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Chrysanthemum morifolium Ramat. (2n=6x=54) is an hexaploid ornamental crop that is thought to be originating from up to 10 wild species in the domestication process. Although it has an expected allopolyploid origin, segregation tested in populations mainly showed a random segregation. To make a start in understanding the complex nature of the hexaploid genome and the use of genomics for breeding, diploid wild species genomes provide a valuable resource. The completion of the de novo genome assemblies of both C. makinoi and C. seticuspe allowed us to look at the synteny between the two species and compared it also to genomes of other Asteraceae. Using resequencing data of other wild species and a hexaploid cultivar provided a first attempt to test the presence of signals from the wild species in the hexaploid gene pool.

In the study, we used an advanced BC3S6 line (and its selfing) originating from a cross between S. arcanum LA2157 and the tomato cv. Moneymaker. Plants in the line were inoculated with Clavibacter michiganensis strain NCPP382. Based on symptom development plants were categorized as susceptible (S) or resistant/tolerant (R). Whole-genome sequencing (WGS) of a susceptible and a resistant pool of 14 plants each was done to identify loci involved in the observed phenotypes. Genomic DNA of plants was extracted from leaves. For each bulk, 28.57 ng of gDNA of each individual were pooled. For the WGS , 400 ng of (pooled) gDNA were used for the library preparation and sequencing. Sequencing was done on an Illumina Novaseq 6000 platform producing 151 bp paired end reads at a 35x depth (Novogene Europe, Cambridge, United Kingdom)., In the study, we used an advanced BC3S6 line (and its selfing) originating from a cross between S. arcanum LA2157 and the tomato cv. Moneymaker. Plants in the line were inoculated with Clavibacter michiganensis strain NCPP382. Based on symptom development plants were categorized as susceptible (S) or resistant/tolerant (R). Whole-genome sequencing (WGS) of a susceptible and a resistant pool of 14 plants each was done to identify loci involved in the observed phenotypes. Genomic DNA of plants was extracted from leaves. For each bulk, 28.57 ng of gDNA of each individual were pooled. For the WGS , 400 ng of (pooled) gDNA were used for the library preparation and sequencing. Sequencing was done on an Illumina Novaseq 6000 platform producing 151 bp paired end reads at a 35x depth (Novogene Europe, Cambridge, United Kingdom).

Climate change seriously impacts global agriculture, with rising temperatures directly affecting the yield. Vegetables are an essential part of daily human consumption and thus have importance among all agricultural crops. The human population is increasing daily, so there is a need for alternative ways which can be helpful in maximizing the harvestable yield of vegetables. The increase in temperature directly affects the plants’ biochemical and molecular processes; having a significant impact on quality and yield. Breeding for climate-resilient crops with good yields takes a long time and lots of breeding efforts. However, with the advent of new omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, the efficiency and efficacy of unearthing information on pathways associated with high-temperature stress resilience has improved in many of the vegetable crops. Besides omics, the use of genomics-assisted breeding and new breeding approaches such as gene editing and speed breeding allow creation of modern vegetable cultivars that are more resilient to high temperatures. Collectively, these approaches will shorten the time to create and release novel vegetable varieties to meet growing demands for productivity and quality. This review discusses the effects of heat stress on vegetables and highlights recent research with a focus on how omics and genome editing can produce temperature-resilient vegetables more efficiently and faster.

