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Phenotypic plasticity is the ability of a genotype to express multiple phenotypes in accordance with different environments. Although variation in plasticity has been observed, there is limited knowledge on how this variation results from natural selection. This thesis analyses how variation in the level of plasticity influences light competition between plants and how this variation could result from selection, driven by light competition, in various environments. As an exemplary case of phenotypic plasticity, this thesis focusses on phenotypic responses of the annual rosette plant Arabidopsis thaliana (Brassicaceae) in response to the proximity of neighbour plants, as signalled through the red : far—red (R:FR) ratio, which are responses associated with the shade avoidance syndrome (SAS). Plant experiments were conducted to measure variation in these plastic responses and a functional-structural plant (FSP) model was created that simulates plant structures in 3D and includes these organ-level plastic responses while simulating explicitly a heterogeneous light environment. Simulating individual plants that explicitly compete for light, while their phenotype changes through plasticity, gave insights in the role of the level of phenotypic plasticity and site of signal perception on plant competitiveness. In addition, an analysis on how natural selection in different environments acts on the level of plasticity was performed by combining FSP simulations and evolutionary game theoretical (EGT) principles.

Projections on the impact of climate change on agricultural productivity foresee prolonged and/or increased stress intensities and enlargement of a significant number of pathogens habitats. This significantly raises the occurrence probability of (new) abiotic and biotic stress combinations. With stress tolerance research being mostly focused on responses to individual stresses, our understanding of plants’ ability to adapt to combined stresses is limited. In an attempt to bridge this knowledge gap, we hierarchized in chapter 1 existing information on individual abiotic or biotic stress adaptation mechanisms taking into consideration different anatomical, physiological and molecular layers of plant stress tolerance and defense. We identified potentially crucial regulatory intersections between abiotic and biotic stress signalling pathways following the pathogenesis timeline, and emphasized the importance of subcellular to whole plant level interactions by successfully dissecting the phenotypic response to combined stress. We considered both explicit and shared adaptive responses to abiotic and biotic stress, which included amongst others R-gene and systemic acquired resistance as well as reactive oxygen species (ROS), redox and hormone signalling, and proposed breeding targets and strategies. In chapter 3 we focused on salt stress and powdery mildew combination in tomato, a vegetable crop with a wealth of genetic resources, and started with a genetic study. S. habrochaites LYC4 was found to exhibit resistance to both salt stress and powdery mildew. A LYC4 introgression line (IL) population segregated for both salt stress tolerance and powdery mildew resistance. Introgressions contributing to salt tolerance, including Na+ and Cl- accumulation, and powdery mildew resistance were precisely pinpointed with the aid of SNP marker genotyping. Salt stress (100mM NaCl) combined with powdery mildew infection increased the susceptibility of the population to powdery mildew in an additive manner, while decreasing the phenotypic variation for this trait. Only a few overlapping QTLs for disease resistance and salt stress tolerance were identified (one on a short region at the top of Chromosome 9 where numerous receptor-like kinases reside). Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance indicating distinct genetic architectures. This enables genetic pyramiding approaches to build up combined stress tolerance. Considering that abiotic stress in nature can be of variable intensities, we evaluated selected ILs under combined stress with salinity ranging from mild to severe (50, 100 and 150mM NaCl) in chapter 4. Mild salt stress (50mM) increased powdery mildew susceptibility and was accompanied by accelerated cell death-like senescence. On the contrary, severe salt stress (150mM) reduced the disease symptoms and this correlated with leaf Na+ and Cl- content in the leaves. The effects of salt stress on powdery mildew resistance may be dependent on resistance type and mechanisms. Near