing. The level of pairing in this mutant, however, is not
ashigh as in the nullisomic for 5B. Intercalary deficiency for Ph1 is
designated ph1bmutant, which permits high level of homeologous pairing. The
terminal deficiency of3D is termed ph2a and is characterized by an
intermediate level of homeologouspairing. Further, ph1c mutant has been found
in durum wheat and is used inpromoting homeologous pairing in intergenomic
hybrids.
Ph.D. Doctor (docere:
a Latin word, which means to teach) of philosophy (philo +sophia;
the Greek words, which imply love and knowledge, respectively). Thus itdenotes
a person having love for knowledge and teaching.
Ph1 Suppressor. The species (T.
searsii) known to suppress the activity of Ph1 in hybridswith bread
wheat, resulting in high homoeologous pairing.
Phage: Short for bacteriophage; a virus for
which the natural host is a bacterialcell. Literally “bacteria eaters.”
Phasmid: A cloning vector that has the
capabilities to replicate as a plasmidor as a phage; the two modes of
replication are usually functional in differentbacterial species
Phenocopy. An
environmentally induced phenotype that resembles the phenotypeproduced by a
mutation. Of course, this effect is not inherited.
Phenome: The sum total of phenotypes at
various levels ranging from molecules to organs and the whole organism.
Phenotype. A description
of all aspects of individual’s morphology, physiology,behaviour, and its
ecological relationships. The phenotype, which is the observableproperties of
an organism, is brought about by its genotype in concert with theenvironment in
which the organism develops. The term has been derived from aGreek word that
literally means “ the form that is shown”. In practice, however, it isused in a
more restricted sense; that is, we say phenotype with respect to a
particulartrait. Contrary to genotype, it is a dynamic entity, which
changes with time.
Phenotype: A biological characteristic or trait
possessed by anorganism that results from the expression of a specific gene.
Phenotype: The visible appearance of an organism.
The phenotype reflects thecombined action of the genotype and the environment
where the individual exists
Phenotypic Assortative Mating. Mating between individuals which resemble eachother more closely
phenotypically than the rest members of the population. The finalresult of
phenotypic assortative mating amounts to that for genetic assortative matingso
long as heritability is complete (that is , 100 per cent). Under condition of
completeheritability, the rate of approach towards homozygosity gets slower
with the increasein the number of loci involved. When heritability is not
complete, 100 per centhomozygosity is not possible (‘F’ cannot reach unity).
Phenotypic Disassortative Mating. Mating between individuals having contrastingphenotypic traits. It tends
to maintain (or even slightly increase) heterozygosity,decrease the population
variance, and reduce correlation between relatives. It may be176used to
compensate for defects by choosing contrasting parents each of which
offsetweaknesses of the other.
Phenotypic segregation: The phenotypic differentiation
patterns of cells orindividuals in segregating populations; as opposed to
genetic segregation
Phenotypic selection: Development of a variety based on its
physical appearance without regard to its genetic constitution
Phenotypic selection: Selection based
on phenotypes of the target traits.
Phenotypic Sex Determination. Sex determination by nongenetic means.
Phenotypic Variance. The total
variance observed in a character.
Phenotypic variance: The total variance observed in a
character; it includesexperimental error, genotype × environment interaction,
and the genotypicvariance
Phenotyping: Evaluation of the individuals of
a mapping population for phenotypic expression of the target trait.
Philadelphia Chromosome. A
translocation between the long arms of chromosomes 9and 22, often found in the
white blood cells of patients with chronic myeloidleukaemia.
Phosphodiester Bond. A bond between
a sugar group and a phosphate group. Suchbonds form the sugar-phosphate
backbone of DNA.
Phosphorylation. The addition
of a phosphate group to ADP for producing ATP.
Photochemical quenching: The part of
light energy used for electron transport and carbon assimilation.
Photophosphorylation. ATP synthesis
by phosphorylation of ADP using the light energyin the chloroplasts of plants.
Phyletic Evolution. Gradual
transformation of one species into another withoutbranching.
Phylogenetic analysisGrouping the
various entities included in a study on the basis of their genetic
relationships indicating the degrees of genetic similarities–dissimilarities
among them.
Phylogenetic trees: A graphic or
textual representation of the evolutionary relationships among various entities
based on similarities and differences in their physical and genetic
characteristics.
Phylogeny. The
evolutionary history of an organism or a taxonomic group.
Physical distance: The distance in terms of base pairs.
Physical map: The genes/molecular markers are depicted in
the same order as they occur in the chromosomes, but the distances between
adjacent genes/markers are depicted in terms of base pairs.
Physical map: A map of the locations of
identifiable landmarkson DNA (e.g., restriction enzyme cutting sites, genes),
regardless of inheritance. Distance is measured inbase pairs.
Physical map: Map of the locations of identifiable
landmarks on DNA (eg: restriction enzyme cutting sites, genes) regardless of
inheritance; the distance ismeasured in base pairs
Physiological Drought. See drought.
Physiological Homeostasis. A type of
buffering reaction of the organism againstfluctuating environmental conditions
by internal self-regulatory systems that resistthose changes either by varying
phenotypically or by remaining constant in the face ofenvironmental changes. It
is frequently associated with heterozygosity of genotypes.
Physiological Races. Pathogens of
the same species with similar or identicalmorphology but differing pathogenic
capabilities.
Physiological Threshold. The limit
beyond which physiological functioning are affectedso adversely that
individuals can no longer survive and thus selection is powerless toeffect any
change even in the presence of substantial genetic variation in thepopulation.
Phytoalexins. The
biochemical substances (phenolic compounds) formed by the hostplant in response
to injury, physiological stimuli, infectious agents or their productsthat
accumulate to levels which inhibit the growth of microorganisms and repel
pestsand pathogens, e.g., DIMBOA in maize and onions, pisatin in
peas, phaseolins inbeans, rishtin and phytotuberin in
potatoes. These biochemical substances confersresistance on the concerned hosts
against respective pests or pathogens.
