GENETICS ASSIGNMENT

PLOIDY

Ploidy is a term from genetics and cell biology. It is used to indicate the number
of chromosome sets in a cell. Most eukaryotes have either one set
(called haploid) or two sets (called diploid). Some other organisms are
polyploidy, they have more than two sets of chromosomes.

Virtually all sexually reproducing organisms are made up of somatic cells that

are diploid or greater, but ploidy level may vary widely between different
organisms, between different tissues within the same organism, and at different
stages in an organism's life cycle. Half of all known plant genera contain
polyploidy species, and about two-thirds of all grasses are polyploidy. Many
animals are uniformly diploid, though polyploidy is common in invertebrates,
reptiles, and amphibians. In some species, ploidy varies between individuals of
the same species (as in the social insects), and in others entire tissues and organ
systems may be polyploidy despite the rest of the body being diploid (as in the
mammalian liver). For many organisms, especially plants and fungi, changes in
ploidy level between generations are major drivers of speciation. In mammals
and birds, ploidy changes are typically fatal. There is, however, evidence of
 polyploidy in organisms now considered to be diploid, suggesting that
polyploidy has contributed to evolutionary diversification in plants and animals
through successive rounds of polyploidization and rediploidization.

Humans are diploid organisms, carrying two complete sets of chromosomes in

their somatic cells: one set of 23 chromosomes from their father and one set of
23 chromosomes from their mother. The two sets combined provide a full
complement of 46 chromosomes. This total number of individual chromosomes
(counting all complete sets) is called the chromosome number. The number of
chromosomes found in a single complete set of chromosomes is called
the monoploid number (x). The haploid number (n) refers to the total number of
chromosomes found in a gamete (a sperm or egg cell produced by meiosis in
preparation for sexual reproduction). Under normal conditions, the haploid
number is exactly half the total number of chromosomes present in the
organism's somatic cells. For diploid organisms, the monoploid number and
haploid number are equal; in humans, both are equal to 23. When a human germ
cell undergoes meiosis, the diploid 46-chromosome complement is split in half
to form haploid gametes. After fusion of a male and a female gamete (each
containing 1 set of 23 chromosomes) during fertilization, the
resulting zygote again has the full complement of 46 chromosomes: 2 sets of 23
chromosomes.

TYPES OF PLOIDY

 Haploid and monoploid.

 Diploid.

 Polyploidy.

 Variable or indefinite ploidy.

 Mixoploidy.
 Dihaploidy and polyhaploidy.

 Euploidy and aneuploidy.

 Homoploid.

Haploid and monoploid

The term haploid is used with two distinct but related definitions. In the most
generic sense, haploid refers to having the number of sets of chromosomes
normally found in a gamete. Because two gametes necessarily combine during
sexual reproduction to form a single zygote from which somatic cells are
generated, healthy gametes always possess exactly half the number of sets of
chromosomes found in the somatic cells, and therefore "haploid" in this sense
refers to having exactly half the number of sets of chromosomes found in a
somatic cell. By this definition, an organism whose gametic cells contain a
single copy of each chromosome (one set of chromosomes) may be considered
haploid while the somatic cells, containing two copies of each chromosome
(two sets of chromosomes), are diploid. This scheme of diploid somatic cells
and haploid gametes is widely used in the animal kingdom and is the simplest to
illustrate in diagrams of genetics concepts. But this definition also allows for
haploid gametes with more than one set of chromosomes.

An alternative usage defines "haploid" as having a single copy of each

chromosome – that is, one and only one set of chromosomes. In this case, the
nucleus of a eukaryotic cell is only said to be haploid if it has a single set
of chromosomes, each one not being part of a pair. By extension a cell may be
called haploid if its nucleus has one set of chromosomes, and an organism may
be called haploid if its body cells (somatic cells) have one set of chromosomes
per cell. By this definition haploid therefore would not be used to refer to the
gametes produced by the tetraploid organism in the example above, since these
gametes are numerically diploid. The term monoploid is often used as a less
ambiguous way to describe a single set of chromosomes; by this second
definition, haploid and monoploid are identical and can be used
interchangeably.

Diploid

Diploid cells have two homologous copies of each chromosome, usually one
from the mother and one from the father. All or nearly all mammals are diploid
organisms. The suspected tetraploid (possessing four chromosome sets) plains
viscacha rat (Tympanoctomys barrerae) and golden viscacha rat
(Pipanacoctomys aureus) have been regarded as the only known exceptions (as
of 2004). However, some genetic studies have rejected any polyploidism in
mammals as unlikely, and suggest that amplification and dispersion of repetitive
sequences best explain the large genome size of these two rodents. All normal
diploid individuals have some small fraction of cells that display polyploidy.
Human diploid cells have 46 chromosomes (the somatic number, 2n) and
human haploid gametes (egg and sperm) have 23 chromosomes (n).
Retroviruses that contain two copies of their RNA genome in each viral particle
are also said to be diploid. Examples include human foamy virus, human T-
lymphotropic virus, and HIV.

