View Full Version : Some breeding stuff
In no apparent order:
Phenotype - literally means "the form that is shown"; it is the outward, physical appearance of a particular trait
Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F1 generation from the cross of two pure lines
Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F1 generation from the cross of two pure lines and reappears in the F2 generation
Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual
Allelic pair - the combination of two alleles which comprise the gene pair
Homozygote - an individual which contains only one allele at the allelic pair; for example DD is homozygous dominant and dd is homozygous recessive; pure lines are homozygous for the gene of interest
Heterozygote - an individual which contains one of each member of the gene pair; for example the Dd heterozygote
Genotype - the specific allelic combination for a certain gene or set of genes
Mendel's First Law - the law of segregation; during gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete
Backcross - the cross of an F1 hybrid to one of the homozygous parents; for pea plant height the cross would be Dd x DD or Dd x dd; most often, though a backcross is a cross to a fully recessive parent
Testcross - the cross of any individual to a homozygous recessive parent; used to determine if the individual is homozygous dominant or heterozygous
Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa)
Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair
Dominance - the ability of one allele to express its phenotype at the expense of an alternate allele; the major form of interaction between alleles; generally the dominant allele will make a gene product that the recessive can not; therefore the dominant allele will express itself whenever it is present
Ploidy is the number of homologous sets of chromosomes in a biological cell. The ploidy of cells can vary within an organism. In humans, most cells are diploid (containing one set of chromosomes from each parent), but sex cells (sperm and egg) are haploid. In contrast, tetraploidy (four sets of chromosomes) is a type of polyploidy and is common in plants, and not uncommon in amphibians, reptiles, and various species of insects.
The number of chromosomes in one of the mutually-homologous sets is called the monoploid number (x). This is the same number for every set in every cell of a given organism.
Diploid (2n) cells have two homologous copies of each chromosome, usually one from the mother and one from the father. The exact number of chromosomes may be one or two different from the 2n number yet the cell may still be classified as diploid (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fraction of cells that display polyploidy. Human diploid cells have 46 chromosomes and human haploid gametes (egg and sperm) have 23 chromosomes.
Polyploidy is the state where all cells have multiple pairs of chromosomes beyond the basic set. These may be from the same species or from closely related species. In the latter case these are known as allopolyploids, amphidiploids or allotetraploids. Allopolyploids can be formed from the hybridisation of two separate species followed by their subsequent chromosome doubling. A good example is the so-called Brassica triangle where three different parent species have hybridized in each pair combination to form three different allopolyploid species. Polyploid plants are probably most often formed from the pairing of meiotically unreduced gametes (Ramsey and Schemske, 2002).
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)
A gamete (from Ancient Greek γαμετης; translated gamete = wife, gametes = husband) is a cell that fuses with another gamete during fertilization (conception) in organisms that reproduce sexually.
A zygote (from Greek zugōtos ‘joined’, from zugoun ‘to join’) is a cell that is the result of fertilization. That is, two haploid cells—usually an ovum from a female and a sperm cell from a male—merge into a single diploid cell called the zygote (or zygocyte).
Dominant trait refers to a genetic feature that hides the recessive trait in the phenotype of an individual. A dominant trait is a phenotype that is seen in both the homozygous AA and heterozygous Aa genotypes. Many traits are determined by pairs of complementary genes, each inherited from a single parent. Often when these are paired and compared, one allele (the dominant) will be found to effectively shut out the instructions from the other, recessive allele. For example, if a person has one allele for blood type A and one for blood type O, that person will always have blood type A. For a person to have blood type O, both their alleles must be O (recessive).
When an individual has two dominant alleles (AA), the condition is referred to as homozygous dominant; an individual with two recessive alleles (aa) is called homozygous recessive. An individual carrying one dominant and one recessive allele is referred to as heterozygous.
A dominant trait when written in a genotype is always written before the recessive gene in a heterozygous pair. A heterozygous genotype is written Aa, not aA.
-Wikipedia
The term "recessive allele" refers to an allele that causes a phenotype (visible or detectable characteristic) that is only seen in homozygous genotypes (organisms that have two copies of the same allele) and never in heterozygous genotypes. Every diploid organism, including humans, has two copies of every gene on autosomal chromosomes, one from the mother and one from the father. The dominant allele of a gene will always be expressed while the recessive allele of a gene will be expressed only if the organism has two recessive forms.[1] Thus, if both parents are carriers of a recessive trait, there is a 25% chance with each child to show the recessive trait.