Phytoene Phytoene
desaturase (Bacterial gene, crt1) ß-carotene
desaturase (Bacterial gene, crt1)
Phytoplankton. Minute
floating plants, usually algae, distributed throughout the pond asdeep as light
penetrates.
Phytosanitary certificate: A certificate from a recognised plant
quarantineservice that indicates that a sample is substantially free from
diseases or pests
Phytotoxins. Chemical
compounds that kill plants. These compounds are produced bypathogens. The
resistant hosts in such cases are insensitive to toxins. For example, thecausal
organism of victoria blight in oat, Drecheslera victoriae,
produces a toxincalled ‘victorin’. Resistant varieties of oats are resistant to
this toxin.
Phytotron. A controlled
environment facility to assist plant scientists in conducting cropbreeding and
crop management studies without any constraint of seasons andlocations. This
unique facility has been created at IARI, New Delhi in 1997. It has anarea of
2500 m2, 22 growth chambers and 10 green houses where temperature,relative humidity,
CO2 levels, and light can be controlled to produce a wide range ofsimulated
conditions. Further, by manipulating these components, plants can be raisedup
to maturity whenever required. It is particularly suited to rain-fed and other
noncongenialproduction regimes inhabited mostly by resource-poor farmers. It
can178provide conditions to facilitate flowering of photosensitive and late
maturinggenotypes and thus provides rapid generation advancement. Conducive
conditions forscreening of genotypes against biotic and abiotic stresses can
also be created.
Pima Cotton. Gossypium
barbadense; also called Egyptian cotton.
Pinocytosis. The process of
active intake of sizable droplets of fluids by the cell.
Plant breeder’s rights: The right granted to a plant breeder,
originator, or owner of a plant variety/hybrid to exclude others from producing
or commercializing the propagating material of that variety/hybrid; the
protection period 15–20 years.
Plant breeder’s rights: The intellectual property rights that
are legally accordedto plant breeders by various laws or international treaties
Plant Breeders’ Right. A system of
intellectual property right (IPR) that provide patenttype protection to
traditionally bred varieties. It is specifically designed to cope withthe
inherent variability of plant materials. It gives to the holder the rights and
abilityto recoup his development costs from the market over a period of years.
Plant breeding: The application of genetic principles
and practices todevelopment of individuals or cultivars more suited to the
needs of humans it uses knowledge from agronomy, botany, genetics,
cytogenetics, moleculargenetics, physiology, pathology, entomology,
biochemistry, or statistics
Plant breeding: The discipline
that aims to change the genetic constitution of crop plants so as to make them
more useful to humans.
Plant introduction (PI): Germplasm brought to the United States
from otherparts of the world to provide new genes for potential improvement of
cropproductivity.
Plant Introduction. Bringing of a
plant species or a variety from one place/environmentto a new place/environment
where it has not been grown previously. Whensuccessful, plant introduction
serves the same purpose as developing varieties in awell-developed breeding
programme. In the past, it has played important roles in themovement of plant
species/varieties from one place to the other, for instance, theintroduction of
soyabeans in India from China. These introductions are utilisedprincipally in
three different ways: (a) direct use by increase in masse (e.g., TaichungNative
1 of rice and Sonoro 64 of wheat), (b) selections made from
introductions(Sonalika from segregating materials of bread wheat), and
(c) use in hybridisation.However, the present role of plant introductions, owing
to emphasis for area-specificbreeding programmes, is limited to providing a
reservoir of germplasm at the disposalof plant breeders.
Plant ontology: It relates to
anatomical features and developmental stages in different plant species.
Plant phenomics: In simple terms,
the study of plant growth, architecture, performance, and composition using
high-throughput methods of data acquisition and analysis.
Plant quarantine: The isolation of newly imported plants
to ensure that theyare not introducing any foreign parasites; the term
quarantine may refer to thequarantine station itself, or to the process of
testing and purifying the plant material
Plant Variety Protection Act: Enacted in 1970 in the United States
to providepatentlike protection for seed plant species; prior to 1970, breeders
in the industryworked primarily with maize and sorghum, with some efforts
directed to alfalfa, cotton, sugarbeet, and certain vegetables; the purpose of
the PVPA was to stimulateprivate plant breeding research and to provide better
seed cultivars to farmers andgardeners
Plant variety rights: The legal rights of a plant breeder
(not necessarily as aperson) who has developed a new variety
Plant-incorporated protectants (PIPs):
Pesticidal
substances introduced intoplants by genetic engineering that are produced and
used by the plant to protectit from pests. The protein toxins of Bt are often
used as PIPs in the formation of Btcrops.
Plaque. A clear area on a
bacterial lawn, left by lysis of the bacteria through progressiveinfections by
a phage and its descendants.
Plaque: In bacterial virus analysis, a clear
area of a petri dish, devoid of bacterialcells, indicating the presence of
viral particles.
Plasma Membrane. A unit
membrane surrounding the outer layer of the cell’scytoplasm. It is selectively
permeable.
Plasmid. Autonomously
replicating extrachromosomal DNA molecule found in bacteria.It is not the
essential component of bacterial genetic material. Its presence iscorrelated
with stress condition and confers resistance to certain antibiotics.
Theseproperties of plasmid make it suitable for exploitation as a vehicle in
geneticengineering.
Plasmid: A small, self-replicating molecule
of DNA that isseparate from the main chromosome. Because plasmids areeasily
moved from cell to cell or to the test tube, scientistsoften cleave them with
restriction enzymes and insert foreignDNA, and then transfer the recombinant
DNA plasmidmolecule (as a vector) into other cells.
Plasmid: Autonomously replicating, extra
chromosomal circular DNAmolecules, distinct from the normal bacterial genome
and nonessential for cellsurvival under nonselective conditions. Some plasmids
are capable of integratinginto the host genome.
Plasmodesma. Any of the
fibrillar plasma connections extending through the cell walland forming the
bridge between adjacent cells.
Plasmogamy. The fusion of
the cytoplasm of two or more cells. It precedes karyogamy inthe process of
fertilization.
Plasmotype. The sum total
of extrachromosomal hereditary determinants. Plasmotypeand genotype together
constitute the idiotype or genetic system of the cell.