Clavibacter michiganensis (Cm) is a tomato phytopathogenic bacterium. Outbreaks of Cm can result in severe yield and economic losses. To date, no resistance to Cm has been identified. Screening of wild tomato accessions has resulted in the identification of several sources of tolerance to Cm. The genetic background of tolerance provided by these sources is polygenic and complex. Previous results from advanced lines of a cross between Solanum arcanum LA2157 and S. lycopersicum showed that introgression lines carrying a locus of S. arcanum LA2157 on chromosome 7 had high levels of tolerance to Cm. We set out to functionally characterize this locus, in an effort to identify the gene(s) underlying the observed tolerance. Testing of near isogenic lines (NILs) containing a fixed LA2157 introgression on chromosome 7 did not lead to the expected results, as high susceptibility was observed in some NILs homozygous for the S. arcanum LA2157 allele. Therefore, we employed whole genome sequencing in combination with a bulk segregant analysis to identify loci involved in the observed tolerant phenotype. Our results suggest that two additional loci on chromosomes 2 and 4 together with the locus on chromosome 7 are required for tolerance to Cm., Clavibacter michiganensis (Cm) is a tomato phytopathogenic bacterium. Outbreaks of Cm can result in severe yield and economic losses. To date, no resistance to Cm has been identified. Screening of wild tomato accessions has resulted in the identification of several sources of tolerance to Cm. The genetic background of tolerance provided by these sources is polygenic and complex. Previous results from advanced lines of a cross between Solanum arcanum LA2157 and S. lycopersicum showed that introgression lines carrying a locus of S. arcanum LA2157 on chromosome 7 had high levels of tolerance to Cm. We set out to functionally characterize this locus, in an effort to identify the gene(s) underlying the observed tolerance. Testing of near isogenic lines (NILs) containing a fixed LA2157 introgression on chromosome 7 did not lead to the expected results, as high susceptibility was observed in some NILs homozygous for the S. arcanum LA2157 allele. Therefore, we employed whole genome sequencing in combination with a bulk segregant analysis to identify loci involved in the observed tolerant phenotype. Our results suggest that two additional loci on chromosomes 2 and 4 together with the locus on chromosome 7 are required for tolerance to Cm.

Background: Genetic diversity is crucial for the success of plant breeding programs and core collections are important resources to capture this diversity. Many core collections have already been constructed by gene banks, whose main goal is to obtain a panel of a limited number of genotypes to simplify management practices and to improve shareability while retaining as much diversity as possible. However, as gene banks have a different composition and goal than plant breeding programs, constructing a core collection for a plant breeding program should consider different aspects. Results: In this study, we present a novel approach for constructing a core collection by integrating both genomic and pedigree information to maximize the representation of the breeding germplasm in a minimum subset of genotypes while accounting for future genetic variation within a strawberry breeding program. Our stepwise approach starts with selecting the most important crossing parents of advanced selections and genotypes included for specific traits, to represent also future genetic variation. We then use pedigree-genomic-based relationship coefficients combined with the ‘accession to nearest entry’ criterion to complement the core collection and maximize its representativeness of the current breeding program. Combined pedigree-genomic-based relationship coefficients allow for accurate relationship estimation without the need to genotype every individual in the breeding program. Conclusions: This stepwise construction of a core collection in a strawberry breeding program can be applied in other plant breeding programs to construct core collections for various purposes.

Hyperhydricity is a physiological anomaly that significantly affects the growth and proliferation rate of crops cultivated by tissue culture techniques. To better understand the mechanisms that govern hyperhydricity incidence, we examined the effects of several media components, particularly cytokinin and gelling agents. These elements were found to be influential in both in vitro propagation and the development of hyperhydricity. Our study revealed that Arabidopsis thaliana seedlings had a greater manifestation of hyperhydricity symptoms when exposed to high cytokinin concentrations compared with the control. The presence of gelrite led to the manifestation of hyperhydric symptoms by elevated water build-up in the apoplast. The phenomenon of stomata closure was observed in the hyperhydric leaves, resulting in an increased ability to retain water and a decrease in the transpiration rates when compared to their respective control leaves. Additionally, histological examinations of the cross sections of hyperhydric leaves revealed an irregular cellular arrangement and large intercellular spaces. Furthermore, hyperhydric seedlings displayed impaired cuticular development in comparison to their normal seedlings.