Isogenic Lines (NILs) that carry different PM resistance genes (Ol-1 (associated with slow hypersensitivity response, HR), ol-2 (an mlo mutant associated with papilla formation) and Ol-4 (an R gene associated with fast HR) indeed exhibited differential responses to combined stress. NIL-Ol-1 resembled the LYC4 ILs response, while NIL-ol-2 and NIL-Ol-4 maintained robust resistance and exhibited no senescence symptoms across all combinations, despite the observed reduction in callose deposition in NIL-ol-2. Increased susceptibility, senescence and fitness cost of NIL-Ol-1 under combined stress coincided with high induction of ethylene and jasmonate biosynthesis and response pathways, highly induced expression of cell wall invertase LsLIN6, and a reduction in the expression of genes encoding for antioxidant enzymes. These observations underlined the significance of stress intensity and mechanism of resistance to the outcome of salt stress and powdery mildew combination, underscoring the involvement of ethylene signalling to the susceptibility response under combined stress. To examine the significance of hormone signalling in combined stress responses we evaluated crosses of tomato hormone mutants notabilis (ABA-deficient), defenseless1 (JA-deficient) and epinastic (ET overproducer) with NIL-Ol-1, NIL-ol-2 and NIL-Ol-4 in chapter 5. The highly pleiotropic epinastic mutant increased susceptibility of NIL-Ol-1, but decreased the senescence response under combined stress, and resulted in partial breakdown of NIL-ol-2 resistance, accompanied by reduced callose deposition. The effects of ET overproduction on susceptibility were more pronounced under combined stress. ABA deficiency in notabilis on the other hand greatly reduced susceptibility of NIL-Ol-1under combined stress at the expense of stronger growth reduction, and induced ROS overproduction. Partial resistance breakdown in the ol-2xnotabilis mutant accompanied by reduced callose deposition was observed, and this was restored under combined stress. Jasmonic acid deficiency phenotypic effects in defenseless mutants were subtle with modest increase in susceptibility for NIL-Ol-1 and NIL-ol-2. For NIL-ol-2 this increased susceptibility was reverted under combined stress. NIL-Ol-4 resistance remained robust across all mutant and treatment combinations. These results highlight the catalytic role of ET and ABA signalling on susceptibility and senescence under combined stress, accentuating concomitantly the importance of signalling fine tuning to minimize pleiotropic effects. The potential of exploiting transcription factors to enhance tolerance to multiple stress factors and their combination was investigated in chapter 6 through the identification and functional characterization of tomato homologues of AtWRKYs 11, 29, 48, 70 and 72. Thirteen tomato WRKY homologues were identified, of which 9 were overexpressed (using transformation with A. tumefaciens) and 12 stably silenced via RNAi in tomato cultivar Money Maker (MM). SlWRKY11-OE and SlWRKY23-OE overexpressors and RNAi lines of SlWRKY7 and SlWRKY9 showed both increased biomass and relative salt tolerance. SlWRKY6-OE exhibited the highest relative salt stress tolerance, but had strongly decreased growth under control conditions. Exceptional phenotypes under control conditions were observed for SlWRKY10-OE (stunted growth) and SlWRKY23-RNAi (necrotic symptoms). These phenotypes were significantly restored under salt stress, and accompanied by decreased ROS production. Both lines exhibited increased resistance to powdery mildew, but this resistance was compromised under salt stress combination, indicating that these genes have important functions at the intersection of abiotic and biotic stress adaptation. SlWRKY23 appears to have a key regulatory role in the control of abiotic stress/defense and cell death control. Experimental observations are critically discussed in the General Discussion with emphasis on potential distinctive responses in different pathosystems and abiotic and biotic stress resistance mechanisms as well as genetic manipulations for effectively achieving combined stress tolerance. This includes deployment of individual common regulators as well as pyramiding of non-(negatively) interacting components such as R-genes with abiotic stress resistance genes, and their translation potential for other abiotic and biotic stress combinations. Understanding and improving plant tolerance to stress combinations can greatly contribute to accelerating crop improvement towards sustained or even increased productivity under stress.