Plasticity. The degree to
which the expression of an individual’s genotype can bemodified by
environmental factors, irrespective of the adaptive value of
thatmodification. The plasticity may be specific to a particular character,
particularenvironment, or specific in direction. It may be under genetic
control, and can befundamentally changed by selection.
Plastid DNA: Organelle DNA that is present in a
plastid
Plastid inheritance: Non-Mendelian inheritance that is
caused by hereditaryfactors present in the plastids plot with or without mass
selection, generallyfollowed by a single-plant selection; it is a procedure for
inbreeding a segregatingpopulation until the desired level of homozygosity is
achieved
Plastid. A cytoplasmic
organelle in plant cells, primarily concerned with the formationand storage of
soluble and insoluble carbohydrates. Plastids include chloroplast(having
chlorophyll pigments), chromoplast (containing carotenoids commonly foundin
fruits and flowers), and leucoplast (with no visible pigments, such as
amyloplast).
Plastogene. Any one of the
hereditary determinants located in the plastids of plant cells.
Plastom. The sum total of
plastogenes present in the plastid DNA.
Pleiotropic Mutation. A mutation
that affects several different characters. For example,a mutation in Sp gene
(to sp one) changes height, position of inflorescence, number
ofpods/cluster and maturity period in fenugreek (Trigonella foenum-graecum L)
inhomozygous condition.
Pleiotropy. A phenomenon
of having more than one seemingly unrelated phenotypicmanifestation of one
gene; such a gene is called pleiotropic gene. Mutation in such agene is called
pleiotropic mutation. For instance, the recessive gene for white-eyecolour in Drosophila
melanogaster also affects the testicular membrane, the shape ofspermatheca,
longevity, and general viability. The well-known - Dee-geo-woo-gen -has
not only shortened the plant height but has also changed angle of inclination
ofleaves, lodging tendency, fertilizer responsiveness, etc. in rice. The
above examplesindicate that each “major” gene could have one or more side
effects; and if sideeffects were favourable, selection for major effect would
be accompanied bycorrelated response for all other side effects. However,
unfavourable side effectswould preclude exploitation of pleiotropy in crop
improvement. It should be notedthat most genes, if not all, affect more than
one characteristic.
Pleiotropy: A single gene influences the
phenotypic expression of more than one trait.
Ploidy. A term referring to
the number of chromosome sets (or genomes) per cell.
Point Mutation. A mutation
that can be mapped to one specific locus.
Point mutation: A change in a single base pair.
Poky. A slow-growing
mitochondrial mutant in Neurospora.
Polar Mutation. A mutation
that affects the transcription or translation of the part of thegene or operon
on only one side of the mutant site, for example, nonsense mutations,frame-shift
mutations, and the like.
Polarity: An overall direction.
Pollen Grain. The male
gametophyte in flowering plants.
Pollination. The transfer
of pollen from the anther to a stigma. Self-pollination is thetransfer of
pollen from an anther to the stigma of the same flower or another floweron the
same plant, or within a clone. Cross-pollination is the transfer of pollen
froman anther on one plant to a stigma of a flower on a genetically different
plant or clone.
Pollination: The transfer of pollen from the
anthers to thestigma of a flower.
Poly(A) Tail. A string of
adenine nucleotides added to mRNA after transcription.
Polyacrylamide gel electrophoresis
(PAGE): A method for
separation ofproteins and amino acids on the basis of their molecule size; the
molecules movethrough the gel under the influence of an electric field
Polyacrylamide. A material
used to make electrophoretic gels for separation of mixturesof macromolecules.
Polycistronic mRNA. An mRNA that
codes for more than one protein. Bacterial genes aremostly polycistronic in the
sense that more than one gene, which are contiguous andrelated, are expressed
together. Thus during transcription, polycistronic mRNA isproduced.
Unlike bacteria, eukaryotic genes (and mRNA) are monocistronic.
Polycistronic RNA: mRNA that codes for more than one polypeptide
Polycross. The progeny
raised from seed of a line outcrossed with selected lines growingin the same
breeding nursery. The evaluation of such progeny is called polycross testthat
provides information about GCA. To ensure that the line is pollinated
equallyfrom other lines, the line should be replicated many times in the
isolated crossingblock in which outcrosses are made. Although widely used owing
to economy ofefforts with precise estimates of GCA, the inherent difficulty is
non-randomness ofpollination.
Polycross: Open pollination of a group of
genotypes (generally selected) inisolation from other compatible genotypes in
such a way as to promote randommating inter se; it is a widely used
procedure for intercrossing parents by naturalhybridization
Polyembryony. A condition of
simultaneous presence of two or more embryos within thesame seed.
Polygenes (Mather, 1943). Genes whose effects are too slight to be identifiedindividually but
which, through similar and supplementary effects, can have largeeffects on
total variability.
Polygenes: Genes producing small individual
effects on the trait phenotype, but the effects of all the polygenes affecting
a given trait are cumulative.
Polygenes: One of a group of genes that together
controls a quantitativecharacter; individually each gene has little effect on
the resulting phenotype, which instead requires the interaction of
Polygenic resistance: Resistance to parasites based on many
genes, i.e. a seriesof genes controlling a quantitative character
Polyhaploid. A haploid of a
polyploid containing more than two genomes (identical ordifferentiated).
Polyhaploid: Haploid plant derived from a polyploid
individual
Polyhybrid: Individuals that are heterozygous with
respect to the alleles ofmany gene loci or of crosses involving parents that
differ with respect to the allelesof more loci
Polylinker. A vector DNA
sequence containing multiple unique restriction-enzyme-cutsites, convenient for
inserting foreign DNA.
Polymerase chain reaction (PCR): A method for amplifying a DNA
basesequence using a heat-stable polymerase and two 20-base primers,
onecomplementary to the (+)-strand at one end of the sequence to be amplified
andthe other complementary to the (-)-strand at the other end. Because the
newlysynthesized DNA strands can subsequently serve as additional templates for
thesame primer sequences, successive rounds of primer annealing, strand
elongation and dissociation produce rapid and highly specific amplification of
the desiredsequence. PCR also can be used to detect the existence of the
defined sequence ina DNA sample.