COGEM has commissioned a research project to obtain insight in the possibilities that gene-editing may offer for the development of abiotic stress tolerant crops. Genetically modified abiotic stress tolerant crops were also included in the research project. The project was carried out by Wageningen University & Research and Wageningen Food Safety Research.The results indicate that most of the effort is put into obtaining drought tolerant crops, followed by crops tolerant to salinity or heat. Worldwide there are a few genetically modified abiotic stress tolerant crops that have been authorised for cultivation. Several genetically modified abiotic stress tolerant crops have been tested in the field.There are only a few examples of gene edited abiotic stress tolerant crops. Results from extensive field testing with these gene edited crops have not been published yet.According to the researchers abiotic stress tolerant crops could be developed faster and more efficient using gene editing. With gene editing gene expression may be changed in a more subtle way, which might allow the development of crops that only express the genes which confer abiotic stress tolerance under stressful conditions. In addition, gene editing may be used to change several genes simultaneously, which may allow signaling routes that play a role in abiotic stress tolerance to be altered in a more balanced way thereby reducing the occurrence of unwanted negative side effects.

In all fruit and vegetable crops, reduction in quality during postharvest storage leads to substantial losses of primary production with enormous economic consequences. Also in tomato, fruit shelf-life is an important quality trait. In this study a collection of tomato accessions, consisting of 92 S. lycopersicum landraces and old cultivars and several S. pimpinellifolium accessions, was phenotyped for several shelf-life parameters and biochemical characterization was performed during the postharvest shelf-life of fruit from selected accessions. This collection was selected based on available genotypic data and represents the genetic diversity present in the EU–SOL tomato core collection (Roohanitaziani, 2020). The core collection was grown in a greenhouse, and fruit were harvested at the breaker-turning stage and stored in a controlled climate chamber for 42 d at 18 ⁰C. The shelf-life attributes firmness loss, weight loss, as well as color pigments, were measured once a week and evaluated over time. All three shelf-life-related parameters varied markedly among accessions, resulting in fruit with different shelf-life. The most promising accessions of the first screen were re-grown and analyzed to validate the initial results and six accessions with contrasting shelf-life were selected for metabolite analysis. Fruit were harvested at the breaker stage and stored for 35 d at 18 ⁰C. Samples were taken at weekly intervals and analyzed for volatile compounds, primary metabolites and cell wall polysaccharide monomers. During storage long and short shelf-life accessions showed considerable differences in their content of sugars, such as galactose and polyamines, such as putrescine in their pericarp. The content of three cell wall sugars, galactose, arabinose and galacturonic acid, underwent considerable changes during postharvest storage. The short shelf-life accessions contained a higher amount of arabinose and galactose in their cell wall than other accessions which is i

Plants have evolved complex defence mechanisms to avoid invasion of potentialpathogens. Despite this, adapted pathogens deploy effector proteins to manipulate host susceptibility (S) genes, rendering plant defences ineffective. Theidentification and mutation of plant S genes exploited by bacterial pathogensare important for the generation of crops with durable and broad-spectrumresistance. Application of mutant S genes in the breeding of resistant crops islimited because of potential pleiotropy. New genome editing techniques openup new possibilities for the modification of S genes. In this review, we focuson S genes manipulated by bacteria and propose ways for their identificationand precise modification. Finally, we propose that genes coding for transporterproteins represent a new group of S genes.

Powdery mildew (PM) is one of the most common plant diseases in the world, occurring in many economically important food and ornamental crops. The characteristic symptoms of this disease are easily recognizable as a white powder that extends across the aerial parts of the plants. The causal pathogens of PM are obligate biotrophic fungi from the Erysiphales order that obtain nutrients from the living tissue of their hosts. To this day, chemical control of PM remains a common practice in many crops. However, the use of fungicides has a negative impact on the environment. For this reason, breeding for resistant varieties stands out as an essential tool to achieve a sustainable management of this disease.In tomato, PM is caused by Oidium neolycopersici (On), a polyphagous fungal species that threatens the production of this crop worldwide. The current understanding of this disease and the mechanisms through which plants are able to withstand it comes from the research done in two pathosystems. On the one hand, in the late 1980’s, an outbreak of On in cultivated tomato in Europe urged researchers to find natural sources of resistance to this disease. This drove the research on the identification of Resistance (R) loci in wild relatives of tomato. On the other hand, On can also infect the model plant Arabidopsis thaliana (Arabidopsis). This model organism offers many advantages for research due to the availability of a large number of scientific resources and information. Apart from On, Arabidopsis is a host for three more PM species. Hence, the Arabidopsis-PM pathosystems have been widely used to identify genetic components of resistance and susceptibility. These latter components are particularly interesting, as they seem to be conserved for several species of PMs and can potentially be extrapolated to other plant species. The plant genes whose absence results in the inability of the pathogen to complete their life cycles, are named Susceptibility (S) genes. The use of

