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Prickly lettuce (Lactuca serriola L., Asteraceae), a wild relative of cultivated lettuce, is an autogamous species which greatly expanded throughout Western and Northern Europe during the last 2 centuries. Here, we present a large-scale biogeographic genetic analysis performed on a dataset represented by 2622 individuals from 110 wild European populations. Thirty-two maternally inherited chloroplast RFLP-markers and 10 nuclear microsatellite loci were used. Microsatellites revealed low genetic variation and high inbreeding coefficients within populations, as well as strong genetic differentiation between populations, which was in accordance with the autogamous breeding system. Analysis of molecular variance based clustering indicated the presence of 3 population clusters, which showed strong geographical patterns. One cluster occupied United Kingdom and part of Northern Europe, and characterized populations with a single predominant genotype. The second mostly combined populations from Northern Europe, while the third cluster grouped populations particularly from Southern Europe. Kriging of gene diversity for L. serriola corroborated northwards and westwards spread from Central (Eastern) Europe. Significant lower genetic diversity characterized the newly colonized parts of the range compared to the historical ones, confirming the importance of founder effects. Stronger pattern of isolation by distance was assessed in the newly colonized areas than in the historical areas (Mantel’s r = 0.20). In the newly colonized areas, populations at short geographic distances were genetically more similar than those in the historical areas. Our results corroborate the species’ recent and rapid northward and westward colonization from Eastern Europe, as well as a decrease of genetic diversity in recently established populations.

Most regulations worldwide stipulate that a new genetically modified (GM) crop event has to be compared to its closest non-GM counterpart as a corner stone of the pre-market risk assessment. To this end the GM crop and its comparator should be grown in field trials for a phenotypic comparison as well as for subsequent detailed analysis of the composition of the two crop varieties. A more in-depth globally harmonised approach for the conduct of these field trials is lacking. Only a few countries have formulated detailed protocols for the set-up of GM field trials. In some countries, commercial non-GM reference varieties need to be included in a field study to compile reliable data that indicate the range of natural variation for the compounds tested at the specific location. Detailed analysis of pre-market assessment reports have so far not shown the added value of including these reference varieties in the field trials. In all cases where specific values were found to be outside of the range of the reference varieties, it proved possible to draw conclusions on the part of the pre-market risk assessment that relates to the compositional analysis, on the basis of already available compositional data. With the increasing quality of several databases on compositional data of a growing number of crop species, it seems unlikely that reference varieties will become more important on future occasions. It was furthermore investigated whether this part of the risk assessment can be related to field trial requirements for variety registration with the explicit intention of reducing the data burden on producers of new GM plant varieties. Field trials for variety registration so far include an assessment of phenotypic characteristics that do not cover safety aspects, with the exception of establishment of the glycoalkaloid content in potatoes in the Netherlands and Sweden. It may, however, under certain conditions be relatively easy to exchange data from compositional measurements between variety registration and GM testing procedures, thus laying a foundation for testing the feasibility of combining both pre-market assessment procedures in a single pre-market evaluation path.

During the 20th century, the economic position of oats (Avena sativa L.) decreased strongly in favour of higher yielding crops including winter wheat and maize. Presently, oat represents only ∼. 1.3% of the total world grain production, and its production system is fragmented. Nonetheless, current interest is growing because of recent knowledge on its potential benefits in food, feed and agriculture. This perspective will serve as a further impetus, with special focus on the recently valued advantages of oats in human food and health.Five approved European Food Safety Authority (EFSA) health claims apply to oats. Four relate to the oat-specific soluble fibres, the beta-glucans, and concern the maintenance and reduction of blood cholesterol, better blood glucose balance and increased faecal bulk. The fifth claim concerns the high content of unsaturated fatty acids, especially present in the endosperm, which reduces the risks of heart and vascular diseases. Furthermore, oat starch has a low glycemic index, which is favourable for weight control. Oat-specific polyphenols and avenanthramides have antioxidant and anti-inflammatory properties. Thus, oats can contribute significantly to the presently recommended whole-grain diet.Next to globulins, oats contain a small fraction of prolamin storage proteins, called 'avenins', but at a much lower quantity than gluten proteins in wheat, barley and rye. Oat avenins do not contain any of the known coeliac disease epitopes from gluten of wheat, barley and rye. Long-term food studies confirm the safety of oats for coeliac disease patients and the positive health effects of oat products in a gluten-free diet. These effects are general and independent of oat varieties. In the EU (since 2009), the USA (since 2013) and Canada (since 2015) oat products may be sold as gluten-free provided that any gluten contamination level is below 20. ppm. Oats are, however, generally not gluten-free when produced in a conventional production chain, because of regular contamination with wheat, barley or rye. Therefore, establishing a separate gluten-free oat production chain requires controlling all steps in the chain; the strict conditions will be discussed.Genomic tools, including a single nucleotide polymorphism (SNP) marker array and a dense genetic map, have recently been developed and will support marker-assisted breeding. In 2015, the Oat Global initiative emerged enabling a world-wide cooperation starting with a data sharing facility on genotypic, metabolic and phenotypic characteristics. Further, the EU project TRAFOON (Traditional Food Networks) facilitated the transfer of knowledge to small- and medium-sized enterprises (SMEs) to stimulate innovations in oat production, processing, products and marketing, among others with regard to gluten-free. Finally, with focus on counteracting market fragmentation of the global oat market and production chains, interactive innovation strategies between customers (consumers) and companies through co-creation are discussed.