Polymerase chain reaction (PCR): A technique to amplify aspecific DNA
sequence in vitro using a DNA replicatingenzyme, specific
oligonucleotide primers, and repeatedcycles of heating and cooling. PCR often
amplifies the startingmaterial many thousands or millions of times.
Polymerase, DNA or RNA: Enzymes that catalyse the synthesis of
nucleicacids on preexisting nucleic acid templates, assembling RNA from
ribonucleotidesor DNA from deoxyribonucleotides.
Polymorphic information content: The probability
of a marker locus being polymorphic between two random individuals/lines
selected from a given population, often referred to as expected heterozygosity.
Polymorphic site: A chromosome site with two or more identifiable
alleleicDNA sequences. Also called a polymorphic locus.
Polymorphism. The regular
and simultaneous presence of more than two distinct formsin the same population
at greater frequencies that cannot be explained by recurrentmutation. It may
occur at the level of protein, enzymes, genes or nucleotide sequencesof the
DNA.
Polymorphism: A Difference in DNA sequence among
individuals. Geneticvariations occurring in more than 1% of a population would
be considered usefulpolymorphisms for genetic linkage analysis. Compare
mutation.
Polymorphism: The simultaneous occurrence of two
or moredistinct forms in a population in a frequency that cannot beaccounted
for by the balance of mutation and selection.
Polynucleotide. A linear
sequence of nucleotides in which 3 position of the sugar
of onenucleotide is linked through a phosphate group to the 5 position of
the sugar of theadjacent nucleotide.
Polypeptide. A chain of
amino acids linked by peptide bonds. It can be a protein as well.
Polyploid. A cell
containing more than two sets of chromosomes (2n = 3x, 4x,
etc) or theindividual composed of such cells. Such a condition is
referred to as polyploidy. It isusually grouped into two classes: (a)
autopolyploid, and (b) allopolyploid. Inautoploids, each of the repeated sets
is considered to be identical or nearly so (as inpeanuts), that is, chromosome
sets are homologous. But in alloploids, chromosomesets are dissimilar or
homeologous (only partially homologous). Since they containgenomes from two or
more species, they are also designated hybrid polyploids.Mackey (1970)
suggested the use of the terms disomic and polysomic for
alloploidsand autoploids, respectively as these terms give a more precise and
conceptual pictureof the nature of polyploids from the viewpoint of cytogenetics
and breeding. Disomicpolyploids (as exemplified by modern wheat) have regular
formation of bivalents,pairing only between homologous chromosomes, disomic
genetics, homozygosity ateach locus, and the chance for heterozygosity and its
consequent heterosis frominteractions between homeologous loci. In contrast, a
polysomic polyploid such as thetetraploid potato can have meiotic pairing
between any two or more of thehomologous chromosomes, tetrasomic genetics and
again the most important, theopportunity for up to four alleles per locus
available for intra- and interlocusinteractions in optimising heterotic
combinations. In general autoploids have not beenvery important in natural
evolution due to aberrant chromosome behaviour duringmeiosis and associated
high degree of sterility. However, from breeding point ofview, they bear
significance in crop species that are propagated by asexual means,such as
potato, banana, and the like. In contrast, hybrid polyploidy has
playedimportant roles in both natural evolution and plant breeding.
Polyploidization: The spontaneous or induced
multiplication of a haploid ordiploid genome of a cell or individual
polyploids, represented by “x”
Polyploidy. A situation or
condition describing occurrence of individuals with more thantwo sets of
chromosomes. It leads to a great increase in allelic diversity, and providesan
opportunity to utilize intra-locus interactions among alleles at the specific
locus.This intra-locus interactions for most loci is analogous to true overdominance.
It alsoprovides even greater opportunity for exploitation of favourable
epistatic interactionsamong alleles of different loci (pseudo-overdominance).
Polyploidy breeding seemsto be more successful in asexually propagated crops,
crop species with lowchromosome number, and cross-pollinated crops.
Polyploidy: A state in which multiple copies of a
complete genome are present. Polyploidy is rare in animals, but common in
plants. In animals (and also plants) some tissues within a diploid organism can
be polyploid. The polyploid seriesis haploid (1 copy), diploid (2 copies),
triploid (3 copies), tetraploid (4 copies), pentaploid (5 copies), hexaploid (6
copies) etc.
Polyploidy: An individual with more than two
sets of chromosomescharacteristic of the species.
Polysaccharide. A biological
polymer composed of several monosaccharides (such asglucose, fructose or
galactose) or sugar subunits, for example, starch or cellulose.
Polysomy: The reduplication of some but not all
of the chromosomes of a setbeyond the normal
Polytene chromosome: A chromosome that is formed by
repeated reduplicationof single chromatids; sections may appear to puff or
swell due to differential geneactivation; it is visible through the light
microscope
Pooled mapping: Plants
homozygous for the recessive phenotype of the target trait are selected from a
large segregating population of a suitable cross and are divided into several
random pools, each pool is analyzed with many markers, and markers closely
linked to the target gene are identified.
Population Density. The number of
individuals of a population per unit area in thehabitat.
Population Genetics. The study of
inherited variation, and thus the behaviour of genes ina population of
organisms. The problem of population genetics is to relate theheritable changes
in population of organisms to the underlying individual processes ofinheritance
and development. It is the translation of Darwin’s three principles
(theprinciple of variation, of heredity, and of selection) into precise genetic
terms.
Population genetics: The study of inherited variation in
populations and itsmodulation in time and space; it relates the heritable
changes in populations to theunderlying individual processes of inheritance and
development
Population mapping: Mapping based on
estimates of linkage disequilibrium (LD) obtained from populations consisting
of a diverse set of individuals/lines drawn from either natural or breeding
populations.
Population structure: The level of
genetic differentiation among different homogeneous groups present in a
population.