-wikipedia
Classical plant breeding uses deliberate interbreeding (crossing) of closely or distantly related individuals to produce new crop varieties or lines with desirable properties. Plants are crossbred to introduce traits/genes from one variety or line into a new genetic background. For example, a mildew-resistant pea may be crossed with a high-yielding but susceptible pea, the goal of the cross being to introduce mildew resistance without losing the high-yield characteristics. Progeny from the cross would then be crossed with the high-yielding parent to ensure that the progeny were most like the high-yielding parent, (backcrossing). The progeny from that cross would then be tested for yield and mildew resistance and high-yielding resistant plants would be further developed. Plants may also be crossed with themselves to produce inbred varieties for breeding.
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According to the theory of Mendelian inheritance, variations in phenotype - the observable physical and behavioral characteristics of an organism - are due to variations in genotype, or the organism's particular set of genes, each of which specifies a particular trait. Different forms of a gene, which may give rise to different phenotypes, are known as alleles. Organisms such as the pea plants Mendel worked on, along with many plants and animals, have two alleles for each trait, one inherited from each parent. Alleles may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, while recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work found that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation.
Multiple sources:
wikipedia
WVU
Inbreeding is breeding between close relatives, whether plant or animal. If practiced repeatedly, it often leads to a reduction in genetic diversity. A concomitant increase in homozygousity of recessive traits can, over time, result in inbreeding depression. This may result in inbred individuals exhibiting reduced health and fitness and lower levels of fertility.
In plant breeding, inbred lines are used as stocks for the creation of hybrid lines to make use of the heterosis effect. Inbreeding in plants also occurs naturally in the form of self-pollination.
Inbreeding depression is reduced fitness in a given population as a result of breeding of related individuals. Breeding between closely related individuals, called inbreeding, results in more recessive deleterious traits manifesting themselves. The more closely related the breeding pair is, the more homozygous deleterious genes the offspring may have
With some exceptions, inbreeding reduces offspring fitness in essentially all naturally outcrossing plants and to a lesser extent in selfing species. The negative effects of mating between relatives have been noticed for many centuries. The careful breeding studies of Darwin (1876) first empirically demonstrated inbreeding depression in a wide variety of taxa. The negative effects of inbreeding have since been observed in both outcrossing and selfing species for a variety of traits with consequences for offspring fitness (Charlesworth and Charlesworth 1987, Keller and Waller 2002). Examples of traits shown to be subjects to inbreeding depression include pollen quantity, number of ovules, amount of seed, germination rate, growth rate and competitive ability (Keller and Waller 2002, Frankham et al. 2003). Genetic models have been developed to functionally explain reduction in fitness-related traits caused by inbreeding.
Here is a good read on inbreeding plants
http://www.as.wvu.edu/~kgarbutt/QuantGen/Gen535_2_2004/Inbreeding_Plants.htm
Heterosis and Inbreeding Depression
by D.A. Cooke
Inbreeding depression is usually defined as the lowered fitness or vigour of inbred individuals compared with their non-inbred counterparts, observed in many (but by no means all) organisms. Its converse is heterosis, the 'hybrid vigour' manifested in increased size, growth rate or other parameters resulting from the increase in heterozygosity in F1 generation crosses between inbred lines.
Problems arise in defining fitness and vigour. So long as we are discussing populations of wild plants, we have the concept of Darwinian fitness: if individuals of one genotype survive to breed more than others, then that genotype confers greater fitness. Fitness is an observed quantity that integrates the effect of all characters that influence the ability of the organism to live and reproduce. As natural selection can only act to increase the frequency of an allele in proportion to the extent to which that allele increases fitness, it was predicted (Falconer, 1989) that the amount of heritable variance for a trait would be inversely proportional to its effect on the organism's fitness. In other words, there would be more inheritable variance in relatively 'neutral' characters than in ones that increased the organism's viability or fecundity. Studies on three very different animal species tended to confirm this prediction regarding individual characters (Kruuk et al., 2000), but the measurement of overall fitness in populations remains problematical.
Vigour is another vague concept: but to most growers it is synonymous with rate of growth or biomass accumulation. In an annual, this is well correlated with production of grain, flowers or fruit since these plants maximise their investment in seed production. But a perennial may increase its growth rate only to reinvest these resources in further vegetative reproduction; examples are bulbil watsonia and crow garlic that have become weeds by the strategy of vegetative reproduction with little or no seeding.