Polyploidy

Polyploidy is the state where all cells have multiple sets of chromosomes
beyond the basic set, usually 3 or more. Specific terms are triploid (3 sets),
tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid or
septaploid(7 sets), octoploid (8 sets), nonaploid (9 sets), decaploid (10 sets),
undecaploid (11 sets), dodecaploid (12 sets), tridecaploid (13 sets),
tetradecaploid (14 sets), etc. Some higher ploidies include hexadecaploid (16
sets), dotriacontaploid (32 sets), and tetrahexacontaploid (64 sets), though
Greek terminology may be set aside for readability in cases of higher ploidy
(such as "16-ploid"). Polytene chromosomes of plants and fruit flies can be
1024-ploid. Ploidy of systems such as the salivary gland, elaiosome, endosperm,
and trophoblast can exceed this, up to 1048576-ploid in the silk glands of the
commercial silkworm Bombyx mori.

Polyploidy occurs commonly in plants, but rarely in animals. Even in diploid

organisms, many somatic cells are polyploid due to a process called
endoreduplication, where duplication of the genome occurs without mitosis (cell
division). The extreme in polyploidy occurs in the fern genus Ophioglossum,
the adder's-tongues, in which polyploidy results in chromosome counts in the
hundreds, or, in at least one case, well over one thousand.

Variable or indefinite ploidy

Depending on growth conditions, prokaryotes such as bacteria may have a

chromosome copy number of 1 to 4, and that number is commonly fractional,
counting portions of the chromosome partly replicated at a given time. This is
because under exponential growth conditions the cells are able to replicate their
DNA faster than they can divide.

In ciliates, the macronucleus is called ampliploid, because only part of the

genome is amplified.

Mixoploidy

Mixoploidy is the case where two cell lines, one diploid and one
polyploid, coexist within the same organism. Though polyploidy in humans is
not viable, mixoploidy has been found in live adults and children.There are two
types: diploid-triploid mixoploidy, in which some cells have 46 chromosomes
and some have 69,and diploid-tetraploid mixoploidy, in which some cells have
46 and some have 92 chromosomes. It is a major topic of cytology.

Dihaploidy and polyhaploidy

Dihaploid and polyhaploid cells are formed by haploidisation of polyploids, i.e.,

by halving the chromosome constitution.

Dihaploids (which are diploid) are important for selective breeding of tetraploid
crop plants (notably potatoes), because selection is faster with diploids than
with tetraploids. Tetraploids can be reconstituted from the diploids, for example
by somatic fusion.

The term "dihaploid" was coined by Bender to combine in one word the number
of genome copies (diploid) and their origin (haploid). The term is well
established in this original sense, but it has also been used for doubled
monoploids or doubled haploids, which are homozygous and used for genetic
research.

Euploidy and aneuploidy

Euploidy  is the state of a cell or organism having one or more than one set of
the same set of chromosomes, possibly excluding the sex-determining
chromosomes. For example, most human cells have 2 of each of the 23
homologous monoploid chromosomes, for a total of 46 chromosomes. A human
cell with one extra set of the 23 normal chromosomes (functionally triploid)
would be considered euploid. Euploid karyotypes would consequentially be a
multiple of the haploid number, which in humans is 23.
Aneuploidy is the state where one or more individual chromosomes of a normal
set are absent or present in more than their usual number of copies (excluding
the absence or presence of complete sets, which is considered euploidy). Unlike
euploidy, aneuploid karyotypes will not be a multiple of the haploid number. In
humans, examples of aneuploidy include having a single extra chromosome (as
in Down syndrome, where affected individuals have three copies of
chromosome 21) or missing a chromosome (as in Turner syndrome, where
affected individuals are missing an X chromosome). Aneuploid karyotypes are
given names with the suffix -somy (rather than -ploidy, used for euploid
karyotypes), such as trisomy and monosomy.

Homoploid

Homoploid means "at the same ploidy level", i.e. having the same number
of homologous chromosomes. For example, homoploid hybridization is
hybridization where the offspring have the same ploidy level as the two parental
species. This contrasts with a common situation in plants where chromosome
doubling accompanies or occurs soon after hybridization. Similarly, homoploid
speciation contrasts with polyploid speciation.