Projections on the impact of climate change on agricultural productivity foresee prolonged and/or increased stress intensities and enlargement of a significant number of pathogens habitats. This significantly raises the occurrence probability of (new) abiotic and biotic stress combinations. With stress tolerance research being mostly focused on responses to individual stresses, our understanding of plants’ ability to adapt to combined stresses is limited. In an attempt to bridge this knowledge gap, we hierarchized in chapter 1 existing information on individual abiotic or biotic stress adaptation mechanisms taking into consideration different anatomical, physiological and molecular layers of plant stress tolerance and defense. We identified potentially crucial regulatory intersections between abiotic and biotic stress signalling pathways following the pathogenesis timeline, and emphasized the importance of subcellular to whole plant level interactions by successfully dissecting the phenotypic response to combined stress. We considered both explicit and shared adaptive responses to abiotic and biotic stress, which included amongst others R-gene and systemic acquired resistance as well as reactive oxygen species (ROS), redox and hormone signalling, and proposed breeding targets and strategies. In chapter 3 we focused on salt stress and powdery mildew combination in tomato, a vegetable crop with a wealth of genetic resources, and started with a genetic study. S. habrochaites LYC4 was found to exhibit resistance to both salt stress and powdery mildew. A LYC4 introgression line (IL) population segregated for both salt stress tolerance and powdery mildew resistance. Introgressions contributing to salt tolerance, including Na+ and Cl- accumulation, and powdery mildew resistance were precisely pinpointed with the aid of SNP marker genotyping. Salt stress (100mM NaCl) combined with powdery mildew infection increased the susceptibility of the population to powdery mildew in an additive manner, while decreasing the phenotypic variation for this trait. Only a few overlapping QTLs for disease resistance and salt stress tolerance were identified (one on a short region at the top of Chromosome 9 where numerous receptor-like kinases reside). Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance indicating distinct genetic architectures. This enables genetic pyramiding approaches to build up combined stress tolerance. Considering that abiotic stress in nature can be of variable intensities, we evaluated selected ILs under combined stress with salinity ranging from mild to severe (50, 100 and 150mM NaCl) in chapter 4. Mild salt stress (50mM) increased powdery mildew susceptibility and was accompanied by accelerated cell death-like senescence. On the contrary, severe salt stress (150mM) reduced the disease symptoms and this correlated with leaf Na+ and Cl- content in the leaves. The effects of salt stress on powdery mildew resistance may be dependent on resistance type and mechanisms. Near Isogenic Lines (NILs) that carry different PM resistance genes (Ol-1 (associated with slow hypersensitivity response, HR), ol-2 (an mlo mutant associated with papilla formation) and Ol-4 (an R gene associated with fast HR) indeed exhibited differential responses to combined stress. NIL-Ol-1 resembled the LYC4 ILs response, while NIL-ol-2 and NIL-Ol-4 maintained robust resistance and exhibited no senescence symptoms across all combinations, despite the observed reduction in callose deposition in NIL-ol-2. Increased susceptibility, senescence and fitness cost of NIL-Ol-1 under combined stress coincided with high induction of ethylene and jasmonate biosynthesis and response pathways, highly induced expression of cell wall invertase LsLIN6, and a reduction in the expression of genes encoding for antioxidant enzymes. These observations underlined the significance of stress intensity and mechanism of resistance to the outcome of salt stress and powdery mildew combination, underscoring the involvement of ethylene signalling to the susceptibility response under combined stress. To examine the significance of hormone signalling in combined stress responses we evaluated crosses of tomato hormone mutants notabilis (ABA-deficient), defenseless1 (JA-deficient) and epinastic (ET overproducer) with NIL-Ol-1, NIL-ol-2 and NIL-Ol-4 in chapter 5. The highly pleiotropic epinastic mutant increased susceptibility of NIL-Ol-1, but decreased the senescence response under combined stress, and resulted in partial breakdown of NIL-ol-2 resistance, accompanied by reduced callose deposition. The effects of ET overproduction on susceptibility were more pronounced under combined stress. ABA deficiency in notabilis on the other hand greatly reduced susceptibility of NIL-Ol-1under combined stress at the expense of stronger growth reduction, and induced ROS overproduction. Partial resistance breakdown in the ol-2xnotabilis mutant accompanied by reduced callose deposition was observed, and this was restored under combined stress. Jasmonic acid deficiency phenotypic effects in defenseless mutants were subtle with modest increase in susceptibility for NIL-Ol-1 and NIL-ol-2. For NIL-ol-2 this increased susceptibility was reverted under combined stress. NIL-Ol-4 resistance remained robust across all mutant and treatment combinations. These results highlight the catalytic role of ET and ABA signalling on susceptibility and senescence under combined stress, accentuating concomitantly the importance of signalling fine tuning to minimize pleiotropic effects. The potential of exploiting transcription factors to enhance tolerance to multiple stress factors and their combination was investigated in chapter 6 through the identification and functional characterization of tomato homologues of AtWRKYs 11, 29, 48, 70 and 72. Thirteen tomato WRKY homologues were identified, of which 9 were overexpressed (using transformation with A. tumefaciens) and 12 stably silenced via RNAi in tomato cultivar Money Maker (MM). SlWRKY11-OE and SlWRKY23-OE overexpressors and RNAi lines of SlWRKY7 and SlWRKY9 showed both increased biomass and relative salt tolerance. SlWRKY6-OE exhibited the highest relative salt stress tolerance, but had strongly decreased growth under control conditions. Exceptional phenotypes under control conditions were observed for SlWRKY10-OE (stunted growth) and SlWRKY23-RNAi (necrotic symptoms). These phenotypes were significantly restored under salt stress, and accompanied by decreased ROS production. Both lines exhibited increased resistance to powdery mildew, but this resistance was compromised under salt stress combination, indicating that these genes have important functions at the intersection of abiotic and biotic stress adaptation. SlWRKY23 appears to have a key regulatory role in the control of abiotic stress/defense and cell death control. Experimental observations are critically discussed in the General Discussion with emphasis on potential distinctive responses in different pathosystems and abiotic and biotic stress resistance mechanisms as well as genetic manipulations for effectively achieving combined stress tolerance. This includes deployment of individual common regulators as well as pyramiding of non-(negatively) interacting components such as R-genes with abiotic stress resistance genes, and their translation potential for other abiotic and biotic stress combinations. Understanding and improving plant tolerance to stress combinations can greatly contribute to accelerating crop improvement towards sustained or even increased productivity under stress.

