Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

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The tomato genome sequence provides insights into fleshy fruit evolution

A vast number of plant pathogens from viroids of a few hundred nucleotides to higher plants cause diseases in our crops. Their effects range from mild symptoms to catastrophes in which large areas planted to food crops are destroyed. Catastrophic plant disease exacerbates the current deficit of food supply in which at least 800 million people are inadequately fed. Plant pathogens are difficult to control because their populations are variable in time, space, and genotype. Most insidiously, they evolve, often overcoming the resistance that may have been the hard-won achievement of the plant breeder. In order to combat the losses they cause, it is necessary to define the problem and seek remedies. At the biological level, the requirements are for the speedy and accurate identification of the causal organism, accurate estimates of the severity of disease and its effect on yield, and identification of its virulence mechanisms. Disease may then be minimized by the reduction of the pathogen's inoculum, inhibition of its virulence mechanisms, and promotion of genetic diversity in the crop. Conventional plant breeding for resistance has an important role to play that can now be facilitated by marker-assisted selection. There is also a role for transgenic modification with genes that confer resistance. At the political level, there is a need to acknowledge that plant diseases threaten our food supplies and to devote adequate resources to their control.

Plant Disease: A Threat to Global Food Security

■ Abstract Many disease resistance (R) proteins of plants detect the presence of disease-causing bacteria, viruses, or fungi by recognizing specific pathogen effector molecules that are produced during the infection process. Effectors are often pathogen proteins that probably evolved to subvert various host processes for promotion of the pathogen life cycle. Five classes of effector-specific R proteins are known, and their sequences suggest roles in both effector recognition and signal transduction. Although some R proteins may act as primary receptors of pathogen effector proteins, most appear to play indirect roles in this process. The functions of various R proteins require phosphorylation, protein degradation, or specific localization within the host cell. Some signaling components are shared by many R gene pathways whereas others appear to be pathway specific. New technologies arising from the genomics and proteomics revolution will greatly expand our ability to investigate the role of R proteins in plant disease resistance.

Understanding the functions of plant disease resistance proteins.

The availability of cheap and abundant molecular
markers in maize (Zea mays L.) has allowed
breeders to ask how molecular markers may
best be used to achieve breeding progress, without
conditioning the question on how breeding
has traditionally been done. Genomewide selection
refers to marker-based selection without
fi rst identifying a subset of markers with signifi -
cant effects. Our objectives were to assess the
response due to genomewide selection compared
with marker-assisted recurrent selection
(MARS) and to determine the extent to which
phenotyping can be minimized and genotyping
maximized in genomewide selection. We simulated
genomewide selection by evaluating doubled
haploids for testcross performance in Cycle
0, followed by two cycles of selection based on
markers. Individuals were genotyped for NM markers,
and breeding values associated with each of
the NM markers were predicted and were all used
in genomewide selection. We found that across
different numbers of quantitative trait loci (20, 40,
and 100) and levels of heritability, the response to
genomewide selection was 18 to 43% larger than
the response to MARS. Responses to selection
were maintained when the number of doubled
haploids phenotyped and genotyped in Cycle
0 was reduced and the number of plants genotyped
in Cycles 1 and 2 was increased. Such
schemes that minimize phenotyping and maximize
genotyping would be feasible only if the
cost per marker data point is reduced to about 2
cents. The convenient but incorrect assumption
of equal marker variances led to only a minimal
loss in the response to genomewide selection.
We conclude that genomewide selection, as
a brute-force and black-box procedure that
exploits cheap and abundant molecular markers,
is superior to MARS in maize.

http://bernardo-group.org/wp-content/uploads/2015/11/Bernardo-and-Yu-2007.pdf

Prospects for genomewide selection for quantitative traits in maize

The oomycetes form a phylogenetically distinct group of eukaryotic microorganisms that includes some of the most notorious pathogens of plants. Oomycetes accomplish parasitic colonization of plants by modulating host cell defenses through an array of disease effector proteins. The biology of effectors is poorly understood but tremendous progress has been made in recent years. This review classifies and catalogues the effector secretome of oomycetes. Two classes of effectors target distinct sites in the host plant: Apoplastic effectors are secreted into the plant extracellular space, and cytoplasmic effectors are translocated inside the plant cell, where they target different subcellular compartments. Considering that five species are undergoing genome sequencing and annotation, we are rapidly moving toward genome-wide catalogues of oomycete effectors. Already, it is evident that the effector secretome of pathogenic oomycetes is more complex than expected, with perhaps several hundred proteins ded...