Zygoidy and azygoidy

Zygoidy is the state in which the chromosomes are paired and can undergo
meiosis. The zygoid state of a species may be diploid or polyploid. In the
azygoid state the chromosomes are unpaired. It may be the natural state of some
asexual species or may occur after meiosis. In diploid organisms the azygoid
state is monoploid. (See below for dihaploidy.)

DNA Ploidy
DNA ploidy analysis of prostate cancer provides important predictive
information that supplements histopathologic examination. Patients
with diploid tumors have a more favorable outcome than those
with aneuploid tumors. Among patients with lymph node metastases treated
with prostatectomy and androgen deprivation therapy, those with diploid tumors
survive 20 years or longer, whereas those with aneuploid tumors die within 5
years. However, the ploidy pattern of prostate cancer is often heterogeneous,
creating potential problems with sampling error.

Analysis of multiple biopsies is important for correct preoperative ploidy

estimation.  A good correlation exists between DNA ploidy and histologic
grade, and DNA ploidy adds clinically useful predictive information for some
patients. The incidence of aneuploidy in high-grade PIN varies from 32% to
68% and is somewhat lower than in carcinoma (55% to 62%). There is a high
level of concordance of DNA ploidy of PIN and coexisting cancer. About 70%
of aneuploid cases of PIN are associated with aneuploid carcinoma; conversely,
only 29% of cases of aneuploid cancer are associated with aneuploid PIN. DNA
ploidy pattern by flow cytometry correlates with cancer grade, volume, and
stage. Most low-stage tumors are diploid and high-stage tumors are nondiploid,
but numerous exceptions occur.

Biopsy ploidy status independently predicts cancer recurrence in patients treated

by prostatectomy. However, 40% of patients with Gleason score ≥ 4 + 4 and
55% of patients with biochemical recurrence have diploid cancer. Patients with
diploid lymph node metastases treated by androgen deprivation therapy alone
have longer progression-free survival and overall survival than those with
aneuploid metastases. Five-year cancer-specific survival is about 95% for
diploid tumors, 70% for tetraploid tumors, and 25% for aneuploid
tumors.1204 Digital image analysis appears to have a high level of concordance
(about 85%) with prostatectomy specimens evaluated by flow cytometry.
PLANT PLOIDY

Genome duplication (polyploidy) is a recurrent evolutionary process in plants,

often conferring instant reproductive isolation and thus potentially leading to
speciation. Outcome of the process is often seen in the field as different
cytotypes co-occur in many plant populations. Failure of meiotic reduction
during gametogenesis is widely acknowledged to be the main mode of
polyploid formation. To get insight into its role in the dynamics of polyploidy
generation under natural conditions, and coexistence of several ploidy levels,
we developed a general gametic model for diploid–polyploid systems.

This model predicts equilibrium ploidy frequencies as functions of several

parameters, namely the unreduced gamete proportions and fertilities of higher
ploidy plants. We used data on field ploidy frequencies for 39 presumably
autopolyploid plant species/populations to infer numerical values of the model
parameters (either analytically or using an optimization procedure). With the
exception of a few species, the model fit was very high. The estimated
proportions of unreduced gametes (median of 0.0089) matched published
estimates well. Our results imply that conditions for cytotype coexistence in
natural populations are likely to be less restrictive than previously assumed. In
addition, rather simple models show sufficiently rich behaviour to explain the
prevalence of polyploids among flowering plants.

 An increase in whole genome chromosome sets is a recurring process in

plant evolution followed by deletion of genes back to a near diploid level.

 Recent genome doubling can consist of genomes from slightly diverged

species and are referred to as allopolyploids.

 Recent genome doubling within a species is referred to as autopolyploids.

 Allopolyploids and autopolyploids have different genetic behaviours.

 Cell size increases with the number of genomes present, as does gene
expression in general.

 Aneuploidy is the change in copy number of part of the genome.

 Aneuploidy produces greater changes in gene expression than does ploidy

variation

Examples of important polyploid plants used for human food include, Triticum

aestivum (wheat), Arachis hypogaea (peanut), Avena sativa (oat), Musa sp.
(banana), many agricultural Brassica species, Solanum tuberosum (potato),
Fragaria ananassa (strawberry), and Coffea arabica (coffee)
POLY PLOIDY

Organisms with more than 2 sets of chromosomes are polyploidy. When there

are 3 sets, this is called triploid, or 3n, and organisms with 4 sets are called
tetraploid, or 4n. Examples of organisms with polyploidy are peanuts, apples,
bananas, and salmon. It is also seen in reptiles, amphibians, and insects

This image shows haploid (single), diploid (double), triploid (triple), and
tetraploid (quadruple) sets of chromosomes. Triploid and tetraploid
chromosomes are examples of polyploidy.
Polyploid types are labeled according to the number of chromosome sets in the
nucleus. The letter x is used to represent the number of chromosomes in a single
set.