Genotyping by high throughput sequencing of mRNA from five different cultivars of Tulip

The increasing nutritional demands of the world as well as the need for crops that perform reliably, in spite of diverse environmental conditions (abiotic and biotic stresses and variable weather conditions), put the plant sciences at the forefront of domains where progress is urgently needed. To be able to do so, plant phenotyping and genotyping are extremely important. Especially in plant phenotyping, research is met with challenges related to poor data management, and thereby inefficient exploitation - let alone reuse of datasets. The challenges to phenotypic data reuse and integration arise due to the highly distributed nature of data in the domain (as there are no central plant phenotypic data repositories) and their multifaceted heterogeneity. The variety of experimental goals and the sheer number of species studied may necessitate different approaches (e.g. for crops, model organisms, forest trees). Experiments may be conducted in open fields, greenhouses or other locations, follow different designs and produce different types of data (e.g. visual observation of a score, images, manual and automatic measurements, molecular assays). Even when everything else matches, the data files produced may have different formats and structures, which is a challenge for data integration. Moreover, good data documentation practices are often lacking, which hinders interpretation and reuse. In the vast majority of cases, plant phenotyping datasets are used only once, solely to address the research question for which they were originally generated. It is the exception, rather than the rule, when different datasets, produced by different, uncoordinated parties, are analyzed to generate further knowledge. Even rarer, though much more useful, are cases where independently created datasets are integrated for the purpose of meta-analyses or improvement of statistical and predictive models. Such work is crucial, for example, for multi-environment studies investigating the adaptabil

Soil salinization is a serious threat to agriculture, jeopardizing global food security and causing huge economic losses every year. Plants face formidable challenges when growing under saline conditions. The high concentration of ions in the root environment hampers water uptake, yet the accumulation of ions in plant tissues induces cytotoxicity. Unfortunately, soil salinization is likely to increase in the context of climate change, which lead to sea level rising and shortage of fresh-water sources. Hence, crop production might rely on irrigation with brackish/ saline water. In addition, the increasing global food demand calls for cultivation in less favourable soils including saline deltas around the world. Improvement of salt tolerance of existing crops might not be sufficient under increasing salinization, so the exploration of new, more salt tolerant crops appears to be essential to ensure food supply. Chenopodium quinoa is -at least outside S. America- a relatively new crop that has gained ground due to its resilience to withstand abiotic stress, especially soil salinity. Quinoa can potentially contribute to ensure food security and it has a healthy balance of proteins with all the essential amino acids, carbohydrates (starch), fibre and seed oil. In this thesis novel insights on the mechanisms and processes that underlie the remarkable salt tolerance of quinoa are provided and traits that may be used to improve crop salt tolerance are described.In Chapter 2 we evaluate responses of quinoa varieties to long-term salinity (0- 400 mM NaCl) with respect to growth and ion homeostasis. We found that salinity reduced the seed yield of the varieties (grown as spaced plants in the greenhouse) by on average 29 % at 100 mM NaCl and up to 88 % at 400 mM NaCl. We observed that quinoa varieties utilise salt exclusion strategies to produce relatively high yields under mild salinity or short-term stress, while tissue tolerance mechanisms enable the plants to survive and eve

