User:Gbaor/Thoughts

• "When assessing the current situation of natural resources in their area, elders cited several problems that were not present, or were less severe, when they were young. These include: less rain, fewer water-catchment ponds and more contamination of the limited available water; diminished plant life, including fewer savannah trees; dramatically fewer wild animals; erosion; and lower soil fertility. They felt that the traditional indigenous knowledge system and communal efforts to manage resources had weakened."

• "In an effort to help ‘modernise’ the culture, outsiders did not recognise traditional leadership structures and did not deal with Karamojong leaders directly."

• "Elderly pastoralists recalled a clan of women, the Ngiyepan, who protected trees in various ways,... they were persuasive verbally and sometimes even physically. It is unclear why they are no longer active,... "

• "They perceived two more recent external innovations – automatic weapons and forced schooling ... The school system also led people to look outside of their own ‘culture-box’ for new answers to the same problems. Elders saw tradition and schooling as mutually exclusive options.
  In endogenous development, people seek a balance between modern and traditional practices.(e.g. ‘modern’ schooling with the traditional system)"

• "One potential bridge to this process is the institution of traditional healers.Because the Karamojong depend on cattle for both subsistence and cultural pride, one of the most important forms of indigenous knowle is ethnoveterinary knowledge ... This includes various different treatments: store-bought, homemade, prescribed and/or prepared by traditional healers, mainly from plant extracts."

• "participatory action research (PAR) approach and an ethnographic framework were used. PAR is ‘research which involves all relevant parties in actively examining together current action (which they experience as problematic) in order to change and improve it. PAR is not just research which is hoped will be followed by action. It is action which is researched, changed and re-researched, within the research process by participants’ (Wadsworth, 1998)"

• "A natural extension of ethnoveterinary knowledge in a damaged environment is medicinal plant agroforestry. ... high priority to multipurpose plants."

• "One component of ethnoveterinary knowledge preservation is documentation and conservation of the medicinal plants. ... Tree planting is not otherwise a part of Karamojong culture. The healers’ associations, however, now promote agroforestry and protection of medicinal plant species. Their agroforestry scheme has focused on domestication of 32 tree species, 24 of which are indigenous."

• "Many make thick fences from thornbush branches to protect crops from wild animals and raiders. ... These fencing plants are medicinal, fruit-producing and/or protective."

• "Dengel Lino, a livestock healer from Bokora: ‘We used to share food and knowledge only with our family, but now I feel comfortable sharing with other healers from Pian and Kenya. It has helped me with my cattle’. ... Peace has been an unintended consequence of these meetings, but is a critical component of development."

• "In the Karamoja culture, after two people have shared a meal, they are like kin and cannot harm one another. ... More peace leads to more sharing, and the virtuous cycle continues."

• "The healers’ associations decided to focus on agroforestry schemes and the prevention of endemic diseases (internal and external parasites), mainly of cattle."

• "The success may be due partly to the fact that it has been an endogenous movement (from within) rather than exogenous (initiated or led from outside). Since indigenous people have led the processes from day one, they have developed the skills and local capacity to continue without help from outside."

• Conservation of a breed is especially important for those breeds which are shown to have a large genetic distance to other breeds.
• Molecular biology
  • Keywords: restriction enzymes, restriction map, DNA cloning, plasmid, genomic library, cDNA library, polymerase chain reaction, human genome project, microsatelite
  • In the future, it will be increasingly difficult to find areas of animal health and production that are not substantially affected by this technology
  • Also sequencing of the genomes of parasites and pathogens will be important, in order to control these organisms.
  • Molecular biology techniques are creating a revolution in veterinary diagnosis, ... the tests can identify the presence of particular species/strains/serogroups of viruses, retroviruses, bacteria, fungi roundworms or tapeworms. They can distinguish between meat from different species of animals.
• Parentage testing and forensic research
  • Keywords: DNA typing, Hardy-Weinberg equilibrium, Linkage equilibrium
• Population substructure
  • Keywords: genetic differentiation, Wright's F statistics, fixation index, Wahlund principle
  • Genetic differentiation may result from natural selection favoring different genotypes in different subpopulations, but it may also result from random processes in the transmission of alleles from one generation to the next of from chance differences in allele frequency among the initial founders of the subpopulations.
  • Fixation index ... equals the reduction in heterozygosity expected with random mating at any one level of population hierarchy relative to another ... it allows an objective comparison of the overall effect of population substructure.
  • In population genetics, a race is a group of organisms in a species that are generally more similar to each other than they are to the members of other such groups.
  • Isolate breaking (Wahlund principle)...(i.e. reduction of homozygosity) - Fusion of subpopulations with random mating and Hardy-Weinberg equilibrium decreases the average frequency of homozygous recessives by an amount equal to the variance in allele frequency among the original subpopulations.
• Interval mapping of QTL
  • Keywords: genetic marker, quantitative trait loci, interval mapping,
  • Mapping of a QTL requires the usage of multiple marker genotypes in the analysis.
  • Interval mapping - term is used for estimating the position of a QTL within two markers (often indicated as "marker-bracket"). Interval mapping is originally based on the maximum likehood, but there are also good approximations with simple regression.
  • Regression on QTL probability - For a given haplotype that was inherited from the sire, we can calculate the probability for having inherited the Q or the q allele It seems therefore natural to regress phenotype on Q-probability. The model is (standard): y=μ+αx where y is the observed phenotype, x is the probability of having inherited a paternal Q, given the observed marker genotype