Types

triploid (three sets; 3x), for example sterile saffron crocus, or seedless
watermelons, also common in the phylum Tardigrada

tetraploid (four sets; 4x), for example Salmonidae fish,[9] the cotton
Gossypium hirsutum

pentaploid (five sets; 5x), for example Kenai Birch (Betula papyrifera var.
kenaica)

hexaploid (six sets; 6x), for example wheat, kiwifruit

heptaploid or septaploid (seven sets; 7x)

octaploid or octoploid, (eight sets; 8x), for example Acipenser (genus of

sturgeon fish), dahlias

decaploid (ten sets; 10x), for example certain strawberries

dodecaploid (twelve sets; 12x), for example the plants Celosia argentea and
Spartina anglica [12] or the amphibian Xenopus ruwenzoriensis.

Animals

Examples. Triploid crops: some apple varieties (such as Belle de Boskoop,

Jonagold, Mutsu, Ribston Pippin), banana, citrus, ginger, watermelon, saffron
crocus. Tetraploid crops: very few apple varieties, durum or macaroni wheat,
cotton, potato, canola/rapeseed, leek, tobacco, peanut, kinnow, Pelargonium.
APPLICATIONS OF PLIODY

Polyploidy describes the case of a cell or an individual possessing entire extra

sets of chromosomes. The type of polyploidy is designated by the number
of haploid (N) sets that are present. Triploid (3N) individuals have three sets of
chromosomes while tetraploid (4N) individuals have four. A karyotype of
a triploid individual can be seen here. Note that there are three copies of
each chromosome.

Polyploidy is extremely common in plants. As a matter of fact, common food

plants such as wheat, seedless grapes and bananas are polyploid.
However, polyploidy is not common in mammals, and it is usually lethal when
it occurs.

 In humans, polyploidy can be caused by at least two mechanisms:

dispermy and unreduced gametes. Dispermy is the term used to describe
the process by which two sperm fertilize a single egg to produce a
triploid zygote. Unreduced gametes are diploid rather than haploid. The
union of an unreduced egg and a haploid sperm would result in a triploid
zygote, while the union of an unreduced egg and an unreduced sperm
would result in a tetraploid zygote.

 Polyploidy only increases this effect in plants and even secures the new

plant breed, as it has the ability to produce multiple copies of the
advantageous genes. Some studies also have suggestions that, when
compared to its diploid relatives, polyploids have an increased level of
heterosis
 In summary, the advantages of polyploidy are caused by the ability to
make better use of heterozygosity, the buffering effect of gene
redundancy on mutations and, in certain cases the facilitation of
reproduction through self-fertilization or asexual means.

 There are three obvious advantages of becoming polyploid: heterosis,

gene redundancy (a result of gene duplication) and asexual reproduction.
Heterosis causes polyploids to be more vigorous than their diploid
progenitors, whereas gene redundancy shields polyploids from the
deleterious effect of mutations. Asexual reproduction, for which the
mechanistic connection to polyploidy is unclear, enables polyploids to
reproduce in the absence of sexual mates.

 There are several disadvantages, documented or conjectured, of

polyploidy. They include the potentially disrupting effects of nuclear and
cell enlargement, the propensity of polyploid mitosis and meiosis to
produce aneuploid cells, and the epigenetic instability that results in
transgressive (non-additive) gene regulation.

 The amount of experimental evidence that addresses these problems

varies considerably. In particular, recent data on gene regulation in
polyploids provide interesting but still incomplete information on the
genetic responses that are involved in polyploidy and on the role of
epigenetic remodelling.
 Transcriptional remodelling in polyploids has two causes. The first is the
interaction of diverged parental genomes that are reunited in the
allopolyploid; this interaction has both genetic and epigenetic effects. The
second, less characterized causal mechanism is genome duplication.
  Triploidy and aneuploidy are unstable states that often lead to or result
from the more stable polyploidy states such as tetraploidy. Both
conditions can have potentially disruptive effects on genome regulation,
some of which might result from meiotically unpaired DNA.

