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Genetic diversity and differentiation

Genetic variation is created by mutation and eroded bay selection and drift. The absence of genetic variation may result in species lacking the adaptive capacity to respond to environmental perturbations which will ultimately lead to extinction.
Genetic variation can be described by three main components:
- genetic diversity: the amount of genetic variation
- genetic differentiation: the amount of genetic variation among populations
- genetic distance: the amount of genetic variation between pairs of populations
Molecular Markers are used to describe and estimate genetic variation.
The measurements of genetic variation include estimating gene flow, taxonomy and identifying bottlenecks.

Factors influencing diversity and differentiation
1 Characteristics of the organism and its environment
1.1 Genetic drift
The random process of allele frequency changes is called genetic drift and is a result of random sampling of gametes. The change in the allele frequencies of a population from one generation to the next is due to the phenomena of probability in which purely chance events determine which alleles within population will be carried forward while others disappear.
Genetic drift can lead to the extinction of alleles and the loss of polymorphism such that a locus becomes fixed for a single allele. Thus in order to eliminate the effects of drift population must be large enough to retain variation.
→ the smaller the population the more likely chance events are to change allele frequencies. In agroecosystems pathogen populations become very large as a result of genetic uniformity of the host plant → genetic drift does not play an important role
In a new founded population genetic drift has a high value (founder effect) so there can be some alleles fixed or lost.
The homozygosity increases as a result of removing allelels. Especially in small populations there is a tendency towards homozygosity of a particular allele. With reproductively isolated homozygous populations, the allele frequency can only change by the introduction of a new allele through mutation. As a result of the homozygosity of some alleles the inbreeding coeficient increases.
Reductions in population size can be through colonization by a small number of individuals (founder effect) or through habitat fragmentation where widespread populations are reduced in size (bottlenecks).

1.2 Gene flow
Gene flow is the proportion of newly immigrant genes moving into a population and out of a population. Only through gene flow populations of species can maintain genetic connectivity because the gene pools of different groups are recombined. Without gene flow populations will diverge and differentiate over time resulting in speciation. Gene flow in stationary organisms comprises movement of gametes (pollen) or zygotes (seeds).
The extent of gene flow is determined by the ode of reproduction, the mobility of the species, dispersal ability of propagules/gametes and the degree of isolation of populations.
The movement of genes from one population to another prevents populations from differentiating over time. Populations with high differentiation should have lower levels of gene flow between them than those with low differentiation.
For small populations where drift is expected to be higher, a single migrant is a relatively high contribution and so often offsets the effect of drift.
Once we understand how the organisms disperse their genes and the ecological requirements for propagule establishment we will be able to predict the likely effects of contemporary environmental change on genetic diversity.
The extend of genetic drift gives an idea how many migrants (sclerotia, basidiospores) were exchanged. For example in rice fields there was a rotation with maize. Then the genotypes were selected to be able to infect maize. With this the allelic/ genetic diversity was reduced in the maize infecting population. Both rice and maize are poacea so it is easier to switch for the pathogen than for example between soybean and rice.

1.2.1 Gene transfer and reproductive system
Gene transfer occurs via sexual or asexual reproduction/ propagation. The viability of clones is limited because of the lack of recombination that would allow adaptation to new environments and the purging of deleterious recessive mutations which may accumulate.

1.2.2 Autogamy
Autogamy or self fertilization produces a zygote following the fusion of two gametes derived from the same individual. Selfing allows the fixation of preferential gene combinations but a lack of recombination can lead to an accumulation of deleterious mutations which are expressed as reduction in an individual fitness and effect known as inbreeding depression. Selfing is also a mechanism that limits the influx of genes from another portion of a species range, which may disrupt adaptive gene complexes adapted to new local environments (outbreeding depression). The problem is to decide whether two individuals are clones or not. For this a high number of polymorphic markers are necessary.

1.2.3 Outcrossing and dioecy
The zygotes of outcrossing are the product o gametes originating from two different individuals. The self-fertilization is prevented and outcrossing promoted. The consequence of outcrossing is that alleles should be distributed amongst individuals of a population according to hardy-Weinberg equilibrium principles. The proportion of heterozygots and homozygots in a population is derived according to the equation p2 + 2pq +q2 where p and q are the allele frequencies. With this it can be tested if the population is random mating or not and the potential inbreeding and assortative mating can be investigated.

1.3 Reproductive system
The assumption is that any single allele is equally likely to fuse with any other allele. So alleles fuse at random (panmixia or non-assortative mating). Random mating includes new combinations of genes which lead to different genotypes and a high genotype diversity. Organisms that reproduce with random mating have a high potential for rapid adaptation to a changing environment.
Positive assortative mating is when mating between individuals of the same type occurs more often than expected. Positive assortative mating leads to a reduction in expected proportion of heterozygous loci than expected.
Negative assortative mating means less mating between individuals than expected. With inbreeding or clonal reproduction the gene combinations are hold together. With this a low genetic diversity exists. The clones are able to keep a well adapted combinations of alleles for a long time. But if the environment changes quickly they need longer to adapt.

1.4 Natural selection
Leads to an in/decrease in the frequency of genes or genotypes: Decrease genetic variation in populations by selecting against a specific gene → prevent genetic speciation. Increase in genetic variation by selecting for genes → speciation. Increases the frequencies of plant resistance alleles as well as the virulence alleles in natural ecosystems through coevolution. In a large population, little change in allele frequencies will result from sampling error, even weak selection forces will push the alleles frequency upwards or downwards (depending on whether the allele’s influence is beneficial or harmful). In small populations, drift will predominate

1.1.5 Mutation
The rate of mutation is low (in the order of 1*10-5 mutations per 100000 cells). Mutation is a change in the DNA at a particular locus in an organism. It is a weak force for changing allele frequencies and strong force for introducing new alleles. These new alleles can produce new genotypes. Some mutations can effect pathogen virulence or sensitivity to fungicides or antibiotics. Large populations are expected to have more alleles than small populations because there are more mutants present for selection. The probability is very low that a mutant can encounter favorable conditions for infection or is able to reproduce

April 23rd, 2009
Topic: Crop health management, Crop Science Tags: None

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