Vigour has sometimes been used as a measure (or even a near-synonym) of fitness in discussions of heterosis. But a plant can be too vigorous for its own good: it can become structurally unstable and vulnerable to destruction by mechanical stress or dependent on a higher and more reliable supply of water and nutrients than the environment can guarantee. And an individual plant whose accelerated growth rate causes it to flower long before the rest of its population may - if it can self-pollinate - have increased its fitness. But its fitness will be reduced to zero if it's a self-incompatible annual.
The relation between fitness and vigour in a wild population is not a straight line, but a curve with a maximum:
In the language of games theory, natural selection might be said to favour strategies that lead to a minimax outcome - the optimum attainable in the real world rather than the theoretical maximum.
Darwinian fitness is not a single character, but the outcome of every trait in an individual that influences the contribution it makes to the next generation. In populations of wild plants, heterosis for a range of quantities presumed to have a strong influence on fitness is more meaningful than heterosis for vigour alone. For example, Buza et al. (2000) measured germination rate, seedling survivorship and vegetative growth rate in their attempt to quantify inbreeding depression in relict Swainsona populations.
Balanced polymorphisms in populations are often due to the heterozygotes having a higher fitness than either homozygote (Ford, 1964).
Possible explanations of this heterosis for overall fitness include:
The formation of homozygotes in which alleles with more or less recessive deleterious effects become fully expressed, but had been masked by the dominants in heterozygotes. Recessive and mildly deleterious mutations are common, and if located close to a beneficial allele they will increase in frequency as it does, being "sheltered" from selection in the heterozygotes. By the time a beneficial mutant is common enough for its homozygotes to occur in significant numbers in the population, it may be linked with enough harmful recessives to make these homozygotes less fit than the heterozygote (Fisher, 1927; Ford, 1965). In this case, heterosis is said to be caused by dominance complementation. This may also be described loosely as epistasis of the harmful genes over the beneficial ones - but only if that term is used in the broadest sense.
Overdominance - the fitness of the heterozygote per se is higher than either homozygote. This could arise because genes normally have pleiotropic effects, contributing to many measurable traits of the plant. If a mutation is selected for a positive effect on fitness or some desired trait, its other effects are likely to be deleterious. Because a mutant allele at first spreads through a population via heterozygotes, selection will tend to modify and optimise its action by making its beneficial effects dominant and its deleterious effects recessive (Gustafsson, 1950; Sheppard, 1953). This hypothesis has been used to explain balanced polymorphisms, for example in the case of Dactylis glomerata (Apirion & Zohary, 1961).
In both explanations, a beneficial dominant effect is associated with a deleterious recessive effect. Whether these correlated effects are due to the same gene, or to closely linked but separate genes may be a difficult point to decide. Both overdominance and dominance complementation may contribute in varying degrees to observed cases of heterosis. But evidence for actual instances of overdominance remains scarce.
Three predictions of the dominance complementation hypothesis suggest how it might be tested:
Inbreeding depression due to genes with deleterious recessive effects that are linked to genes with beneficial dominant effects may be removed by selection; but if it is due to overdominance it cannot.
A period of inbreeding can 'purge' deleterious recessive alleles from a population since these will have an increased chance of appearing in homozygotes than can be eliminated by selection (Barrett & Charlesworth, 1991).
If two strains of a plant are each selected for heterosis in the F1 produced by crossing them with a third strain, heterosis will also increase in the F1 between these selected strains because they are being purged of deleterious alleles. But if heterosis was due to overdominance, the two strains would converge, since each would be selected for alleles that differed from those of the tester strain at each locus, and their hybrid will show inbreeding depression instead of heterosis.
Wild plants that are normally inbreeders, or have a mixed inbreeder/outbreeder strategy, might be expected to have a genetic architecture that minimises inbreeding depression. In one experiment confirming this, the inbred seeds from cleistogamous flowers of Viola species had only slightly lower fitness than the outcrossed seeds from chasmogamous flowers on the same plants (Berg & Redbo-Torstensson, 1999).
Inbreeding depression is caused mainly by deleterious recessive alleles in both Mimulus guttatus (an outbreeder) and the closely related inbreeder M. micranthus (Dudash & Carr, 1998). Natural selection in experimentally inbred lines of M. guttatus purged the few alleles with major deleterious effects, but numerous other alleles, each with a small effect, accounted for almost all the depression (Willis, 1999).
Cultivated plants
But most of the practical interest in heterosis centres on cultivated plants, and when plant breeders say 'fitness' they really mean 'crop yields'. It is more useful to speak of heterosis for a particular statistic of the crop: for example, leaf area or seed size.