Many tobacco (Nicotiana tabacum) cultivars are salt-tolerant and thus are potential model plants to study the mechanisms of salt stress tolerance. The CALCINEURIN B-LIKE PROTEIN (CBL) is a vital family of plant calcium sensor proteins that can transmit Ca2+ signals triggered by environmental stimuli including salt stress. Therefore, assessing the potential of NtCBL for genetic improvement of salt stress is valuable. In our studies on NtCBL members, constitutive overexpression of NtCBL5A was found to cause salt supersensitivity with necrotic lesions on leaves. NtCBL5A-overexpressing (OE) leaves tended to curl and accumulated high levels of reactive oxygen species (ROS) under salt stress. The supersensitivity of NtCBL5A-OE leaves was specifically induced by Na+, but not by Cl−, osmotic stress, or drought stress. Ion content measurements indicated that NtCBL5A-OE leaves showed sensitivity to the Na+ accumulation levels that wild-type leaves could tolerate. Furthermore, transcriptome profiling showed that many immune response-related genes are significantly upregulated and photosynthetic machinery-related genes are significantly downregulated in salt-stressed NtCBL5A-OE leaves. In addition, the expression of several cation homeostasis-related genes was also affected in salt-stressed NtCBL5A-OE leaves. In conclusion, the constitutive overexpression of NtCBL5A interferes with the normal salt stress response of tobacco plants and leads to Na+-dependent leaf necrosis by enhancing the sensitivity of transgenic leaves to Na+. This Na+ sensitivity of NtCBL5A-OE leaves might result from the abnormal Na+ compartmentalization, plant photosynthesis, and plant immune response triggered by the constitutive overexpression of NtCBL5A. Identifying genes and pathways involved in this unusual salt stress response can provide new insights into the salt stress response of tobacco plants., Frontiers in Plant Science

The button mushroom Agaricus bisporus is represented mainly by two varieties, a secondarily homothallic variety with predominantly two heterokaryotic spores per basidia and a heterothallic variety with predominantly four homokaryotic spored basidium. Both varieties also differ in their recombination landscape with the former showing crossovers (CO) predominantly at chromosome ends whereas the latter has a more evenly distribution of CO over the chromosomes. The two varieties are compatible, and this has been used to study segregation of the basidial spore number (BSN) and the genomic positions of recombination, i.e., the CO landscape, in order to find the underlying genetic determinants. Knowledge on genes controlling CO positions might facilitate either the conservation of favorable allele combinations or the disruption of unwanted allele combinations to reduce linkage drag. For BSN, in total seven QTL were found with the major QTL on chromosome 1 explaining ca. 55% of the phenotypic variation. It appeared, however, difficult to map the recombination landscape. This phenotype can only be assessed in the meiotic offspring of an intervarietal hybrid which is a laborious and difficult task. Nevertheless, this was done, and we were able to map three QTLs for this trait, two on chromosome 1 and one on chromosome 2 not overlapping with the QTL for BSN. The hurdles encountered are discussed and a new strategy is proposed that can solves these. We propose to use two genetically unrelated mapping populations both offspring of a cross between a var. bisporus and a var. burnettii homokaryon and thus segregating both for CO and BSN. Homokaryotic offspring of both populations can be intercrossed without limitation of mating incompatibility and marker homozygosity and the hybrid mushrooms directly used to map BSN. Homokaryotic offspring of these hybrid mushrooms can be genotypes to assess CO positions using next generation sequencing technologies that will solve marker problems, Frontiers in Fungal biology

MotivationThe investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement.ResultsHere, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed., Bioinformatics

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Ingestion of gluten proteins (gliadins and glutenins) from wheat, barley and rye can cause coeliac disease (CD) in genetically predisposed individuals. The only remedy is a strict and lifelong gluten-free diet. There is a growing desire for coeliac-safe, whole-grain wheat-based products, as consumption of whole-grain foods reduces the risk of chronic diseases. However, due to the large number of gluten genes and the complexity of the wheat genome, wheat that is coeliac-safe but retains baking quality cannot be produced by conventional breeding alone. CD is triggered by immunogenic epitopes, notably those present in α-, γ-, and ω-gliadins. RNA interference (RNAi) silencing has been used to down-regulate gliadin families. Recently, targeted gene editing using CRISPR/Cas9 has been applied to gliadins. These methods produce offspring with silenced, deleted, and/or edited gliadins, that overall may reduce the exposure of patients to CD epitopes. Here we review methods to efficiently screen and select the lines from gliadin gene editing programs for CD epitopes at the DNA and protein level, for baking quality, and ultimately in clinical trials. The application of gene editing for the production of coeliac-safe wheat is further considered within the context of food production and in view of current national and international regulatory frameworks.