Stopped at 5-10 - put aside, more background knowledge needed

Full title: Genomic selection : marker assisted selection on a genome wide scale (Editorial by Theo. Meuwissen)

• Genomic selection (GS) may be defined as the simultaneous selection for many (tens or hundreds of thousands of) markers, which cover the entire genome in a dense manner so that all genes are expected to be in linkage disequilibrium with at least some of the markers.
• A variety of methods have been suggested for the calculation of GS-estimated breeding values (EBV), ranging from BLUP (Kolbehdari et al.), Bayesian methods such as BayesB (Meuwissen et al., Genetics 157:1819–1829), and machine learning techniques (Long et al.). These methods differ in their assumptions about the underlying genetic model. ... The method that reflects the biological nature of the gene effects closest is expected to yield the most accurate GS-EBV. Thus, more research into the distribution of gene effects is warranted.
• Traditional selection is successfully improving a large number of traits in ongoing breeding schemes, but it requires widespread (all selection candidates), reasonably accurate and preferably early in life recording of the traits. Especially, functional traits only partially fulfill these requirements, and their rates of genetic gain are therefore much lower than that of production traits. As mentioned in several of the papers, GS may overcome these problems, although Calus and Veerkamp found substantially reduced accuracies of GS-EBV for lowly heritable traits.
• As GS has the potential to achieve a more balanced selection response (balanced over production and functional traits), and substantially reduced inbreeding rates (Daetwyler et al.), its main effect on future breeding schemes may be an increased sustainability.

Full title: Genomic selection

• The ideal method to estimate the breeding value from genomic data is to calculate the conditional mean of the breeding value given the genotype of the animal at each QTL. This conditional mean can only be calculated by using a prior distribution of QTL effects so this should be part of the research carried out to implement genomic selection.
• Meuwissen et al. (2001) proposed a variant of MAS that they called genomic selection. The key features of this method are that markers covering the whole genome are used so that potentially all the genetic variance is explained by the markers; and the markers are assumed to be in LD with the QTL so that the number of effects per QTL to be estimated is small. Using simulation, they showed that the breeding value could be predicted with an accuracy of 0.85 from marker data alone.
• Statistical analysis to calculate EBV from genome-wide DNA markers It is convenient to think of the process in three steps: 1. Use the markers to deduce the genotype of each animal at each QTL. 2. Estimate the effects of each QTL genotype on the trait. 3. Sum all the QTL effects for selection candidates to obtain their genomic EBV (GEBV).
• An advantage of using the correct prior is that the estimates of the biggest or most significant QTL are not overestimated. This means that the effects can be estimated from all available data regardless of whether the data was part of that used to discover the QTL or not.
• The requirements to implement genomic selection in breeding programmes are relatively simple. Generally there will be a discovery dataset where a large number of SNP have been assayed on a moderate number of animals who have phenotypes for all the relevant traits. A prediction equation that uses markers as input and predicts BV is derived from this data. There should then be a validation sample ... The prediction equation is tested to assess its accuracy on this independent sample.
• ...the estimation of QTL effects can be carried out on animals that are completely separate from the selection candidates. In fact the selection candidates do not need to have phenotypes recorded at all.
• Interbull provides EBV that compare bulls from around the world. This situation is favorable to livestock producers but is threatened by genomic selection. Unless all genomic EBV are calculated using the same prediction equation(s), they will no longer be comparable.
• [Database held by organizations responsible for national genetic evaluation] ... this may inhibit commercialization of genomic selection because it makes it difficult for a company to recover the investment needed to develop and market a set of markers for genomic selection. The alternative would be for each company to have its own markers, database and EBV. How the future will unfold is not clear.
• Genomic selection has the potential to radically alter the structure of livestock breeding programmes. ... formal progeny testing will disappear ... [it could] potentially cut the cost of operating dairy breeding companies by 92% (Schaeffer 2006). More generally, genomic selection will cause a tendency to shorten generation intervals because the markers can be genotyped at birth or even before.
• Except for the cost of genotyping, "stud" animals could be produced as cheaply as commercial animals. Then traditional stud breeders who record their animals with a breed association would be unable to compete with breeders who relied entirely on marker data.
• Genomic selection means that all selection candidates can be evaluated for any environment for which the prediction equation is known. Consequently, many divergent populations, each specialized to a particular environment, are likely to be replaced by one general purpose population with a decrease in the total effective population size. [Is this an advantage or disadvantage? Decreased effective population size should mean loss of genetic diversity...]

Full title: Prediction of response to marker-assisted and genomic selection using selection index theory

Path coefficient diagram illustrating the relationships among components contributing to phenotype with marker-assisted selection for a single trait [changed a little due to technical difficulties]:

Where: P, phenotype; G, total genetic value; E, environmental component of P; Q, component of G that is associated with markers; R, component of G that is independent of markers; Q^, estimated breeding value (EBV) for Q based on marker data; e, prediction error of Q^; h₂, heritability of P; q₂, proportion of genetic variance associated with markers; r_Q', accuracy of Q^ as a predictor of Q;

Stopped at: p. 334 - Extension to multiple traits