Population Theory (Malthus 1798). A theory related to human population growth inresponse to means of
subsistence. It states that the increase in human population willbe controlled
by hunger in absence of wars or any other forms of disaster. ModernMalthusians
maintain that the catastrophe has only been delayed, and that the
miseryassociated over population is still the fate of modern civilization. They
believe thatpopulation growth may proceed at a faster rate (geometric progression)
than means ofsubsistence (which may increase only at a arithmetic rate).
Population variance: A measure of dispersion defined as the
average of thesquared deviations between the observed values of the elements of
a populationand the corresponding mean of those values
Population. A term
originally coined to denote a group of people. However, it has beenbroadened to
include groups of individuals of any one kind of organism. The term asused in
Genetics & Plant Breeding includes a reproductive community of sexual
andcross-fertilizing organisms, which share in a common gene pool. Since
Mendel’s lawsof inheritance still apply to the transmission of genes among
individuals of such agroup, it is also referred to as Mendelian population. As
a consequence of itsreproductive systems and its previous evolutionary history,
each population in thiscategory is believed to possess an integrated genetic
structure, which may bedescribed in terms of systems of gene and genotypic
frequencies. In autogamouscrops, it refers to a group of segregating
individuals, pure lines and/or families. Ittends to maintain their individual
integrity by virtue of special reproductivemechanism that precludes (within
limits) free interbreeding among themselves. Instatistics, population is a
hypothetical and infinitely large series of potentialobservations among which
observations actually made constitute a sample.
Position Effect. A term used to
describe a situation in which the phenotypic influence ofa gene is altered by
changes in the position of that gene within the genome.
Positional candidate gene: A gene known to be located in the same
regionas a DNA marker that has been shown to be linked to a single-locus trait
or to aquantitative trait locus and whose function suggests that it could be
the source ofgenetic variation in the trait in question
Positional cloning: Isolation and
cloning of a gene on the basis of its close linkage with a DNA marker involves
identification of a pair of markers flanking the mutant allele, identification
and isolation of the DNA fragment containing the mutant allele, and
determination of function of the concerned gene.
Positional cloning: The process where researchers obtain
the clone of a genewithout prior knowledge of its protein product or function;
it uses large-scalephysical and formal genetic linkage maps to find specific
genes.
Position-Effect Variegation. Variegation caused by the inactivation of a gene in somecells through
its abnormal juxtaposition with heterochromatin.
Positive Assortative Mating. A situation in which like individuals mate more commonlythan expected by
chance. If the mating-individuals are related by descent/ancestry (AA× AA),
it is called genetic assortative mating. If mating of like-to-like (tall
× tall) isbased on appearance, it is referred to as phenotypic assortative
mating. The ultimateeffect of assortative mating is an increase in the
homozygosity of the population.
Positive assortative mating: A type of nonrandom mating in which
individualsof similar phenotype mate more often than predicted under random
matingconditions
Positive Control. Regulation
mediated by a protein that is required for the activation of atranscription
unit. Expression of the gene requires activating signal.
Positive false discovery rate: The expected
ratio of the wrongly rejected null hypotheses (H0) to the total number of H0
rejected in the experiment when positive findings have occurred.
Post-transcriptional gene silencing
(PTGS): Silencing of an
endogenous genecaused by the introduction of a homologous dsRNA, transgene, or
virus; in PTGS, the transcript of the silenced gene is synthesized but does not
accumulate becauseit is rapidly degraded; this is a more general term than RNAi
Potential Variability. A kind of
bound variability that is released slowly in subsequentgenerations when it gets
converted into free variability following segregation. In mostcases, it occurs
in the heterozygotes. However, if two or more genes affect the sametrait in
completely additive manner, potential variability will occur in AaBb, AAbband
aaBB. The latter two genotypes contain homozygotic potential variability
that isreleased very slowly because it is first converted into heterozygotic
potentialvariability by crossing and then converted into free variability.
Power of association mapping: The probability
of detecting “true” marker–trait associations in a sample using AM.
Power of QTL detection: The probability
of detecting a QTL with a given effect size and the stated level of Type I
error.
Pre amplification step: Amplification of
fragments using two AFLP primers, each having one selection nucleotide at its
30 end.
Pre-Breeding. The sum total
of all the activities related to germplasm enhancement forfuture use in
varietal development.Precision Agriculture. Agriculture that makes an
effective use of informationtechnology through data available on soil, water,
environment and other relatedvariables.
Prebreeding: All research and screening activities
before a plant material entersthe directed breeding process (eg. the
development of germplasm to a state whereit is viable for breeder’s use);
primarily, it involves the evaluation of traits fromexotic material and their
introduction into more cultivated backgrounds
Precision of QTL mappingThe dispersion
of repeated independent estimates of the QTL position or that of the genetic
effects of the QTL alleles.
Preformation. The belief
that the egg, sperm, or zygote contains a preformed adult inminiature form,
which becomes unfolded during development.
Prepotency. The capacity
of a parent to impress its characteristics on its offspring sothey are more
alike than usual. Differences in prepotency depend on homozygosity,dominance,
epistasis, and linkage. A homozygote dominant at all loci would excel
inprepotency because its close relatives would be unusually alike. Such an
individualproduces only one kind of gamete; therefore, upon selfing or crossing
inter se ofindividuals with the same genotype will produce individuals
of the same kind, that is,genetic correlations among relatives will be very high.
Multiple heterozygotes, whichproduce many kinds of gametes (and hence, many
kinds of individuals upon selfing),are generally not highly prepotent.
Primary Gene Pool. Genetic
resources of a crop that include both cultivated and wildraces wherein exchange
of genetic information among individuals is possible throughroutine breeding.
Primary gene pool: Includes the cultivated species of a
crop and related speciesfrom which useful genes can be most readily obtained
for breeding; in general, itis the total sum of all the genetic variation in
the breeding population of a speciesand closely related species that commonly
interbreed with, or can be routinelycrossed with, the species
Primary mapping populationsPopulations
created by hybridization between two homozygous lines usually having
contrasting forms for the traits of interest.
Primary Species. See monogenomic species.
Primary Structure. The sequence
of amino acids in the polypeptide chain.
Primary study: A study that
enables a discovery, e.g., detection and mapping of a QTL governing a trait of
interest.