Cultivation of spinach requires high amounts of nitrogen (N), which puts a strain on the environment. A sustainable solution to this problem is to breed for crops with higher N use efficiency (NUE). The aim of this study was to provide tools for molecular breeding and to elucidate the genetic variation of factors contributing to NUE in spinach. A cross was made between two F1 hybrid cultivars contrasting in NUE. Several F1 progeny were self-pollinated and based on evaluation of the F2 generation, a mapping F2 population (335 individuals) of a single F1 was selected. SNP markers for the genetic map were discovered by RNA sequencing of the two parent cultivars, and 283 SNP markers were used to produce a genetic map comprising of six linkage groups (P01–P06), ranging in size from 46 to 116 cM. NUE related traits were determined for a set of F2:3 families grown under low and high N conditions in a hydroponics system under an Ingestad N-addition model. Interval mapping analysis detected 39 trait-specific QTLs, with several QTLs accumulating on P01 and P02 of the linkage map. The QTLs and in particular the P01 and P02 regions provide potential targets for the improvement of NUE in spinach.

The world’s third most important food crop, potato, suffers yield reductions during drought stress. Drought scenarios are predicted to become more frequent and severe due to climate change. Therefore, we investigated the feasibility of improving drought tolerance in potato using a set of 103 European potato cultivars. We employed a multidisciplinary approach in our study including the phenotyping of multi-location and multi-year field trials, modelling of potato canopy growth and tuber size distribution, association mapping of tuber size distribution parameters with a 14K SNP array, magnetic resonance imaging of xylem and phloem conduits, microscopic study of stem cross-sections and transcriptomic analyses. We observed that late foliage maturity and a delayed attainment of maximum canopy cover favoured tuber yield during drought conditions. We found a marker-trait association of a region on chromosome three with marketable tuber size and spread of tuber size distribution under drought. Our findings indicate that water and assimilate transport are critical for carbon partitioning to tubers during drought. We observed that increased xylem density per unit stem area and reduction of xylem vessel diameter under drought contributed to tolerance. An integration of these findings in potato breeding programs will facilitate the improvement of drought tolerance in potato.

Potato is an important food crop with high yields. However when exposed to drought it suffers major yield losses. Considering its global importance and the increasing incidence of drought due to climate change, research toward drought tolerance in potato remains imperative. We have studied a set of 103 commercial cultivars representing the genetic diversity in the European potato market. The cultivars were grown in different field locations in three subsequent years (2013–2015). Our aim was to understand how different field drought regimes affect canopy growth in potato, and how these effects translate to tuber yield. The field environmental conditions were monitored, and pictures of canopy ground cover during the growing season were taken. Canopy growth parameters were extracted by an iterative method using the beta sigmoid growth function to model canopy growth. At harvest, tuber yield was scored and tuber size was graded. The GGE (Genotype and Genotype-by-Environment) bi-plot and Finlay Wilkinson’s Regression were used to investigate Genotype x Environment interactions. We observed that the timing of the drought occurrence differentially affected canopy growth and tuber yield. Under drought stress, fast attainment of exponential growth and maximum canopy cover had negative effects on tuber formation and tuber bulking. Growth rate, maximum canopy cover, and area under the canopy curve (photosynthetic capacity over the growth season) were more important for tuber bulking than they were for tuber formation under drought stress. Cultivars with high yield were identified as potential material for improvement to drought tolerance. These findings will contribute to the breeding for drought-tolerant potato amidst the threats of climate change.

In the field, plants constantly face a plethora of abiotic and biotic stresses that can impart detrimental effects on plants. In response to multiple stresses, plants can rapidly reprogram their transcriptome through a tightly regulated and highly dynamic regulatory network where WRKY transcription factors can act as activators or repressors. WRKY transcription factors have diverse biological functions in plants, but most notably are key players in plant responses to biotic and abiotic stresses. In tomato there are 83 WRKY genes identified. Here we review recent progress on functions of these tomato WRKY genes and their homologs in other plant species, such as Arabidopsis and rice, with a special focus on their involvement in responses to abiotic and biotic stresses. In particular, we highlight WRKY genes that play a role in plant responses to a combination of abiotic and biotic stresses.