Heterosis is also modified by the interactions between genotype and environment in cultivation. Hybrid sorghum can show heterosis for yield; but this effect varies widely between trials conducted at sites differing in seasonal water supply (Chapman et al., 2000), so that it is more meaningful to characterise a particular hybrid line as showing heterosis for yield at a specific locality or under certain environmental conditions.
In practice, yield and other measurable traits desired by breeders are often correlated with traits that increase the fitness of the plant: increased efficiency of metabolism, photosynthesis etc. As a convenient approximation, we can speak loosely of 'beneficial' and 'deleterious' effects.
Heterosis for size, vigour or yield is most evident in outbreeding crops. The classic case is maize, in which heterosis has long been exploited in the production of uniformly high-yielding F1 seed in commercial quantities.
The definitive experiment by Sprague (1983) showed that this instance of heterosis is due wholly or mainly to dominance complementation. Over many years, two maize populations were each selected for increased yield in the hybrids produced by crossing them with another inbred 'tester' strain. F1 hybrids between the two selected strains showed increased yield, as predicted by the dominance complementation hypothesis. They also produced increased yields in hybrids with other testers.
If dominance complementation is the only factor involved in heterosis for yield, the high productivity of hybrid maize may have been matched by open-pollinated cultivars if enough work had been invested in their development. However, Fu & Dooner (2002) have reported the surprising discovery that maize cultivars differ in the set of genes they carry: some loci in one cultivar lack corresponding alleles in another line. In this case, any component of the heterosis effect due to complementation between different loci could never be fixed in an open-pollinated line, since these loci would remain on separate chromosomes. Maize may be a special case among crop plants - both because its genome has been doubled in size by retrotransposon activity that produced multiple paralogs of some genes, and also because it has been more radically changed by the domestication process than have other crops such as rice.
Xiao et al. (1995) demonstrated that overdominance is not a major cause of heterosis for yield in a cross between the two subspecies of rice, because there was no correlation between most traits and overall genome heterozygosity, heterozygotes were never superior to both homozygotes in analysis of quantitative trait loci, and some F8 inbred lines were actually superior to the F1 for all traits evaluated.
Trials support the hypothesis that heterosis in wheat is due to dominance complementation, with linkage and interaction of alleles (Pickett & Galwey, 1997) - to the loss of those who would like to exploit hybrid wheat as they have done hybrid maize. In some other outbreeding crop plants, such as cucumbers (Cramer & Wehner, 1999), crossing inbred lines rarely leads to heterosis.
The hypothesis of dominance complementation is also supported by evidence that polyploids are to some extent buffered against inbreeding depression because they have additional copies of each gene (Bingham et al., 1994; Husband & Schemske, 1997).
A third explanation of heterosis
An alternative theory was proposed by Milborrow (1998). He suggested that growth of a plant may be limited by the genes that regulate certain metabolic pathways down to lower levels than the maximum possible. Heterozygotes may partially escape this regulation because they have two slightly different alleles for these genes, allowing greater flow on these pathways. This is not overdominance; but, like the overdominance hypothesis, it predicts that heterozygotes have an inherent advantage in vigour that cannot be duplicated by any amount of selection in open-pollinated homozygous lines.
The most interesting part of Milborrow's theory is the implication as to why there are so many "weak" alleles in a population to start with. These are not sublethal mutants that have accumulated under the protection of closely linked genes that are strongly selected, but a necessary part of the genetic adaptation of the population.
Natural selection will maintain weak alleles because an individual with all the strong alleles will be vigorous but of lower fitness. Therefore, selection maintains the average individual in the population at that level of vigour which maximises fitness. This may explain observations that the level of heterosis in wild populations depends on their habitat, sometimes termed habitat-dependent heterosis (Lloyd, 1980). The fitness advantage of heterozygotes is often greater under more severe conditions (eg., Dudash, 1990).
Genetic variation allows more vigorous and less vigorous individuals to exist and take advantage of changing conditions under which they may have the advantage. This is a mixed strategy; and as Von Neumann & Morgenstern (1953) showed, mixed strategies are necessary to achieve minimax outcomes.
But artificial selection of plants in cultivation aims to maximise desired parameters - yield, size etc - within an artificial, optimum environment. It may therefore be possible to purge the alleles that cause inbreeding depression from cultivated lines.