Advantages of Polyploidy

Due to the high incidence of polyploidy in some taxa, such as plants, fish, and
frogs, there clearly must be some advantages to being polyploid. A common
example in plants is the observation of hybrid vigor, or heterosis, whereby the
polyploid offspring of two diploid progenitors is more vigorous and healthy
than either of the two diploid parents. There are several possible explanations
for this observation. One is that the enforced pairing
of homologous chromosomes within an allotetraploid
prevents recombination between the genomes of the original progenitors,
effectively maintaining heterozygosity throughout generations (Figure 3). This
heterozygosity prevents the accumulation of recessive mutations in the genomes
of later generations, thereby maintaining hybrid vigor. Another important factor
is gene redundancy. Because the polyploid offspring now have twice as many
copies of any particular gene, the offspring are shielded from the deleterious
effects of recessive mutations. This is particularly important during
the gametophyte life stage. One might envision that, during the haploid stage of
the life cycle, any allele that is recessive for a deleterious mutation will not be
masked by the presence of a dominant, normally functioning allele, allowing the
mutation to cause developmental failure in the pollen or the egg sac.
Conversely, a diploid gamete permits the masking of this deleterious allele by
the presence of the dominant normal allele, thus protecting the pollen or egg sac
from developmental dysfunction. This protective effect of polyploidy might be
important when small, isolated populations are forced to inbreed.
Another advantage conferred by gene redundancy is the ability to diversify
gene function over time. In other words, extra copies of genes that are not
required for normal organism function might end up being used in new and
entirely different ways, leading to new opportunities in
evolutionary selection (Adams & Wendel, 2005).

Interestingly, polyploidy can affect sexuality in ways that provide selective

advantages. One way is by disrupting certain self-incompatibility systems,
thereby allowing self-fertilization. This might be the result of the interactions
between parental genomes in allopolyploids (Comai et al., 2000). Another way
is by favoring the onset of asexual reproduction, which is associated with
polyploidy in both plants and animals. This switch in reproductive strategies
may improve fitness in static environments.

Disadvantages of Polyploidy

For all the advantages that polyploidy can confer to an organism, there are also
a great number of disadvantages, both observed and hypothesized. One of these
disadvantages relates to the relative changes between the size of the genome and
the volume of the cell. Cell volume is proportional to the amount of DNA in the
cell nucleus. For example, doubling a cell's genome is expected to double the
volume of space occupied by the chromosomes in the nucleus, but it causes only
a 1.6-fold increase in the surface area of the nuclear envelope (Melaragno et al.,
1993). This can disrupt the balance of factors that normally mediate interactions
between the chromosomes and nuclear components, including envelope-bound
proteins. The peripheral positioning of telomeric and
centromeric heterochromatin may be disturbed as well, because there is less
relative surface space on the nuclear envelope to accommodate this positioning
(Fransz et al., 2002).
Polyploidy can also be problematic for the normal completion
of mitosis and meiosis. For one, polyploidy increases the occurrence
of spindle irregularities, which can lead to the chaotic segregation of chromatids
and to the production of aneuploid cells in animals and yeast. Aneuploid cells,
which have abnormal numbers of chromosomes, are more readily produced in
meioses involving three or more sets of chromosomes than in diploid cells.
Autopolyploids have the potential to form multiple arrangements of
homologous chromosomes at meiotic metaphase I (Figure 2), which can result
in abnormal segregation patterns, such as 3:1 or 2:1 plus one laggard. (Laggard
chromosomes do not attach properly to the spindle apparatus and thus randomly
segregate to daughter cells.) These abnormal segregation patterns cannot be
resolved into balanced products, and random segregation of multiple
chromosome types produces mostly aneuploid gametes (Figure 3).
Chromosome pairing at meiosis I is more constrained in allopolyploids than in
autopolyploids, but the stable maintenance of the two parental chromosomal
complements also requires the formation of balanced gametes.
Another disadvantage of polyploidy includes potential changes in gene
expression. It is generally assumed that an increase in the copy number of all
chromosomes would affect all genes equally and should result in a uniform
increase in gene expression. Possible exceptions would include genes that
respond to regulating factors that do not change proportionally with ploidy. We
now have experimental evidence for such exceptions in several systems. In one
interesting example, investigators compared the mRNA levels per genome for
18 genes in 1X, 2X, 3X, and 4X maize. While expression of most genes
increased with ploidy, some genes demonstrated unexpected deviations from
expected expression levels. For example, sucrose synthase showed the expected
proportional expression in 2X and 4X tissues, but its expression was three and
six times higher, respectively, in 1X and 3X tissues. Two other genes showed
similar, if less extreme, trends. Altogether, about 10% of these genes
demonstrated sensitivity to odd-numbered ploidy (Guo et al., 1996).