Primary Trisomics. Trisomics
having a particular homologue in triplicate. Total numberof primary trisomics
is equal to the haploid number of chromosomes of a species.
Primary Triticales. See triticales.
Primase. An enzyme that makes
RNA primers during DNA replication.
Primer extension In case of SNP
genotyping, a specially designed primer is annealed to the target PCR product,
extended by one to few nucleotides using DNA polymerase, and the products of
the extension are analyzed to deduce the SNP allele.
Primer Walking. The use of a
primer based on a sequenced area of a genome tosequence into a flanking
unsequenced area.
Primer. A short
single-stranded RNA or DNA that can act as a start site for 3’ chaingrowth when
bound to a single-stranded template.
Primer: Short pre-existing polynucleotide
chain to which newdeoxyribonucleotides can be added by DNA polymerase.
Primer: Short, pre-existing oligonucleotide or
polynucleotide cahin to whichnew DNA can be added by DNA polymerase.
Primer-dimers: Occur when single stranded primer
oligonucleotides bind toeach other rather than the DNA template
Primordium. An embryonic
structure, which eventually forms an adult part or organ.
Prior index An index based on marker genotype
and trait phenotype data from materials other than the population being
subjected to selection.
Probability. The number of
times an event is likely to occur in the total number of trials.For instance,
the probability of rolling a four on a die in a single trial is 1/6 (becausethe
die has six sides).
Probe. Defined nucleic acid
segment that can be used to identify specific DNA moleculesbearing the
complementary sequence, usually through autoradiography.
Probe: Single-stranded DNA or RNA molecules
of a specificbase sequence, labeled either radioactively or immunologically,
that are used to detect the complementary basesequence by hybridization.
Probe: Single-stranded DNA or RNA molecules
of specific base sequence, labeled either radioactively or immunologically,
that are used to detect thecomplementary base sequence by hybridisation.
Probes Small DNA or RNA fragments of, usually,
500–3,000 bp; used for hybridization to detect specific fragments from among
mixture of many different fragments.
Processed pseudogene: A copy of a functional gene which has
no promoter, nointrons, and which, consequently, is not itself transcribed;
pseudogenes are thoughtto originate from the integration into the genome of
cDNA copies synthesized frommRNA molecules by reverse transcriptase;
pseudogenes therefore have a poly(dA) sequence at their 5′ ends; because they
are not subject to any evolutionarypressure to maintain their coding potential,
pseudogenes accumulate mutationsand often have stop codons in all three reading
frames
Product Rule. A statistical
rule to predict probability of occurrence of two or moreindependent events. The
probability of two independent events occurringsimultaneously is the product of
their individual probabilities. For example, with twodice we have independent
objects, and thus probability of two fours is 1/36 (1/6 × 1/6= 1/36).
Production Environment. A complex of
several biotic and abiotic factors that affectgrowth and production of a
particular crop. Abiotic factors include various edaphicand climatic factors.
Edaphic factors are predictable, and breeding ideotype on thisground is easy
for this stress; however, it is not true owing to other reasons.
Productivity. The rate at
which radiant energy is converted into organic substances byphotosynthetic and
chemosynthetic activity of producer organisms (chiefly greenplants). This is
also called gross primary productivity, total photosynthesis or totalassimilation.
The rate of storage of organic matter in plant tissues exceeding therespiratory
use by the plants during the period of measurement is called net
primaryproductivity, apparent photosynthesis or net assimilation.
Here the term productivity186and the phrase rate of production have
been used interchangeably. In agriculture,production per unit area is called
productivity.Proflavin. A mutagen that tends to produce frame-shift
mutations.
Progeny Selection. A type of
selection in which individuals are chosen to produce thenext generation on the
basis of performance of their progeny, rather than on their ownphenotypic
appearance. The procedure is similar to ear-to-row selection.
Progeny selection: Selection based on progeny
performance.
Progeny Test. A test of the
breeding value of a genotype based on the performance of itsoffspring produced
in some definite system of mating. It could be indicative ofwhether the
genotype in question is heterozygous (which will produce variableoffspring) or
its obvious superiority was due primarily to better
micro-environmentalconditions. Early progeny test is usually advocated for the
monogenic or oligogenictraits owing to two obvious reasons: (1) perfect
population size for expression of eachgenotype is usually small, and
consequently, the chance of obtaining a desirablegenotype is more, and (2) such
a small-sized population requires little space. Early -testing has also been
recommended for a large scale screening of inbred lines so thatresources can be
saved for a final stage evaluation; however, objections have alsobeen raised on
the grounds that it will lead to a loss of many worth-while inbred lines.Early
progeny test is also useful for traits having higher heritability. If a hybrid
isdiffering for many genes and the trait in question has lower heritability,
progeny testsin early segregating generations (F2/F3/F4) are not conducted.
Plant selections made inthe F5/F6 are likely to be homozygous, or nearly so,
and the performance of theirprogeny consequently more predictable than the
performance of progeny of theheterozygotes that earlier dominated the
population and were under influence ofdominance and non-allelic interaction.
Progeny test: A test of the value of a genotype
based on the performance of itsoffspring produced in some definite system of
mating.
Progeny. The offspring of a
particular mating or of a particular individual (in case ofapomictic
reproduction).
Prokaryote. The kingdom
(including viruses, bacteria and blue-green algae) lackingmembrane-bounded
eukaryotic organization of the genetic material. It can also bedefined as an
organism composed of a prokaryotic cell(s).
Prokaryote: Organisms whose genetic material is
notenclosed by a nucleus. eubacteria, archaebacteria, and blue-green algae.
Prokaryotic Cell. A cell having
no nuclear membrane and hence no separate nucleus.
Promoter. A regulator
region of a short distance from the 5’ end of a gene that acts as thebinding
site for RNA polymerase (for the initiation of transcription).
Promoter: A DNA sequence preceding a gene that
containsregulatory sequences controlling the rate of RNA transcriptionof that
gene. In effect, promoters control when and inwhich cells a given gene will be
expressed.
