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The world needs more than double its current agricultural productivity by 2050 to produce enough food and feed, as well as to provide feedstock for the bioeconomy. These future increases will not only need to be sustainable but without comprommising the nutritional quality, and ideally also need to decrease greenhouse gas emissions and increase carbon sequestration to help mitigate the consequences of global climate change. These challenges could be tackled by developing and integrating new future‐proof crops into our food system. The H2020 CropBooster‐P project sets out plant‐centered breeding approaches guided by a broad socio‐economic and societal support. First, the potential approaches for breeding crops with sustainably increased yields adapted to the future climate of Europe are identified. These crop‐breeding options are subsequently prioritized and their adoption considered by experts across the agri‐food system and the wider public, taking into account environmental, economic and other technical criteria. In this way, a specific research agenda to future‐proof our crops was developed, supported by an eventual implementation plan. [ABSTRACT FROM AUTHOR]

Plant scientists and farmers are facing major challenges in providing food and nutritional security for a growing population, while preserving natural resources and biodiversity. Moreover, this should be done while adapting agriculture to climate change and by reducing its carbon footprint. To address these challenges, there is an urgent need to breed crops that are more resilient to suboptimal environments. Huge progress has recently been made in understanding the physiological, genetic and molecular bases of plant nutrition and environmental responses, paving the way towards a more sustainable agriculture. In this review, we present an overview of these progresses and strategies that could be developed to increase plant nutrient use efficiency and tolerance to abiotic stresses. As illustrated by many examples, they already led to promising achievements and crop improvements. Here, we focus on nitrogen and phosphate uptake and use efficiency and on adaptation to drought, salinity and heat stress. These examples first show the necessity of deepening our physiological and molecular understanding of plant environmental responses. In particular, more attention should be paid to investigate stress combinations and stress recovery and acclimation that have been largely neglected to date. It will be necessary to extend these approaches from model plants to crops, to unravel the relevant molecular targets of biotechnological or genetic strategies directly in these species. Similarly, sustained efforts should be done for further exploring the genetic resources available in these species, as well as in wild species adapted to unfavourable environments. Finally, technological developments will be required to breed crops that are more resilient and efficient. This especially relates to the development of multiscale phenotyping under field conditions and a wide range of environments, and use of modelling and big data management to handle the huge amount of information provided by the new molecular, genetic and phenotyping techniques. [ABSTRACT FROM AUTHOR]

A growing world population as well as the need to enhance sustainability and health create challenges for crop breeding. To address these challenges, not only quantitative but also qualitative improvements are needed, especially regarding the macro‐ and micronutrient composition and content. In this review, we describe different examples of how the nutritional quality of crops and the bioavailability of individual nutrients can be optimised. We focus on increasing protein content, the use of alternative protein crops and improving protein functionality. Furthermore, approaches to enhance the content of vitamins and minerals as well as healthy specialised metabolites and long‐chain polyunsaturated fatty acids are considered. In addition, methods to reduce antinutrients and toxins are presented. These approaches could help to decrease the 'hidden hunger' caused by micronutrient deficiencies. Furthermore, a more diverse crop range with improved nutritional profile could help to shift to healthier and more sustainable plant‐based diets. [ABSTRACT FROM AUTHOR]

Within the framework of the International Solanaceae Genome Project, the genome of tomato ( Solanum lycopersicum) is currently being sequenced. We follow a ‘BAC-by-BAC’ approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome. [ABSTRACT FROM AUTHOR]

We have developed the software package Tomato and Potato Assembly Assistance System (TOPAAS), which automates the assembly and scaffolding of contig sequences for low-coverage sequencing projects. The order of contigs predicted by TOPAAS is based on read pair information; alignments between genomic, expressed sequence tags, and bacterial artificial chromosome (BAC) end sequences; and annotated genes. The contig scaffold is used by TOPAAS for automated design of nonredundant sequence gap-flanking PCR primers. We show that TOPAAS builds reliable scaffolds for tomato (Solanum lycopersicum) and potato (Solanum tuberosum) BAC contigs that were assembled from shotgun sequences covering the target at 6- to 8-fold coverage. More than 90% of the gaps are closed by sequence PCR, based on the predicted ordering information. TOPAAS also assists the selection of large genomic insert clones from BAC libraries for walking. For this, tomato BACs are screened by automated BLAST analysis and in parallel, high-density nonselective amplified fragment length polymorphism fingerprinting is used for constructing a high-resolution BAC physical map. BLAST and amplified fragment length polymorphism analysis are then used together to determine the precise overlap. Assembly onto the seed BAC consensus confirms the BACs are properly selected for having an extremely short overlap and largest extending insert. This method will be particularly applicable where related or syntenic genomes are sequenced, as shown here for the Solanaceae, and potentially useful for the monocots Brassicaceae and Leguminosea. [ABSTRACT FROM AUTHOR]