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A Catalogue of the Effector Secretome of Plant Pathogenic Oomycetes

Late blight caused by the oomycete Phytophthora infestans is the most destructive disease in potato cultivation worldwide. New, more virulent P. infestans strains have evolved which overcome the genetic resistance that has been introgressed by conventional breeding from wild potato species into commercial varieties. R genes (for single-gene resistance) and genes for quantitative resistance to late blight are present in the germplasm of wild and cultivated potato. The molecular basis of single-gene and quantitative resistance to late blight is unknown. We have cloned R1, the first gene for resistance to late blight, by combining positional cloning with a candidate gene approach. The R1 gene is member of a gene family. It encodes a protein of 1293 amino acids with a molecular mass of 149.4 kDa. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain. The most closely related plant resistance gene (36% identity) is the Prf gene for resistance to Pseudomonas syringae of tomato. R1 is located within a hot spot for pathogen resistance on potato chromosome V. In comparison to the susceptibility allele, the resistance allele at the R1 locus represents a large insertion of a functional R gene.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2001.01292.x

The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes.

Late blight caused by the oomycete Phytophthora infestans is the economically most important and destructive disease in potato cultivation. Quantitative resistance to late blight available in tetraploid cultivars is correlated with late maturity in temperate climates, which is an undesirable characteristic. A total of 30 DNA-based markers known to be linked to loci for pathogen resistance in diploid potato were selected and tested as polymerase chain reaction-based markers for linkage with quantitative trait loci (QTL) for late blight resistance and plant maturity in two half-sib families of tetraploid potatoes. Most markers originated from within or were physically closely linked to candidate genes for quantitative resistance factors. The families were repeatedly evaluated in the field for quantitative resistance to late blight and maturity. Resistance was corrected for the maturity effect. Nine of eleven different map segments tagged by the markers harbored QTL affecting maturity-corrected resistance. Interactions were found between unlinked resistance QTL, providing testable strategies for marker-assisted selection in tetraploid potato. Based on the linkage observed between QTL for resistance and plant maturity and based on the genetic interactions observed between candidate genes tagging resistance QTL, we discuss models for the molecular basis of quantitative resistance and maturity.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/MPMI.2004.17.10.1126

Tagging quantitative trait loci for maturity-corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers.

Potatoes (Solanum tuberosum L.) and humans (Homo sapiens L.) are both outcrossing species. The phenotypic variation of both is controlled by environnemental factors and by natural DNA polymorphisms between individuals. Therefore we adopt similar approaches as used in human population genetics, such as association mapping, to identify loci and their alleles that are causal for complex agronomic characters such as quantitative resistance to pathogens or tuber sugar content. Fonctional analysis of genes operating in resistance to pests and pathogens or in carbohydrate metabolism, either in potato itself or in other plants including the model species Arabidopsis thaliana (L). Heynh, provides many functional candidates for these complex agronomic traits. In our approach, fonctional candidate genes are tested for linkage to quantitative trait locl (QTL) for pathogen resistance or tuber quality traits, thereby selecting positional candidates (genes colocalizing with a QTL). DNA polymorphisme in or physically linked to positional candidate genes are then evaluated in populations of tetraploid potato genotypes and tested for association with phenotypes evaluated in the same populations. We have used the candidate gene approach to identify DNA-based markers that are diagnostic for quantitative resistane in late blight caused by Phytophthora infestans (Mont) de Bary, to the root cyst nematode Globodera pallida (Stone), and for chip color in tetraploid potato cultivars and in advanced breeding clones.

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Christina Angelika Bormann

Papers

The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes.

Tagging quantitative trait loci for maturity-corrected late blight resistance in tetraploid potato with PCR-based candidate gene markers.

Candidate Gene Approach to Identify Genes Underlying Quantitative Traits and Develop Diagnostic Markers in Potato