Promoter: A region of DNA involved in binding of
RNA polymerase to initiatetranscription.
Propagule. The means of
propagation and/ or dissemination. It may be unicellular ormulticellular agent
(seed, for example).
Proper Plot Technique. A technique to
minimize experimental error as much aspossible. Some common plot techniques are
proper choice of plot size and shape,block size and shape, number of
replication, and the like.
Prophage. A phage
“chromosome” inserted as a part of the linear structure of the DNAchromosome of
a bacterium.
Prophase. The early
stage of nuclear division during which chromatins condense andchromosomes
become visible.
Proplastid. An immature
plastid.
Protandry. A mating
system that involves maturation of anthers before pistils (pollenshed first as
in maize, carrots, etc.).
Protandry: The maturation of anthers before
carpels (eg. in sugarbeet, sunflower, or carrot)
Protein quantity QTLs They govern
variation in the cellular contents of specific proteins.
Protein: A large molecule composed of one or
more chains of amino acids in aspecific order; the order is determined by the
base sequence of nucleotides in thegene coding for the protein. Proteins are
required for the structure, function, andregulation of the bodys cells,
tissues, and organs, and each protein has uniquefunctions. Examples are
hormones, enzymes, and antibodies.
Protein: A molecule composed of amino acids
arranged in aspecial order determined by the genetic code. Proteins arerequired
for the structure and function of all living organisms.
Protein-based markers Electrophoretic
variants of proteins, including enzymes.
Protein-for-Protein Hypothesis (Van der Plank 1976, ’78). A hypothesis pertaining tohost-parasite interaction. The products of
genes of both host and pathogen recognizeand interact with each other that lead
either to incompatibility (resistance) orcompatibility (diseased condition).
According to Van der Plank, the protein-forproteinhypothesis is applied to diseases
to which the gene-for-gene hypothesis hasbeen applied. The two hypotheses
differ somewhat in emphasis; the latter centresaround genes for resistance,
whereas the former is concerned primarily, albeit notexclusively, with
compatible host - pathogen combinations. Strobel (1975) objectedthe explanation
made by Van der Plank. According to him, it is the protein from thesusceptible
allele that recognizes and binds the toxin produced by the pathogen, andthus
the explanation of Van der Plank (1978) that pathogen protein copolymerizeswith
that of host protein giving rise to compatibility reaction, cannot be
true.According to Samborski (1978), it also does not account for the fact
observed by Flor(1956) that interaction of recessive alleles of host and dominant
alleles of pathogen inflax rust could lead to compatibility. Therefore,
according to him, compatibility ariseswhen either the host or the pathogen, or
both produce wrong products or nothing atall.
Proteome The complete set of proteins
expressed in a cell during a specific developmental stage and under the given
environmental conditions.
Proteome. The complete
set of protein-coding genes in a genome.
Proteome: The complete set of proteins
detectable in a tissue; it is the functionalrepresentation of the genome that
includes the types, functions, and interactionsof proteins that are present in
a cell; it is not a fixed characteristic of a cell, butvariable depending on
developmental stage, hormonal status, etc.
Proteomics The study of proteome using a
diverse array of techniques.
Proteomics. The cloning
and molecular characterization of the complete set of proteincodinggenes in a
genome.Protogyny. Just reverse of protandry. It is a mechanism in which
stigma becomesreceptive first, (i.e., before pollen shed; for example,
pearl millet, walnuts, etc).Notice that both protandry and protogyny
are analogous in that both fosters crosspollination.
Proteomics: A system for identifying proteins
within a cell or tissue sample, i.e. systematic characterization of proteins,
which are found in a tissue or in a specificphysiological condition; the
proteins can be identified using mass spectroscopy
Protoclonal variation: Variability of somatic cells derived
from protoplast culture.
Protogyny: A condition in which the female parts
develop first (eg. in bajra)
Proto-oncogene. The normal
cellular counterpart of genes that can be mutated to becomedominant oncogenes.
Proto-oncogene: A gene that can mutate to an allele,
an oncogene, that causesa cell to become cancerous.
Protoplasm. The cytoplasm
and nucleoplasm of the cell.
Protoplast culture: The isolation and culture of plant
protoplasts by mechanicalmeans or by enzymatic digestion of plant tissue,
organs, or cultures derived fromthese; protoplasts are utilised for selection
or hybridisation at the cellular level andfor a variety of other purposes
Protoplast Fusion. Also called somatic
hybridisation; the fusion of protoplasts from twodiverse sources aided by
suitable fusogenic treatments. It is one of the important usesof protoplast culture.
A variety of fusogenic treatments are available, which includeNaNO3, high pH
with Ca++, polyethylene glycol and electrical impulse. Such agentsbring the
protoplasts together, cause them to adhere with one another for bringingfusion.
It is used to hybridise otherwise sexually incompatible (cross
incompatible).Somatic hybridisation has been used in Nicotiana, Datura,
Petunia, Solanum, and thelike.
Protoplast fusion: A technique used in somatic
hybridisation experiments; it isused for overcoming crossing barriers;
protoplasts are placed together and inducedto fuse, applying fusogenic agents,
such as polyethylene glycol or physical means; subsequent regeneration of the
cell wall allows the propagation and regenerationof a somatic hybrid plant
Protoplast. A plant cell
devoid of the wall. The wall of the cell is digested by an enzyme,called cellulase
(and macerozyme). Enzymatic treatments yield a large quantity
ofprotoplasts without cell breakage and osmotic shrinkage. Viability of the
protoplastscan be tested by the presence of photosynthetic and respiratory
activity; however,fluoroscein diacetate is frequently used to test the
viability. Cultured protoplasts canbe used not only for somatic cell fusion but
also for taking up foreign DNA.
Protoplast: Cell without a cell wall; protoplasts
are produced by enzymes, which digest the wall; they are used for production of
hybrid cells by protoplastfusion or for injection of foreign DNA
Prototroph. A strain of
organisms that will proliferate on minimal medium (without anysupplemented
nutrient such as an amino acid, a vitamin or a hormone).
Provirus. A virus
“chromosome” integrated into the DNA of the host cell.