Over 30 million people in East Africa depend on East African highland bananas for food and income. The bananas are grown with limited additions of nutrients and no irrigation, despite widespread poor soil fertility and regular dry seasons. This thesis describes the effect of increasing rainfall and application of potassium and nitrogen fertilizers on banana growth and yields. In areas that receive less than 1100 mm of rainfall per year, additional rainfall increases yields by 65%. Application of potassium increases yields by 88%, while nitrogen is not required. A framework for computing banana growth and yield in response to the amount of water stored in the soil is described. Where the soil water storage capacity is low, mulching increases yields by 10% but it has no effect in areas where the soil water storage is high. This framework is envisaged to guide improvements in banana management and productivity in East Africa.

Over 30 million people in East Africa depend on East African highland bananas for food and income. The bananas are grown with limited additions of nutrients and no irrigation, despite widespread poor soil fertility and regular dry seasons. This thesis describes the effect of increasing rainfall and application of potassium and nitrogen fertilizers on banana growth and yields. In areas that receive less than 1100 mm of rainfall per year, additional rainfall increases yields by 65%. Application of potassium increases yields by 88%, while nitrogen is not required. A framework for computing banana growth and yield in response to the amount of water stored in the soil is described. Where the soil water storage capacity is low, mulching increases yields by 10% but it has no effect in areas where the soil water storage is high. This framework is envisaged to guide improvements in banana management and productivity in East Africa.