The application of Good Agricultural Practice (GAP) contributes to many aspects of sustainable farming, including integrated control of weeds, diseases, and pests, and optimization of fertilization and irrigation. It is a relatively neglected issue in debates regarding the application of new technology, such as genetic modification (GM), which often revolve around the intrinsic properties of a GM crop allegedly leading to unsatisfactory performance. However, the performance largely depends on the agronomic and institutional embedding of applying new technology, which generally applies to all crops, whether conventional or GM. We describe and discuss four cases in which the government or private partners in the production chain regulate this, using legal measures, incentives, or mutual agreements, or a combination thereof. These cases serve as a starting point for a discussion on how GAP can be stimulated, organized, and guaranteed. We argue that next to the government, also seed suppliers, NGOs, and buyers, as well as farmers can be drivers for the application of GAP when tools are available that enable farmers to make optimal farming choices.

Genetics, biochemistry, and crop modelling are independently evolving disciplines; however, they complement each other in addressing some of the important challenges that crop science faces. One of these challenges is to improve our understanding of crop genotype-to-phenotype relationships in order to assist the development of high-yielding and resource-use efficient genotypes that can adapt to particular (future) target environments. Crop models are successful in predicting the impact of environmental changes on crop productivity. However, when critically tested against real experimental data, crop models have been shown to be less successful in predicting the impact of genotypic variation and genotype-by-environment interactions exhibited in genetic populations. In order to better model gene-trait-crop performance relationships in support of breeding and genetic engineering programmes, crop models need to be improved in terms of both model parameters and model structure. We argue that integration of quantitative genetics and photosynthesis biochemistry with modelling is a first step towards a new generation of improved crop models. With genetic information and biochemical understanding incorporated, crop modelling also generates new insights and concepts that can in turn be used to improve genetic analysis and biochemical modelling of complex traits. This modelling-genetics-biochemistry framework (the MGB triangle framework) stresses the synergy among the three disciplines, and may best serve as a step to achieve the ultimate goal of the more broadly framed “Crop Systems Biology” approach to improve efficiency of both classical breeding and genetic engineering programmes.

Crop plants are subjected to a variety of stresses during their lifecycle, including abiotic stress factors such as salinity and biotic stress factors such as pathogens. Plants have developed a multitude of defense and adaptation responses to these stress factors. In the field, different stress factors mostly occur concurrently resulting in a new state of stress, the combined stress. There is evidence that plant resistance to pathogens can be attenuated or enhanced by abiotic stress factors. With stress tolerance research being mostly focused on plant responses to individual stresses, the understanding of a plant's ability to adapt to combined stresses is limited. In the last few years, we studied powdery mildew resistance under salt stress conditions in the model crop plant tomato with the aim to understand the requirements to achieve plant resilience to a wider array of combined abiotic and biotic stress combinations. We uncovered specific responses of tomato plants to combined salinity-pathogen stress, which varied with salinity intensity and plant resistance genes. Moreover, hormones, with their complex regulation and cross-talk, were shown to play a key role in the adaptation of tomato plants to the combined stress. In this review, we attempt to understand the complexity of plant responses to abiotic and biotic stress combinations, with a focus on tomato responses (genetic control and cross-talk of signaling pathways) to combined salinity and pathogen stresses. Further, we provide recommendations on how to design novel strategies for breeding crops with a sustained performance under diverse environmental conditions.

High throughput plant phenotyping facilities are rapidly becoming essential for significant advancements in plant breeding. Wageningen ur combines all of the necessary expertises in Phenomics nl and is involved in several (inter) national phenotyping initiatives to lead and explore the field of plant phenomics.

Gewassen beïnvloeden de bodem waarop ze geteeld worden. In deze verkennende literatuurstudie is onderzocht wat er bekend is over variatie tussen verschillende genotypen/plantenrassen met betrekking tot hun effect op bodemkwaliteit voor een aantal ruwvoedergewassen, in het bijzonder Maïs (Zea mays), Engels raaigras (Lolium perenne) en Witte klaver (Trifolium repens). Dergelijke variatie zou mogelijkheden kunnen bieden om via veredeling en het inzetten van specifieke rassen de bodemkwaliteit te verbeteren. Er is betrekkelijk weinig onderzoek vanuit deze invalshoek gedaan. De focus van de studie was gericht op variatie in wortelarchitectuur, en wortelexudatie en wortelafsterving/nieuwvorming in relatie tot het organische stof gehalte en beschikbaarheid van nutriënten, en de bodem biota, met name mycorrhiza.