Pseudoallele: Genes that behave as alleles in the
allelism test but that can beseparated by crossingover
Pseudocompatibility. The occurrence
of fertilization in otherwise incompatible plantsunder exceptional
environmental or genotypic conditions. Also see pseudofertility.
Pseudodominance. The sudden
appearance of a recessive phenotype in a pedigree due todeletion of a masking
dominant gene (from one of the homologs in a deletionheterozygote). It is one
of the marking phenomena for the occurrence of a deletionevent.
Pseudodominance: The apparent dominance of a recessive
gene (allele), owingto a deletion of the corresponding gene in the homologous
chromosome
Pseudofertility. The ability of
an otherwise self-incompatible plant to produce viableoffspring under specific
environmental condition (at the end of the growing season). Itso happens (e.g.
tobacco) because the efficiency of the incompatibility reactionweakens with
age.
Pseudogamy. Formation of
seeds after stimulation by a male gamete (seemingpollination). In this case,
pollen does not make any genetic contribution to embryoformation, but is
necessary to initiate the growth of ovary or to form endospermnucleus. The
progeny shows the characteristics of the female parent.
Pseudogamy: A type of apomixis in which the
diploid egg cell develops intothe embryo without fertilisation of the egg cell,
although only after fertilization ofthe polar nuclei with one of the sperm
cells from the male gamete to form a normaltriploid endosperm
Pseudogene. An inactive
gene derived from an ancestral active one.
Pseudo-overdominance Heterozygote
superiority is due to repulsion phase linkage.
Pseudo-Self-Compatibility. Partial seed
setting following self-pollination in anotherwise self-incompatible plant. This
usually occurs at the end-of-the-seasonbecause the strength of
self-incompatibility system weakens due to aging.
PSGMS. Photoperiod-Sensitive
Genetic Male-sterility; photoperiod mediated malesterilitycondition observed in
certain genotypes of rice. Such genotypes may bemaintained (propagated) under
short-day condition, and become male sterile duringlong-day condition. Such
lines offer opportunity for replacing the widely used threelinesystem for
producing hybrid varieties involving male-sterile, maintainer andrestorer
lines. However, in PSGMS, temperature also plays an important role in
thefertility of PSGMS rice. Two loci have been identified; one controls PSGMS
system,and the other conditions temperature sensitivity.
PSI-BLAST It is used to identify all the
members of a very large gene family, which
PUC18 vector: A plasmid cloning vector; size: 2.7
kb; ~100 copies perchromosome; it shows ampicillin resistance for selection and
alpha complementingfragment of beta-galactosidase
Pulse–Chase Experiment. An experiment
in which cells are grown in a radioactivemedium for a brief period (the pulse)
and then transferred to a nonradioactive one fora longer period (the chase).
Pulsed-field gel electrophoresis: An electrophoretic technique in which
thegel is subjected to electrical fields alternating between different angles,
allowingvery large DNA fragments to move through the gel, and hence permitting
efficientseparation of mixtures of such large fragments
Punnett Square. A grid used as
a graphic representation of the progeny zygotes (F2)resulting from different
gamete fusions in a specific cross.
Pure line: The progeny of a single homozygous individual
produced by repeated selfing.
Pure-Line Breeding. A system of
breeding in which the new variety is made up of theprogeny of a single
self-fertilized homozygous individual. Although agriculturallyadvanced
countries have already exploited its full potential, however, it has still
aplace wherein land varieties still exist.
Pure-Line theory (Johannsen 1903). A theory of breeding based on progeny of singleself-fertilized
homozygous individual. The proposed theory can be summarized as: (a)a
population of self-pollinated crop consists of a mixture of pure lines, (b) a
pure-linebreeds true to the type, (c) a pure-line may become “impure” owing to
naturalcrossing, mutation and mechanical mixing, (d) variation between
pure-lines isheritable in nature, and (e) variation within a pure-line does not
have a genetic basis,and is caused due to slight differences in the
environment. All plants within a purelineare virtually homozygous for the same
gene pairs, and thus selection within apure-line is not effective.
Pure-Line. Progeny of a
single self-fertilised homozygous individual. A pure line breedstrue for the
specific character being studied; that is, all offspring produced by selfingor
crossing within the progeny show the same form for this trait. It is a
strainhomozygous at all loci, ordinarily obtained by successive
self-fertilizations.
Purine. A type of nitrogen
base with the presence of two rings in the structure. Thepurine bases of
nucleic acids are adenine and guanine.
Purine: A nitrogen-containing, single-ring,
basic compound that occurs innucleic acids. The purines in DNA and RNA are
adenine and guanine.
Purity. The ratio of sucrose
to total solids (brix) dissolved in juice of sugar cane or sugarbeet.
p-value: The probability of Type I error
or the probability of null hypothesis, e.g., a lack of marker–trait
association, being wrongly rejected.
PVP. Plant Variety
Protection; legal protection to newly bred varieties. The bill underIPRs
(India) was passed on 9. 8. 2001 and called Protection of Plant Varieties
andFarmers’ Rights Bill 2001. Under the new regime of PVP, for granting a legal
right toa variety, it must conform to the criteria of novelty and distinctness,
uniformity andstability (DUS). The legal protection is valid for 9 and 6 years
for trees and vines, andfield crops, respectively. It can be renewed; however,
the total period will not exceed18 and 15 years for trees and vines, and field
crops, respectively.
Pyramiding of genes: The process of bringing together
several diseaseresistance or agronomically important genes from different
sources into onegenetic background (genotype)
Pyrimidine. A type of
nitrogen base with a single ring forming its chemical structure.The pyrimidine
bases in DNA are cytosine and thymine, whereas in RNA are cytosineand
uracil.
Pyrimidine: A nitrogen-containing, double-ring,
basic compound that occursin nucleic acids. The pyrimidines in DNA are cytosine
and thymine; in RNA,cytosine and uracil.
PyrosequencingA method of DNA sequencing based on the use of pyrophosphate released on
addition of a nucleotide to a growing chain for generation of, ultimately,
light by luciferase that is detected.
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