We discuss options to reform the EU genetically modified organisms (GMO) regulatory framework, make risk assessment and decision-making more consistent with scientific principles, and lay the groundwork for international coherence. The first in a three-part series, this article focuses on reform options related to the scope of the legislation and the GMO definition.

On a global scale, potato is an important crop for both consumption and the starch industry. At present, the starch industry is keen to create economic value and to reduce its impact on the environment by valorising all resources in potatoes. One way to contribute towards this goal is to develop new potato varieties with elite traits, i.e. a high level of tuber protein content and a reduced level of fibre hydration. Improving these traits is however challenging due to their complex nature. Therefore, a better understanding of the genetics and biological processes underlying tuber protein content and fibre hydration are relevant. The objectives of this study were to shed light on the genetic and molecular architectures of tuber protein content and fibre hydration and to pinpoint key factors (i.e. biological processes, molecular structures, genes and alleles) that are involved in modulation of these traits.Chapter 1 provides a description of the potato crop and the starch industry. We present protein and fibre as key resources, where improvement of their quantity and quality will lead to a better valorisation of the potato crop. The principles of potato genetics, potato breeding and modern tools for trait improvement are described.In Chapter 2 we studied the genetics of tuber protein content in a panel of tetraploid potato varieties. We estimated a moderate level of trait heritability, identified marker-trait associations (QTLs), haplotypes and candidate genes. Our findings showed that alleles of StCDF1 were associated with tuber protein content. The results provide resources for genomics-enabled breeding.In Chapter 3 we performed a multi-allelic QTL analysis of tuber protein content in a large bi-parental population of tetraploid potato. We estimated a moderate level of trait heritability and identified QTLs. The alleles underlying the QTLs provided both positive and negative effects on the level of tuber protein content. Our results showed that tuber protein content

Potato wart disease, caused by the obligate biotrophic Chytrid fungus Synchytrium endobioticum, is one of the most important quarantine diseases of potato. This disease was named after the symptoms caused by the pathogen, which are the proliferation of meristematic tissues leading to the formation of warts, mainly on the below-ground sprouts of potato plants. The quarantine status of S. endobioticum is due to the production of spores that can remain viable in the soil for more than 40 years, the lack of chemical control and the severe yield losses. In Europe, more than 40 different pathotypes of S. endobioticum have been recorded and only resistance to pathotype 1 is commonly deployed in the breeding germplasm. The breeding and cultivation of potato varieties resistant to a wider spectrum of pathotypes is crucial for quarantine practice to reduce the propagation of the pathogen. Therefore, the identification of genes bringing resistance to the most frequent pathotypes of the pathogen and the development of diagnostic markers for marker assisted selection (MAS) is urgently needed.In this thesis, genes involved in resistance to pathotypes 1, 2, 6 and 18 of S. endobioticum were identified to make an inventory of the different resistance sources at hand for potato breeders. In Chapter 2, we investigated the distribution of the pathotype 1 resistance in a variety panel representative of the potato breeding material. Breeding programs of the 20th century were very successful in producing varieties resistant to pathotype 1 as 77% of the panel varieties were found to be resistant. To identify markers linked with pathotype 1 resistance, we used previously produced genotypic and phenotypic data to perform a Genome-Wide Association Study (GWAS). The GWAS resulted in the identification of markers associated with pathotype 1 resistance on the north arm of chromosome 11. In this region, the major effect gene Sen1 was previously identified. Sen1 is the main source of pathotype 1 r