Sell-Kubiak, E. (2015). Non-genetic variance in pigs: genetic analysis of reproduction and production traits. PhD thesis, Wageningen University, The Netherlands The main objective of this thesis was to study the origin of random variance in reproduction and production traits of pigs. In pig breeding for many traits it is important not only to improve the reproduction and production trait itself, but also its variation. The variance of traits can be used to improve pigs’ productivity, and potentially also to improve uniformity of traits. Results presented in Chapters 2 and 3 show that the proposed approach to explore the origin of common litter variance was not successful. The impact of various sow features on growth rate and feed intake of grow-finish pigs was very small. More importantly, sow features did not explain the phenotypic variance due to common litter effects found in production traits of pigs. In Chapters 4 and 5 the residual variance of birth weight and litter size were found to have a genetic component. The genetic coefficient of variation at residual standard deviation level (GCVSDe) was proposed as a measure of expressing the potential response to selection (Chapter 4). For both traits the estimated GCVSDe was about 10%, indicating sufficient potential for response to selection. In Chapter 4 it was shown that analyzing variation in traits with Double Hierarchical Generalized Linear model (DHGLM) was highly comparable with the conventional analysis of standard deviation of a trait. The correlation between the additive genetic effects for birth weight and the residual variance was 0.6 (Chapter 4), whereas for litter size (TNB) and its residual variance (varTNB) this correlation was 0.5 (Chapter 5). Those moderate correlations are an important indication of the direction of correlated selection response in the mean of those traits. In Chapter 5 in a genome-wide association study for litter size variation, the significant SNPs explained 0.83% of total genetic variance in TNB and 1.44% in varTNB. The most significant SNP explained 0.4% of genetic variance in TNB (chromosome 11) and 0.5% in varTNB (chromosome 7). One of the possible candidate genes for varTNB on chromosome 7 is heat shock protein (HSPCB). Studying the residual variance of traits with DHGLM has a great potential to serve as an alternative to conventional analysis to study and to select for improved uniformity of various traits. Lastly, Chapter 6 focuses on discussion of the findings of this thesis and their overall importance for pig breeding, as well as highly relevant topics for breeding uniform and robust pigs (macro-micro sensitivity analysis and application of genomic selection).

Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.

Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.

Forty accessions, forming a core collection of mainly bush type of the common bean (Phaseolus vulgaris L.) germplasm in the Netherlands, were evaluated for 14 qualitative and quantitative traits at the Agricultural University, Wageningen (WAU), the Netherlands in 1992. These and an additional 117 Dutch accessions, mainly collected in private home gardens, were also evaluated for phaseolin seed protein pattern, and morphological and agronomic traits at the International Center for Tropical Agriculture (CIAT, Spanish acronym), Cali, Columbia between 1987 and 1997. Multivariate and principal component analyses at both WAU and CIAT indicated existence of one large group with no discernable patterns among Dutch common bean collections of landraces, garden forms and cultivars. However, when phaseolin, an evolutionary, biochemical marker, was used as an initial classification criterion followed by use of morphological markers, the two major gene pools; Andean and Middle American with two races in each (Chile and Nueva Granada in Andean, and Durango and Mesoamerica in Middle American) were identified

The first introduction of common bean from Central/South America into Western Europe most likely took place around 1500. The attractive bean seeds and their easy transportation warranted numerous additional introductions, not only from the Americas, but also from other areas where the common bean had been introduced. Bean seeds also must have been transported all over Europe both locally and internationally. Natural and human selection took place in and among introductions as well as in hybrid populations. Strong human selection may have led to pure garden forms which often occur in The Netherlands. In the period 1945–1948 a dry-bean collection of some 1500 accessions was made in The Netherlands. These have been classified into various criteria: 1. landraces, ‘primitive’ garden forms and cultivars, 2. (semi)climbing or bush types, 3. various seed colour types, including whitish, brownish, yellowish, black and variegated