Again multiple sources:
Wikipedia again
some stuff in my archives
and some stuff gotten off the net I saved
Backcrossing is a crossing of a hybrid with one of its parents or an individual genetically similar to its parent, in order to achieve offspring with a genetic identity which is closer to that of the parent. It is used in horticulture, animal breeding and in production of gene knockout animals.
Advantages
If the recurrent parent is an elite genotype, at the end of the backcrossing programme an elite genotype is recovered
As there is no "new" recombination, the elite combination is not lost
Disadvantages
Works poorly for quantitative traits
Is more restricted for recessive traits
In practice, sections of genome from the non-recurrent parents are often still present and can have deleterious traits associated with them
For very wide crosses, limited recombination may maintain thousands of ‘alien’ genes within the elite cultivar
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BackCrossing
Backcrossing is where you breed an individual (your special clone) with it's progeny.
1) Your first backcross is just a backcross.
2) Your second backcross where you take the progeny from the first backcross and cross back to the SAME parent (grandparent now) is often called SQUARING by plant breeders.
3) Your third backcross where you take the progency (squared) from the second backcross and cross back to the SAME parent (great grandparent now) is often called CUBING by plant breeders. You can continue the backcrossing but we just call this backcrossing. Cubing is in reference to the number three, as in 3 backcrosses
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Note:
Inbreeding depression can occur when backcrossing
Cranky
03-26-2008, 03:40 PM
good info there bro;)
nice one
cranks
IMO this is an important read for anybody doing random pollenation. ;)
(aka hybrid crosses)
same sources as in previous posts
Outcrossing is the practice of introducing unrelated genetic material into a breeding line. It increases genetic diversity, thus reducing the probability of all individuals being subject to disease or reducing genetic abnormalities(only within the first generation). It actually can serve to increase the number of individuals who carry a disease recessively.[1]
It is used in line breeding to restore vigor or size and fertility to a breeding line.
Outcrossing is now the norm of most purposeful breeding, contrary to what is commonly believed.[2][3][4] [5] The outcrossing breeder intends to remove the traits by using "new blood". With dominant traits, one can still see the expression of the traits and can remove those traits whether one outcrosses, line breeds or inbreds. With recessives, outcrossing allows for the recessive traits to migrate across a population. It may actually increase the number of individuals carrying a disease.
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Now the kick in the nuts..screwed if ya do and screwed if ya don't :p (see inbreeding depression)
OUTBREEDING DEPRESSION
In evolutionary biology, outbreeding depression refers to cases when offspring from crosses between individuals from different populations have lower fitness than progeny from crosses between individuals from the same population. This phenomenon can occur in two ways. First, selection in one population might produce a large body size, whereas in another population small body size might be more advantageous. Gene flow between these populations may lead to individuals with intermediate body sizes, which may not be adaptive in either population.
A second way outbreeding depression can occur is by the breakdown of biochemical or physiological compatibilities between genes in the different populations. Within local, isolated populations, alleles are selected for their positive, overall effects on the local genetic background. Due to nonadditive gene action, the same genes may have rather different average effects in different genetic backgrounds--hence, the potential evolution of locally coadapted gene complexes.
In other words, individuals from Population A will tend to have genes selected for the quality of combining well with gene combinations common in Population A. However, genes found in Population A will not have been selected for the quality of crossing well with genes common in Population B. Therefore outbreeding can undermine vitality by reducing positive epistasis and/or increasing negative epistasis.
However, it is critical to understand that reduced inbreeding depression in first generation hybrids can, in some circumstances, be strong enough to more than make up for outbreeding depression. This is why farmers keep purebred strains for the purpose of outcrossing (while not usually breeding the hybrids).
As a general rule of thumb, hybrid vigor (another way of saying a reduction of inbreeding depression) is strongest in first generation hybrids and gets weaker over time. In contrast, outbreeding depression can be relatively weak in the first generation. But outside the context of ruthless selective pressure, outbreeding depression will increase in power through the further generations as co-adapted gene complexes are broken apart without the forging of new co-adapted gene complexes to take their place.
It is important to keep in mind that these two mechanisms of outbreeding depression can be operating at the same time. However, determining which mechanism is more important in a particular population is very difficult.
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I will prolly start a new thread over this concept on over crossing and no selective pollenation.
BTW Heterosis=hybrid vigor ;)
Whats the difference?
(from the wiki)
"Genotype" is an organism's full hereditary information, even if not expressed.
"Phenotype" is an organism's actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.
The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype-phenotype map.
The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911.
Will post more later...