Miscanthus is a woody rhizomatous C4 grass that can be used as a CO2 neutral biofuel resource. It has potential to grow in marginal areas such as saline soils, avoiding competition for arable lands with food crops. This study explored genetic diversity for salt tolerance in Miscanthus and discovered mechanisms and traits that can be used to improve the yield under salt stress. Seventy genotypes of Miscanthus (including 57 M. sinensis, 5 M. sacchariflorus, and 8 hybrids) were evaluated for salt tolerance under saline (150 mM NaCl) and normal growing conditions using a hydroponic system. Analyses of shoot growth traits and ion concentrations revealed the existence of large variation for salt tolerance in the genotypes. We identified genotypes with potential for high biomass production both under control and saline conditions that may be utilized for growth under marginal, saline conditions. Several relatively salt tolerant genotypes had clearly lower Na+ concentrations and showed relatively high K+/Na+ ratios in the shoots under salt stress, indicating that a Na+ exclusion mechanism was utilized to prevent Na+ accumulation in the leaves. Other genotypes showed limited reduction in leaf expansion and growth rate under saline conditions, which may be indicative of osmotic stress tolerance. The genotypes demonstrating potentially different salt tolerance mechanisms can serve as starting material for breeding programs aimed at improving salinity tolerance of Miscanthus.

Aan dit rollenspel nemen deel: een maïsteler, een manager van FrieslandCampina, een verkoper van gewasbeschermingsmiddelen en een actievoerder van Greenpeace. Voor elk van de vier rollen is een informatieblad. Doel is niet te winnen maar samen te leren om voor- en nadelen goed af te wegen. Voorbereidingstijd, duur van het gesprek en de evaluatie in overleg met de docent.

One of the most promising New Plant Breeding Techniques is genome editing (also called gene editing) with the help of a programmable site-directed nuclease (SDN). In this review, we focus on SDN-1, which is the generation of small deletions or insertions (indels) at a precisely defined location in the genome with zinc finger nucleases (ZFN), TALENs, or CRISPR-Cas9. The programmable nuclease is used to induce a double-strand break in the DNA, while the repair is left to the plant cell itself, and mistakes are introduced, while the cell is repairing the double-strand break using the relatively error-prone NHEJ pathway. From a biological point of view, it could be considered as a form of targeted mutagenesis. We first discuss improvements and new technical variants for SDN-1, in particular employing CRISPR-Cas, and subsequently explore the effectiveness of targeted deletions that eliminate the function of a gene, as an approach to generate novel traits useful for improving agricultural sustainability, including disease resistances. We compare them with examples of deletions that resulted in novel functionality as known from crop domestication and classical mutation breeding (both using radiation and chemical mutagens). Finally, we touch upon regulatory and access and benefit sharing issues regarding the plants produced.

Aan dit rollenspel nemen deel: een maïsteler, een manager van FrieslandCampina, een verkoper van gewasbeschermingsmiddelen en een actievoerder van Greenpeace. Voor elk van de vier rollen is een informatieblad. Doel is niet te winnen maar samen te leren om voor- en nadelen goed af te wegen. Voorbereidingstijd, duur van het gesprek en de evaluatie in overleg met de docent.

Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

This paper describes the complete findings of the EU-funded research project OPTIMISC, which investigated methods to optimize the production and use of miscanthus biomass. Miscanthus bioenergy and bioproduct chains were investigated by trialing 15 diverse germplasm types in a range of climatic and soil environments across central Europe, Ukraine, Russia, and China. The abiotic stress tolerances of a wider panel of 100 germplasm types to drought, salinity, and low temperatures were measured in the laboratory and a field trial in Belgium. A small selection of germplasm types was evaluated for performance in grasslands on marginal sites in Germany and the UK. The growth traits underlying biomass yield and quality were measured to improve regional estimates of feedstock availability. Several potential high-value bioproducts were identified. The combined results provide recommendations to policymakers, growers and industry. The major technical advances in miscanthus production achieved by OPTIMISC include: (1) demonstration that novel hybrids can out-yield the standard commercially grown genotype Miscanthus x giganteus; (2) characterization of the interactions of physiological growth responses with environmental variation within and between sites; (3) quantification of biomass-quality-relevant traits; (4) abiotic stress tolerances of miscanthus genotypes; (5) selections suitable for production on marginal land; (6) field establishment methods for seeds using plugs; (7) evaluation of harvesting methods; and (8) quantification of energy used in densification (pellet) technologies with a range of hybrids with differences in stem wall properties. End-user needs were addressed by demonstrating the potential of optimizing miscanthus biomass composition for the production of ethanol and biogas as well as for combustion. The costs and life-cycle assessment of seven miscanthusbased value chains, including small- and large-scale heat and power, ethanol, biogas, and insulation material production, revealed GHG-emission- and fossil-energy-saving potentials of up to 30.6 t CO2eqC ha(-1) y(-1) and 429 GJ ha(-1)y(-1), respectively. Transport distance was identified as an important cost factor. Negative carbon mitigation costs of-78 epsilon t(-1) CO2eq C were recorded for local biomass use. The OPTIMISC results demonstrate the potential of miscanthus as a crop for marginal sites and provide information and technologies for the commercial implementation of miscanthus-based value chains.

Plant hormones are paramount to plant adaptation to changing environmental conditions and interactions with microorganisms. There is currently limited knowledge on their significance in the response to stress combination. Using near isogenic lines (NILs) that carry the Ol-1, ol-2 and Ol-4 gene for resistance to tomato powdery mildew caused by Oidium neolycopersici, this study focused on the responses of these NILs to powdery mildew and salt stress combination. In these NILs, marker genes for monitoring hormonal pathways showed differential expression pattern upon powdery mildew infection. Further by crossing these NILs with tomato mutants notabilis (ABA-deficient), defenseless1 (JA-deficient) and epinastic (ET overproducer) the cross-talk among hormonal pathways was further investigated. Among the mutants, epinastic resulted in increased susceptibility of NIL-Ol-1 and breakdown of NIL-ol-2 resistance, accompanied by reduced callose deposition, effects that were more pronounced under combination with salt stress. On the other hand notabilis, resulting in H2O2 overproduction greatly reduced susceptibility of NIL-Ol-1 under combined stress accompanied however by heightened sensitivity to salt stress. Callose deposition reduction led to partial resistance breakdown in NIL-ol-2 which was reversed under combined stress. NIL-Ol-4 resistance remained robust across all mutant and treatment combinations. We discuss the critical role that hormone signalling appears to have for the outcome of combined stress and powdery mildew in terms of resistance and plant fitness integrating observations from physiological, histochemical and gene expression analyses. These significant insights obtained extend our understanding of hormonal regulation of combined stress responses and can aid in narrowing down targets for improving crop performance under stress combinations.

Nitrogen (N) fertilizers increased food production over the last 60 years, but also contributed significantly to the use of fossil energy and the total amount of reactive N in the environment. Agriculture needs to reduce N input and increase nitrogen use efficiency (NUE). Legislation like the Nitrate Directive (91/767/EEC) and the Water Framework Directive (2000/60/EC) forces a reduction in N supply in crop production. The effects of this constraint on yield and quality of potato are expected to be significant since N plays an important role in the vegetative development and production of potato. Considerable amounts of N are needed as N recovery is notoriously low due to the small and shallow roots. The overall aim of this thesis is to improve the nitrogen use efficiency of potato under low nitrogen supply. Specific aims are i) to understand the N effects on potato performance, especially under low N input, ii) to quantify the genotypic variation under contrasting N inputs, iii) to identify quantitative trait loci associated with the crop’s response to nitrogen. We used ecophysiological models to dissect the canopy development into biological meaningful parameters as phenotyping tools. Two potato populations (a set of tetraploid cultivars and a biparental diploid population) were phenotyped in the field under two contrasting N levels. Additionally, a set of 6 cultivars from three maturity groups (early, middle and late) were phenotyped in more detail under 5 nitrogen conditions combining two input levels and two fertilizers types plus a control without nitrogen fertilisation. The curve-fit parameters were, together with other agronomical traits, used in the agronomic and genetic analysis. Our approach using the ecophysiological models captured the phenotypic response to N, enhancing the interpretation of the nitrogen effects and of the differences among maturity types. The nitrogen effects on canopy development resulted in large differences in light interception, tuber yield, tuber size distribution and nitrogen uptake. There were differences in the response to nitrogen between the diploid biparental population and the set of tetraploid cultivars. In general, in the diploid population, having less vigour and therefore less potential to respond to the extra nitrogen, the time required to complete each phase of the canopy development was longer than in the set of tetraploids. In the set of cultivars the rate of early vegetative growth was higher, the onset of the phase with maximum canopy cover was earlier, and the duration of maximum canopy was longer than for the diploid population. However, in both the diploid and the tetraploid population maturity was the major factor accounting for genetic variation in canopy development and tuber development traits. The genotypic differences were reflected in quantitative trait loci that were either N dependent or N independent, with pleiotropic regions affecting most of the maturity-related traits. Few traits showed quantitative trait loci on common regions that were not maturity related like those on chromosomes 2 and 6 (association mapping) or linkage groups ma_VI, pa_VIII pa_XI. Maturity obscures other genotype-dependent physiological traits; therefore it is imperative to find traits that are responsible for genotypic variation, but not related to maturity type. Moreover the results showed that nitrogen use efficiency under low nitrogen input is higher than under high nitrogen input, and higher for late cultivars than for early cultivars. Therefore, breeding for nitrogen use efficiency under low input requires direct selection combined with good response to extra nitrogen and should be done within each maturity group. Finally in a broader context we discussed the need of high-throughput phenotyping in breeding for complex traits, like those involving efficiency, to make the most of the large amount of genetic data, all possible based on advances in technology in remote sensing and images analysis. Keywords: Association mapping, Breeding for low input, Canopy development, Maturity type, Nitrogen use efficiency, Potato, Solanum tuberosum, Quantitative trait loci.

Phosphorus (P) is often an important limiting factor for crop yields, but rock phosphate as fertilizer is a non-renewable resource and expected to become scarce in the future. High P input levels in agriculture have led to environmental problems. One of the ways to tackle these issues simultaneously is improving phosphorus use efficiency (PUE) of the crops through breeding. In this review, we describe plant architectural and physiological traits important for PUE. Subsequently, we discuss efficient methods of screening for PUE traits. We address targeted cultivation methods, including solid and hydroponic systems, as well as testing methods, such as image analysis systems, and biomass and photosynthesis measurements. Genetic variation for PUE traits has been assessed in many crops, and genetics of PUE has been studied by quantitative trait loci (QTL) analyses and genome-wide association study. A number of genes involved in the plant’s response to low P have been characterized. These genes include transcription factors, and genes involved in signal transduction, hormonal pathways, sugar signalling, P saving metabolic pathways, and in P scavenging, including transporters and metabolites and/or ATP-ases mobilizing P in the soil. In addition, the role of microorganisms promoting PUE of plants, particularly arbuscular mycorrhizal fungi is discussed. An overview is given of methods for selecting for optimal combinations of plant and fungal genotypes, and their genetics, incl. QTLs and genes involved. In conclusion, significant progress has been made in selecting for traits for PUE, developing systems for the difficult but highly relevant root phenotyping, and in identifying QTLs and genes involved.

Plant breeding has resulted in numerous high-quality crop varieties being cultivated nowadays. Breeding based on crossing and selection remains an important and ongoing activity for crop improvement, but needs innovation to be able to address urgent future challenges, including increasing crop production in a rapidly changing environment.

WRKY is a transcription factor family unique to plants with diverse functions in defense pathways, abiotic stress tolerance and developmental programs. Family members are characterized by the conserved WRKY domain and significant sequence variation in the remainder of the protein, which is translated into distinct functions even for closely related genes. We utilized the extensive functional characterization of the Arabidopsis thaliana WRKY family to identify tomato homologues of Arabidopsis WRKY genes that are involved in defense responses (AtWRKY 11, 29, 48, 70 and 72). In total 13 tomato WRKY homologues were identified for these genes, of which 9 were successfully over-expressed, and 12 stably silenced via RNAi in transgenic tomato lines. The transgenic lines were evaluated for their response to salt stress, powdery mildew resistance and the combination of these stresses. Lines overexpressing SlWRKY11 and SlWRKY23, and RNAi lines of SlWRKY7 and SlWRKY9 showed both increased biomass and improved salt tolerance. For SlWRKY11 and SlWRKY23 overexpression (OE) lines, this was accompanied by a moderate increase in oxidative stress tolerance. The SlWRKY6-OE line showed strongly improved salt stress tolerance, but a growth penalty under control conditions. Exceptional phenotypes were observed for the SlWRKY10-OE line (stunted growth) and the RNAi line SlWRKY23-RNAi (necrotic symptoms), but these phenotypes were partly restored to normal under salt stress. Both these lines exhibited increased resistance to powdery mildew, but this was compromised when the plants were put under salt-stress as well. Important functions for tomato WRKY genes were revealed in both the abiotic and biotic stress response and several genes should be further explored to elucidate their downstream regulatory functions that lead to increased stress tolerance.

Background Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. Results Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. Conclusions Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0879-0) contains supplementary material, which is available to authorized users.

Stress conditions in agricultural ecosystems can occur in variable intensities. Different resistance mechanisms to abiotic stress and pathogens are deployed by plants. Thus, it is important to examine plant responses to stress combinations under different scenarios. Here, we evaluated the effect of different levels of salt stress ranging from mild to severe (50, 100 and 150mM NaCl) on powdery mildew (PM) resistance and overall performance of tomato introgression lines with contrasting levels of partial resistance, as well as isogenic lines carrying the PM resistance genes Ol-1 (associated with slow Hypersensitivity Response; HR), ol-2 (a mlo mutant associated with papilla formation) and Ol-4 (a R gene associated with fast HR). PM resistance was affected by salt stress in a genotype and stress intensity dependent manner. In susceptible and partial resistant lines, increased susceptibility was observed under mild salt stress (50mM) which was accompanied with accelerated cell death-like senescence. On the contrary, severe salt stress (150mM) reduced disease symptoms. Na+ and Cl- accumulation in the leaves was linearly related to the decreased pathogen growth under severe stress, suggesting a more direct role for the salt in suppressing PM growth. In contrast, complete resistance mediated by ol-2 and Ol-4 was unaffected under all treatment combinations, and was associated with a decreased growth penalty. Increased susceptibility and senescence under combined stress of the variety Moneymaker (MM) and the NIL Ol-1 was associated with the induction of ethylene and jasmonic acid pathway genes as well as of the cell wall invertase gene LIN6. These results highlight the significance of stress severity and resistance type on the plant’s performance under abiotic and biotic stress combination.

Nitrogen (N) fertilizers increased food production over the last 60 years, but also contributed significantly to the use of fossil energy and the total amount of reactive N in the environment. Agriculture needs to reduce N input and increase nitrogen use efficiency (NUE). Legislation like the Nitrate Directive (91/767/EEC) and the Water Framework Directive (2000/60/EC) forces a reduction in N supply in crop production. The effects of this constraint on yield and quality of potato are expected to be significant since N plays an important role in the vegetative development and production of potato. Considerable amounts of N are needed as N recovery is notoriously low due to the small and shallow roots. The overall aim of this thesis is to improve the nitrogen use efficiency of potato under low nitrogen supply. Specific aims are i) to understand the N effects on potato performance, especially under low N input, ii) to quantify the genotypic variation under contrasting N inputs, iii) to identify quantitative trait loci associated with the crop’s response to nitrogen. We used ecophysiological models to dissect the canopy development into biological meaningful parameters as phenotyping tools. Two potato populations (a set of tetraploid cultivars and a biparental diploid population) were phenotyped in the field under two contrasting N levels. Additionally, a set of 6 cultivars from three maturity groups (early, middle and late) were phenotyped in more detail under 5 nitrogen conditions combining two input levels and two fertilizers types plus a control without nitrogen fertilisation. The curve-fit parameters were, together with other agronomical traits, used in the agronomic and genetic analysis. Our approach using the ecophysiological models captured the phenotypic response to N, enhancing the interpretation of the nitrogen effects and of the differences among maturity types. The nitrogen effects on canopy development resulted in large differences in light interception, tuber yield, tuber size distribution and nitrogen uptake. There were differences in the response to nitrogen between the diploid biparental population and the set of tetraploid cultivars. In general, in the diploid population, having less vigour and therefore less potential to respond to the extra nitrogen, the time required to complete each phase of the canopy development was longer than in the set of tetraploids. In the set of cultivars the rate of early vegetative growth was higher, the onset of the phase with maximum canopy cover was earlier, and the duration of maximum canopy was longer than for the diploid population. However, in both the diploid and the tetraploid population maturity was the major factor accounting for genetic variation in canopy development and tuber development traits. The genotypic differences were reflected in quantitative trait loci that were either N dependent or N independent, with pleiotropic regions affecting most of the maturity-related traits. Few traits showed quantitative trait loci on common regions that were not maturity related like those on chromosomes 2 and 6 (association mapping) or linkage groups ma_VI, pa_VIII pa_XI. Maturity obscures other genotype-dependent physiological traits; therefore it is imperative to find traits that are responsible for genotypic variation, but not related to maturity type. Moreover the results showed that nitrogen use efficiency under low nitrogen input is higher than under high nitrogen input, and higher for late cultivars than for early cultivars. Therefore, breeding for nitrogen use efficiency under low input requires direct selection combined with good response to extra nitrogen and should be done within each maturity group. Finally in a broader context we discussed the need of high-throughput phenotyping in breeding for complex traits, like those involving efficiency, to make the most of the large amount of genetic data, all possible based on advances in technology in remote sensing and images analysis. Keywords: Association mapping, Breeding for low input, Canopy development, Maturity type, Nitrogen use efficiency, Potato, Solanum tuberosum, Quantitative trait loci.

High throughput plant phenotyping facilities are rapidly becoming essential for significant advancements in plant breeding. Wageningen ur combines all of the necessary expertises in Phenomics nl and is involved in several (inter) national phenotyping initiatives to lead and explore the field of plant phenomics.

Abiotic and biotic stress factors are the major constrains for the realization of crop yield potential. As climate change progresses, the spread and intensity of abiotic as well as biotic stressors is expected to increase, with increased probability of crops being exposed to both types of stress. Shielding crops from combinatorial stress requires a better understanding of the plant’s response and its genetic architecture. In this study, we evaluated resistance to salt stress, powdery mildew and to both stresses combined in tomato, using the S. habrochaites LYC4 introgression line (IL) population. The IL population segregated for both salt stress tolerance and powdery mildew resistance. Using SNP array marker data, QTLs were identified for salt tolerance as well as Na+ and Cl- accumulation. Salt stress increased the susceptibility of the population to powdery mildew in an additive manner. Phenotypic variation for disease resistance was reduced under combined stress as indicated by the coefficient of variation (CV). No correlation was found between disease resistance and Na+ and Cl- accumulation under combined stress Most genetic loci were specific for either salt stress tolerance or powdery mildew resistance. These findings increase our understanding of the genetic regulation of responses to abiotic and biotic stress combinations and can provide leads to more efficiently breeding for tomatoes and other crops with a high level of disease resistance while maintaining their performance in combination with abiotic stress.

Breeding for stress-resilient crops strongly depends on technological and biological advancements that have provided a wealth of information on genetic variants and their contribution to stress tolerance. In the context of the upcoming challenges for agriculture due to climate change, such as prolonged and/or increased stress intensities, CO2 increase and stress combinations, hierarchizing this information is key to accelerating crop improvement towards sustained or even increased productivity. We propose traits with high scalability to yield and crop performance that can be targeted for improvement and provide examples of recent discoveries with potential applicability in breeding. Critical to success is the integrated analysis of the phenotypes of genetic variants across different environmental variables using modelling approaches and high-throughput phenotyping.

In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co-expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid- and environmental stress-inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection.

Highlight Salt stress severity differentially affected partial powdery mildew resistance. Stress combination uniquely resulted in accelerated senescence. mlo-based and R-gene-mediated resistance maintained robustness across salt treatments., Stress conditions in agricultural ecosystems can occur at variable intensities. Different resistance mechanisms against abiotic stress and pathogens are deployed by plants. Thus, it is important to examine plant responses to stress combinations under different scenarios. Here, we evaluated the effect of different levels of salt stress ranging from mild to severe (50, 100, and 150mM NaCl) on powdery mildew resistance and overall performance of tomato introgression lines with contrasting levels of partial resistance, as well as near-isogenic lines (NILs) carrying the resistance gene Ol-1 (associated with a slow hypersensitivity response; HR), ol-2 (an mlo mutant associated with papilla formation), and Ol-4 (an R gene associated with a fast HR). Powdery mildew resistance was affected by salt stress in a genotype- and stress intensity-dependent manner. In susceptible and partial resistant lines, increased susceptibility was observed under mild salt stress (50mM) which was accompanied by accelerated cell death-like senescence. In contrast, severe salt stress (150mM) reduced disease symptoms. Na+ and Cl− accumulation in the leaves was linearly related to the decreased pathogen symptoms under severe stress. In contrast, complete resistance mediated by ol-2 and Ol-4 was unaffected under all treatment combinations, and was associated with a decreased growth penalty. Increased susceptibility and senescence under combined stress in NIL-Ol-1 was associated with the induction of ethylene and jasmonic acid pathway genes and the cell wall invertase gene LIN6. These results highlight the significance of stress severity and resistance type on the plant’s performance under the combination of abiotic and biotic stress.

Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.

In the original publication of the article, Li et al. has been incorrectly cited in the following sentence “Interestingly, a complex trait par excellence, yield, was also shown to be amenable to an SDN-1 approach. Li et al. (2017) used CRISPR-Cas9 in rice to mutate the regulatory genes Gna1, DEP1, and GS3 and obtained plants with increased grain numbers, dense erect panicles plus semi-dwarf phenotype, and larger grains, respectively.”.

For crops that are grown for their fruits or seeds, elevated temperatures that occur during flowering and seed or fruit set have a stronger effect on yield than high temperatures during the vegetative stage. Even short-term exposure to heat can have a large impact on yield. In this study, we used Arabidopsis thaliana to study the effect of short-term heat exposure on flower and seed development. The impact of a single hot day (35°C) was determined in more than 250 natural accessions by measuring the lengths of the siliques along the main inflorescence. Two sensitive developmental stages were identified, one before anthesis, during male and female meiosis, and one after anthesis, during fertilization and early embryo development. In addition, we observed a correlation between flowering time and heat tolerance. Genome-wide association mapping revealed four quantitative trait loci (QTLs) strongly associated with the heat response. These QTLs were developmental stage specific, as different QTLs were detected before and after anthesis. For a number of QTLs, T-DNA insertion knockout lines could validate assigned candidate genes. Our findings show that the regulation of complex traits can be highly dependent on the developmental timing.

This brochure gives an overview of new plant breeding techniques. This overview is based on a more technical review of the scientific literature, published in a separate report. The overview presents the opportunities and limitations of these techniques from the point of view of potential applications in plant breeding with promising results for improving agricultural sustainability.

This brochure gives an overview of new plant breeding techniques. This overview is based on a more technical review of the scientific literature, published in a separate report. The overview presents the opportunities and limitations of these techniques from the point of view of potential applications in plant breeding with promising results for improving agricultural sustainability.

Plant breeding has resulted in numerous high-quality crop varieties being cultivated nowadays. Breeding based on crossing and selection remains an important and ongoing activity for crop improvement, but needs innovation to be able to address urgent future challenges, including increasing crop production in a rapidly changing environment.