This research presents the effect of the 10-year long civil war in Sierra Leone on rice genetic resources, using farmers and their seed systems in three selected districts as reference points. The war disrupted all forms of production and development in the country and like other sectors of the economy, agricultural production and the conservation of plant genetic resources at the farm level was severely affected. It emerged that farmers’ effectiveness to cultivate and manage their seed systems and the options to grow rice under insecure conditions were disrupted at different levels in the three districts studied. However, the general consequence of the war in all of the districts was that farmers lost considerable amounts of their seed stocks. Total losses for some rice varieties was averted because of the occurrence of a number of varieties in more than one village in the same region, which was a result of farmers seed exchange systems, and also due to farmer movement during the war. The majority of the varieties that were reported lost were actually “dispersed” in the regions, indicating good options for post-war recovery. There was little evidence that the genetic composition of rice varieties were significantly altered as a consequence of the war, except for the total loss of upland varieties in one of the districts. The varieties that had the highest survival were those that had wider pre-war distribution, showed plasticity in growing habits wherein they demonstrated the potential to grow in both agro-ecosystems and in the different districts, and the fact that they existed in many different forms. Statistical analysis showed a clear distinction between upland and lowland varieties, which demonstrated the effectiveness of farmer selection with regard to the two production ecosystems. This was different for the periods defined as pre-war and post-war. Pre-war varieties were less well defined in this respect. Further to this, there was evidence of a change in rice genetic resources between the pre-war and post-war situations, which was demonstrated in the number of varieties for each of the two ecosystems. Despite these changes, and the losses in seed stocks as a consequence of the war, genetic diversity increased in post-war rice varieties. AFLP results indicated that rice varieties in Sierra Leone possess different levels of intra-variety variation, which makes it difficult to identify homogenous genotypes at the seed unit level. This was attributed to genetic exchanges caused by farmers’ practices of growing different varieties in mixtures. The variation however does not alter the profile of inter-variety genetic differences, which remains large enough to distinguish one variety from the other. It demonstrates that the genetic composition of rice varieties remains distinct from one another, and that variety names in Sierra Leone are good indicators for genetic diversity of rice at the farm level.

Forty accessions, forming a core collection of mainly bush type of the common bean (Phaseolus vulgaris L.) germplasm in the Netherlands, were evaluated for 14 qualitative and quantitative traits at the Agricultural University, Wageningen (WAU), the Netherlands in 1992. These and an additional 117 Dutch accessions, mainly collected in private home gardens, were also evaluated for phaseolin seed protein pattern, and morphological and agronomic traits at the International Center for Tropical Agriculture (CIAT, Spanish acronym), Cali, Columbia between 1987 and 1997. Multivariate and principal component analyses at both WAU and CIAT indicated existence of one large group with no discernable patterns among Dutch common bean collections of landraces, garden forms and cultivars. However, when phaseolin, an evolutionary, biochemical marker, was used as an initial classification criterion followed by use of morphological markers, the two major gene pools; Andean and Middle American with two races in each (Chile and Nueva Granada in Andean, and Durango and Mesoamerica in Middle American) were identified

The first introduction of common bean from Central/South America into Western Europe most likely took place around 1500. The attractive bean seeds and their easy transportation warranted numerous additional introductions, not only from the Americas, but also from other areas where the common bean had been introduced. Bean seeds also must have been transported all over Europe both locally and internationally. Natural and human selection took place in and among introductions as well as in hybrid populations. Strong human selection may have led to pure garden forms which often occur in The Netherlands. In the period 1945–1948 a dry-bean collection of some 1500 accessions was made in The Netherlands. These have been classified into various criteria: 1. landraces, ‘primitive’ garden forms and cultivars, 2. (semi)climbing or bush types, 3. various seed colour types, including whitish, brownish, yellowish, black and variegated