Tomato is one of the most important vegetable crops in the world. The Netherlands, despite of its relatively small land area, is a leading player in producing and exporting tomato at a global scale. Due to the temperate climate in the Netherlands, the cultivation of tomato, as well as other major vegetables such as sweet pepper and cucumber, is mostly done in greenhouses. In this manner, the growth conditions, such as temperature, lighting, CO2 enrichment, humidity, can be maintained optimally in order to maximize yield of harvestable parts of the crops, i.e. fruits in this case. This type of cultivation in temperate climate areas requires very much energy, mainly for heating which take up 20 – 30% of the total production costs. This high energy consumption for cultivation is deemed to have also a high impact on the environment. Therefore, many efforts have been put into finding solutions to decrease the energy consumption in the greenhouse horticultural sector. For instance, several companies and research institutes have been looking into ways to make novel building materials, optimize light types and intensities to improve photosynthesis efficiency, develop new greenhouse architectures that can become energy-neutral in the future. In this thesis, we looked into the biological side of this issue, in which we set out to understand more about how tomato copes with sub-optimal temperatures (SOT), and explore the genetic variation that can be used to breed new tomato cultivars that perform well at SOT. SOT in this thesis is defined as the temperature below the current economical optimum growth temperature in heated greenhouses in the Netherlands of 19-20°C and above the chilling temperature of 12°C.In Chapter 1 I presented an introduction about why it is important to develop resilient crops for a sustainable economy in the current situation where the climate changes can have negative impact on food production. The importance of photosynthesis and sucrose metabolism as

In conventional plant micropropagation exogenous sucrose is generally taken up by plants from the medium. Any treatment that improves sucrose assimilation or translocation might promote plant growth and micropropagation efficiency. Transpiration is widely believed to be at a very low level in vitro and subsequently the water flow and nutrient translocation are supposed to be marginal. We investigated the relation between growth and sucrose translocation on the one hand and leaf transpiration on the other hand in vitro. It was found that both transpiration, including the transpiration roles of surface cuticle and of stomatal activity, and sucrose assimilation attributed by water transport contributed to biomass accumulation in plants as the main reason for growth. It was also examined the role of sucrose transporter genes in the process of exogenous sucrose translocation in roots. The results demonstrated the importance of SWEET11 and SWEET12 genes in exogenous sucrose assimilation and translocation in vitro. In addition we emphasized the contribution of aquaporin plasma membrane intrinsic proteins PIP1 to the growth of in vitro plants through investigating physiological characteristics in miRNA-induced-PIP1s-silenced plants. As a woody plant Malus domestica ‘Gala’ was used to test whether increased transpiration generally can lead to improved plantlet growth in shoot culture and to demonstrate the relationship between transpiration, stomatal and cuticular transpiration, and plantlet growth in vitro. A follow up of this research should focus on plantlet growth promotion by cuticle manipulation and sucrose assimilation and translocation via fresh cut section.

Many ornamental crops are polyploid or even exist at different ploidy levels. Polyploid QTL analysis tools have been developed in recent years, yet they are limited in the population types they accept. Biparental populations are nowadays being regarded as a limited tool for QTL discovery, as only a limited number of QTLs occurs in an experimental cross and their effects might not be stable across genetic backgrounds. Genome-Wide Association Studies include more genetic diversity but suffer from (hidden) genetic structure and low frequency of QTL alleles. Both factors influence QTL detection and effect estimation, decreasing the sensitivity of QTL analysis. Alternatively, multiparental populations (MPP) can be used, potentially combining multiple QTLs and QTL alleles with known population structure and balanced allele frequencies. Breeding populations of interconnected crosses also constitute a form of MPP and QTLs identified in them might be more applicable to commercial cultivars. To perform QTL analysis in polyploids, mixed models or Bayesian approaches that consider pedigree information are recommended. During the analysis, QTL effects are ideally estimated using Identity by Descent (IBD) alleles (genomic regions that originate from the same ancestor) which can be obtained through haplotype estimation. Although MPPs could thus be a powerful set-up to estimate polyploid haplotypes, a software gap was identified as no current polyploid haplotyping tools are able to utilize MPP pedigree information to obtain haplotypes across an MPP. In order to utilize MPPs to their full extent and expand polyploid QTL analyses to encompass typical breeding populations, new haplotyping tools must be developed.

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement.