Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Continuation and discontinuation of local institution in community based natural resource management

Currently the push toward frontier areas, which until twenty years ago were still largely untouched by commercial agriculture, is taking place on a massive scale. This push is being driven not the least by global economic developments, such as the price increase of agriculture commodities like coffee and cocoa. In most cases the indigenous communities become trapped between the state monopoly in natural resource management and the competition for resources by external actors. In this processes the indigenous communities start to lose their access to resources. Another victim in this process is the environment where the natural resources are imbedded. International and national organizations working to conserve environment have became conscious of the important role that indigenous people could fulfill as partners in this endeavour. This partnership in struggle has produced a new discourse on the relationship between indigenous people and their environment. As a further consequence, programs were set up to develop what became known as Community Based Natural Resource Management (CBNRM) with its numerous variations. Based on a case study in a village on the eastern border of the Lore Lindu National Park in Central Sulawesi, this study questioned the basic assumption behind the concept of Community Based Natural Resource Management (CBNRM). Namely the assumption that communities living at the margin of forest are socially and culturally homogenous, still more or less egalitarian, and basically living in harmony with their natural environment. This study was inspired by the persistent critique – although still a minority – on the basic assumption the CBNRM from academicians and practitioners working through the Entitlement perspective. Another inspiration was the mounting critique toward the participatory approach. In its effort the study explore further the usefulness of certain approaches. One of the approach much relied on in this study was the local history of the community studied, through exerting oral and local written documents on local history, legends and local stories. These sources proofed quite capable in bringing the local history into the light. Another was the actor oriented approach, which later came to be supported by the concept of Social Pool Resources. The latter concept proofed to be useful as analytical instrument to integrate social institutions and the common pool resources, as a field of action for the different actors as human agencies.

Genetic variation of and environmental effects on inducibility of resistance in tomatoes (Solanum lycopersicum L.) to Phytophthora infestans (Mont) de Bary

Many plant strengtheners are promoted for their supposed effects on nutrient uptake and/or resistance induction (IR). In addition, many organic fertilizers are supposed to enhance plant health and several studies have shown that tomatoes grown organically are more resistant to late blight, caused by Phytophthora infestans to tomatoes grown conventionally. Much is known about the mechanisms underlying IR. In contrast, there is no systematic knowledge about genetic variation for IR. Therefore, the following questions were addressed in the presented dissertation: (i) Is there genetic variation among tomato genotypes for inducibility of resistance to P. infestans? (ii) How do different PS compare with the chemical inducer BABA in their ability to IR? (iii) Does IR interact with the inducer used and different organic fertilizers? A varietal screening showed that contrary to the commonly held belief IR in tomatoes is genotype and isolate specific. These results indicate that it should be possible to select for inducibility of resistance in tomato breeding. However, isolate specificity also suggests that there could be pathogen adaptation. The three tested PS as well as two of the three tested organic fertilisers all induced resistance in the tomatoes. Depending on PS or BABA variety and isolate effects varied. In contrast, there were no variety and isolate specific effects of the fertilisers and no interactions with the PS and fertilisers. This suggests that the different PS should work independent of the soil substrate used. In contrast the results were markedly different when isolate mixtures were used for challenge inoculations. Plants were generally less susceptible to isolate mixtures than to single isolates. In addition, the effectiveness of the PS was greater and more similar to BABA when isolate mixtures were used. The fact that the different PS and BABA differed in their ability to induce resistance in different host genotype -pathogen isolate combinations puts the usefulness of IR as a breeding goal in question. This would result in varieties depending on specific inducers. The results with the isolate mixtures are highly relevant. On the one hand they increase the effectiveness of the resistance inducers. On the other hand, measures that increase the pathogen diversity such as the use of diversified host populations will also increase the overall resistance of the hosts. For organic tomato production the results indicate that it is possible to enhance the tomato growing system with respect to plant health management by using optimal fertilisers, plant strengtheners and any measures that increase system diversity.

Pesticide-handling practices of smallholder coffee farmers in Eastern Jamaica

Pesticide use among smallholder coffee producers in Jamaica has been associated with significant occupational health effects. Research on pesticide handling practices, however, has been scarce, especially in eastern Jamaica. This explorative study aims at filling this gap and provides a first basis to develop effective interventions to promote a safer pesticide use. A random sample of 81 coffee farmers was surveyed. The majority of farmers reported to suffer from at least one health symptom associated with pesticide handling, but safety practices were scarcely adopted. There was also the risk that other household members and the wider local community are exposed to pesticides. The lack of training on pesticide management, the role of health services and the cost for protective equipment seemed to be the most significant factors that influence current pesticide handling practices in eastern Jamaica. Further research is recommended to develop a systemic understanding of farmer’s behaviour to provide a more solid basis for the development of future intervention programmes.