A prevailing view in ecotoxicology is that toxicants affect organisms by impairing lifecycle traits that arc most sensitive to these toxicants, a concept also adopted by national and international legislative authorities for deriving safe standards for contaminants in soil and water. For example, a classic approach in toxicity testing is to quantify juvenile survival or reproduction, since these are often known to be the most sensitive traits with respect to toxicants. However, organisms can tolerate stressors such as toxicants by having plastic life-cycle traits thus enabling them to maintain population growth rate or fitness.The main objective was to test the classic premise on the most sensitive life-cycle trait by investigating toxicant-induced plasticity in life-cycle traits and fitness alterations.Using theoretical life-cycle models, Chapter 2 showed that the impact of toxicants on fitness was determined by its relationship with plastic responses in life-cycle traits and the life-history strategy. These results were compared with experimental observations using nematodes as a case study. The nematode Plectus acuminatus was selected for chronic life-cycle investigations in Chapter 3 on the basis of its moderate sensitivity to cadmium and pentachlorophenol. Chapter 4 presented a mathematical life-cycle model for P.acuminatus to estimate fitness reductions from plastic responses in life-cycle traits to cadmium. This model was used in Chapter 5 to evaluate the impact of critical effect concentrations (EC 20 ) for cadmium and pentachlorophenol on fitness. It was demonstrated that fitness in P.acuminatus was not determined by the most sensitive life-cycle trait.Moreover, less sensitive traits appeared to have a stronger impact on fitness. In addition it was found that P.acuminatus was able to maintain fitness due to plasticity in life-cyle traits when exposed to cadmium. Finally Chapter 6 explored the effect of copper onfitness in two nematode species with divergent life-history strategies ( P.acuminatus and Heterocephalobus pauciannulatus). From a toxicological point of view the reproductive period in P.acuminatus was 6 times more sensitive to copper than in H.pauciannulatus. However, the relationship between plasticity in the reproductive period and fitness showed that fitness was equally reduced in both species.The present findings agree with the theoretical results obtained in Chapter 2 and it can be concluded that the impact of toxicants on fitness depends on: 1) the plasticity of lifecycle traits to toxicants, 2) the relationship between the plastic responses in life-cycle traits to fitness and 3) the life-history strategy of the organism. These conclusions do not support the general premise in ecotoxicology that the impact of toxicants on organisms is determined by the most sensitive life-cycle trait. It is therefore advocated that future ecotoxicological research with other organisms should put more emphasis on the ability of species to adapt to toxic stress by having plastic life-cycle traits in order to enhance the predictive value of toxicity tests which provide the basis for ecological risk assessment procedures.

A prevailing view in ecotoxicology is that toxicants affect organisms by impairing lifecycle traits that arc most sensitive to these toxicants, a concept also adopted by national and international legislative authorities for deriving safe standards for contaminants in soil and water. For example, a classic approach in toxicity testing is to quantify juvenile survival or reproduction, since these are often known to be the most sensitive traits with respect to toxicants. However, organisms can tolerate stressors such as toxicants by having plastic life-cycle traits thus enabling them to maintain population growth rate or fitness.The main objective was to test the classic premise on the most sensitive life-cycle trait by investigating toxicant-induced plasticity in life-cycle traits and fitness alterations.Using theoretical life-cycle models, Chapter 2 showed that the impact of toxicants on fitness was determined by its relationship with plastic responses in life-cycle traits and the life-history strategy. These results were compared with experimental observations using nematodes as a case study. The nematode Plectus acuminatus was selected for chronic life-cycle investigations in Chapter 3 on the basis of its moderate sensitivity to cadmium and pentachlorophenol. Chapter 4 presented a mathematical life-cycle model for P.acuminatus to estimate fitness reductions from plastic responses in life-cycle traits to cadmium. This model was used in Chapter 5 to evaluate the impact of critical effect concentrations (EC 20 ) for cadmium and pentachlorophenol on fitness. It was demonstrated that fitness in P.acuminatus was not determined by the most sensitive life-cycle trait.Moreover, less sensitive traits appeared to have a stronger impact on fitness. In addition it was found that P.acuminatus was able to maintain fitness due to plasticity in life-cyle traits when exposed to cadmium. Finally Chapter 6 explored the effect of copper onfitness in two nematode species with divergent life-history strategies ( P.acuminatus and Heterocephalobus pauciannulatus). From a toxicological point of view the reproductive period in P.acuminatus was 6 times more sensitive to copper than in H.pauciannulatus. However, the relationship between plasticity in the reproductive period and fitness showed that fitness was equally reduced in both species.The present findings agree with the theoretical results obtained in Chapter 2 and it can be concluded that the impact of toxicants on fitness depends on: 1) the plasticity of lifecycle traits to toxicants, 2) the relationship between the plastic responses in life-cycle traits to fitness and 3) the life-history strategy of the organism. These conclusions do not support the general premise in ecotoxicology that the impact of toxicants on organisms is determined by the most sensitive life-cycle trait. It is therefore advocated that future ecotoxicological research with other organisms should put more emphasis on the ability of species to adapt to toxic stress by having plastic life-cycle traits in order to enhance the predictive value of toxicity tests which provide the basis for ecological risk assessment procedures.