Tomato spotted wilt virus is an important threat to tomato production worldwide. A single dominant resistance gene locus, Sw5, originating from Lycopersicon peruvianum, has been identified and introgressed in cultivated tomato plants. Here we present the genomic organization of a 35 250 bp fragment of a BAC clone overlapping the Sw5 locus. Two highly homologous (95%) resistance gene candidates were identified within 40 kb of the CT220 marker. The genes, tentatively named Sw5-a and Sw5-b, encode proteins of 1245 and 1246 amino acids, respectively, and are members of the coiled-coil, nucleotide-binding-ARC, leucine-rich repeat group of resistance gene candidates. Promoter and terminator regions of the genes are also highly homologous. Both genes significantly resemble the tomato nematode and aphid resistance gene Mi and, to a lesser extent, Pseudomonas syringae resistance gene Prf. Transformation of Nicotiana tabacum cv. SR1 plants revealed that the Sw5-b gene, but not the Sw5-a gene, is necessary and sufficient for conferring resistance against tomato spotted wilt virus. [ABSTRACT FROM AUTHOR]

Simple Summary: Our climate is changing and the world population is growing to an estimated 10 billion people by 2050. This may cause serious problems in global food supply, protection of the environment and safeguarding Earth's biodiversity. To face these challenges, agriculture will have to adapt and a key element in this will be the development of "future-proof" crops. These crops will not only have to be high-yielding, but also should be able to withstand future climate conditions and will have to make very efficient use of scarce resources such as water, phosphorus and minerals. Future crops should not only sustainably give access to sufficient, nutritious, and diverse food to a worldwide growing population, but also support the circular bio-based economy and contribute to a lower atmospheric CO2 concentration to counteract global warming. Future-proofing our crops is an urgent issue and a challenging goal that only can be realized by large-scale, international research cooperation. We call for international action and propose a pan-European research and innovation initiative, the CropBooster Program, to mobilize the European plant research community and all interested actors in agri-food research and innovation to face the challenge. The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation's Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge. [ABSTRACT FROM AUTHOR]

Beet cyst nematode-resistant sugar beet plants, containing the Hs1pro-1 locus from Beta procumbens, show a female transmission frequency of the resistance of ca. 90%. Such plants often suffer from tumour formation on leaves and root systems, and from the occurrence of a so-called ‘multi-top’ phenotype. With the aim of obtaining resistant sugar beet material lacking these negative traits, nematode-resistant plants with a reduced size of the chromosome segment of the wild beet that carries the Hs1pro-1 gene were selected from backcrosses between the resistant stocks B883 or AN1-65-2 and susceptible sugar beet (Beta vulgaris). Analysis of such plants, referred to as Sat-minus plants, showed that the transmission frequency of the resistance to subsequent generations had dropped dramatically to ca. 0.5%. The multi-top phenotype was still present in the newly selected material, indicating that improvement of the resistant sugar beet material by further backcrossing will be hard to achieve. Two of the selected resistant offspring plants were analysed at the molecular level. With the aid of AFLP markers it was found that the size of the alien chromosome segment had decreased to 35% and 17% of the original size, respectively. Surprisingly, both plants had lost the Hs1pro-1 nematode resistance gene that recently was isolated from the original introgression material. This shows that more than one gene conferring resistance must be present in the locus in B883 and AN1-65-2 carrying the resistance gene Hs1pro-1. [ABSTRACT FROM AUTHOR]

DNA fingerprinting with three repetitive DNA sequences (OPX2, PB6-4 and Sat-121) was carried out on a set of 10 monosomic additions of Beta procumbens and 75 anonymous B. patellaris-derived monosomic additions in B. vulgaris, for characterization of the alien chromosomes at the DNA level. The probes are Procumbentes-specific and distributed over all chromosomes. Morphological characteristics were also used for the classification of B. patellaris monosomic addition families and for comparison with the morphology of the addition families of B. procumbens. DNA fingerprinting revealed unique patterns for almost all individual addition chromosomes of B. procumbens. However, it was concluded that chromosomes 1 and 6 of B. procumbens may be identical with the only difference that the chromosome referred to as 6 carries a susceptible allele for beet cyst nematode (BCN) resistance. In contrast, it was concluded that the two addition types with chromosome 2 are carrying different chromosomes of B. procumbens, so that one of them was renumbered to become the new chromosome 6. DNA fingerprinting of 75 anonymous B. patellaris-derived monosomic additions facilitated the identification and characterization of the alien chromosomes and the grouping of these additions into nine different groups. Several of these groups could be divided in two sub-groups on the basis of small differences in banding patterns. The results of the DNA fingerprinting led to the conclusion that B. patellaris most likely is an allotetraploid. It was also deduced that the BCN gene(s) in this species are homozygous and located on chromosome 1, while the pair of homoeologous chromosomes does not carry such BCN gene(s). Because of the allotetraploid nature of B. patellaris, preferential association occurs between the two homologous chromosomes containing the allele(s) for BCN resistance. Each group of B. patellaris addition families united by DNA fingerprinting had comparable morphological characteristics. Some of these morphological traits appeared to be chromosome-specific and were very useful for primary classification of the addition families. However, the present study showed that these morphological traits are not adequate for the identification of all alien chromosomes without the aid of additional markers. Because of similarities observed between molecular characteristics or the effects on plant morphology of several chromosomes of B. procumbens and B. patellaris it was concluded that B. procumbens could have been involved in the evolutionary history of B. patellaris. [ABSTRACT FROM AUTHOR]