Steve Tanksley

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

BackgroundPhylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species.ResultsAmong potatoes, when total evidence is invoked, one single predominant history is highlighted with complete resolution within and among the three main clades. It also supports the hypothesis of the North and Central American B-genome origin of the tuber-bearing members of Solanum sect. Petota and shows a clear division between A genomes in clades 3 and 4, and B genomes in clade 1+2. On the other hand, when a prior agreement approach is invoked other potato evolutionary histories are revealed but with less support. These alternative histories could be explained by past hybridization, or fast rates of speciation. In the case of tomato, the analyses with all sequence data completely resolved 19 of 21 clades, for the first time revealed the monophyly of five clades, and gave further support for the recent segregation of new species from the former Solanum peruvianum. Concordance analyses revealed and summarized the extensive discordance among COSII markers. Some potential reasons for discordance could be methodological, to include systematic errors due to using a wrong model of sequence evolution, coupled with long branches, or mixtures of branch lengths within COSII, or undetected paralogy or alignment bias. Other reasons could be biological processes such as hybridization or lineage sorting.ConclusionThis study confirms and quantifies the utility of using DNA sequences from different parts of the genome in phylogenetic studies to avoid possible bias in the sampling. It shows that 11–18 loci are enough to get the dominant history in this group of Solanum, but more loci would be needed to discern the distribution of gene genealogies in more depth, and thus detect which mechanism most likely shaped the discordance.

Differential regulation of grain sucrose accumulation and metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta) revealed through gene expression and enzyme activity analysis.

* Coffea arabica (Arabica) and Coffea canephora (Robusta) are the two main cultivated species used for coffee bean production. Arabica genotypes generally produce a higher coffee quality than Robusta genotypes. Understanding the genetic basis for sucrose accumulation during coffee grain maturation is an important goal because sucrose is an important coffee flavor precursor. * Nine new Coffea genes encoding sucrose metabolism enzymes have been identified: sucrose phosphate synthase (CcSPS1, CcSPS2), sucrose phosphate phosphatase (CcSP1), cytoplasmic (CaInv3) and cell wall (CcInv4) invertases and four invertase inhibitors (CcInvI1, 2, 3, 4). * Activities and mRNA abundance of the sucrose metabolism enzymes were compared at different developmental stages in Arabica and Robusta grains, characterized by different sucrose contents in mature grain. * It is concluded that Robusta accumulates less sucrose than Arabica for two reasons: Robusta has higher sucrose synthase and acid invertase activities early in grain development - the expression of CcSS1 and CcInv2 appears to be crucial at this stage and Robusta has a lower SPS activity and low CcSPS1 expression at the final stages of grain development and hence has less capacity for sucrose re-synthesis. Regulation of vacuolar invertase CcInv2 activity by invertase inhibitors CcInvI2 and/or CcInvI3 during Arabica grain development is considered.

Exploitation of Natural Biodiversity Through Genomics

The genetic improvement of crop plants is the most viable approach to meeting the increasing demand for agricultural output. This goal may be achieved by using the wealth of genetic variation provided by nature. Until now, scientists have been unable to exploit the genetic potential warehoused in plant germplasm repositories for quantitative traits associated with agricultural yield. Here we review the development and application of the advanced-backcross and introgression-line breeding populations for the identification of wild species derived chromosome segments that improve agricultural performance of elite germplasm. The results of studies in a wide range of crops indicate that, unlike their domestic relatives, which are often depleted in genetic variation, wild populations of plants carry a tremendous wealth of potentially valuable alleles, many of which would not have been predicted from the phenotype of the wild plants. The results from these studies may help open up new sources of genetic variation for plant breeding and biotechnology and shed light on the nature of quantitative trait variation.

A genomic search for the gene conferring resistance to fusarium wilt in tomato

Fusarium wilt is an economically important disease of tomatoes, caused by the soil-born fungus Fusarium oxysporum f. sp. lycopersici. There are three host-specific races of this pathogen. The dominant tomato gene I-2 confers resistance to race 2. The I-2 fusarium resistance gene was mapped genetically to chromosome 11 of tomato, between the RFLP markers TG105 and TG36, 0.4 centiMorgan (cM) from TG105. A mean value of 43 kb for each cM was assigned in the vicinity of I-2. We have generated new RFLP markers in the region by chromosome walking from TG105 towards I-2 on lambda clones, and by subcloning a 350 kb long YAC clone (YAC 8) that contains TG105. These RFLP markers were mapped physically on YAC 8 by PFGE. The location of I-2 relative to these markers was genetically estimated using a recombinant inbred (RI) segregating population. The order of the markers according to the RI population is inconsistent with their order on the physical map. A cDNA clone, D14, that was isolated by YAC 8, turned out to be 53% similar to xanthine dehydrogenase from mammals and flies. Antibodies raised against a part of the protein encoded by D14 recognize cross reacting material of MW 80 kD, that is highly enriched in nodules of legumes, and seems to be induced by various environmental and pathogenic stress conditions.

SolGenes — a Solanaceae database

Biological investigations have the potential to produce large volumes of data, much of which is condensed or omitted from publications, and which may not be readily accessible to researchers outside that discipline. Bringing together in a single repository information whose common thread is the Solanaceae family gives researchers a valuable, multidisciplinary tool. The SolGenes (Solanaceae) database project, a part of the USDA Plant Genome Research Program, is meant to be such a tool. The database has facilities for handling genetic and physical maps, DNA sequences, pathologies and germplasm stocks, as well as other types of information. It currently contains tomato, potato and pepper genetic maps based on a common set of probes, tomato germplasm data including wild species and stocks, autoradiogram images of distributed probes and much more. Current efforts are focused on loading images of tomato mutants, expanding the germplasm data, and setting up a gopher server. The database software (ACEDB) provides a user-friendly, graphical interface with links between logically related pieces of information, allowing the user to view data from multiple sources with just a few clicks of the mouse. The database and software are freely available to interested parties.

Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta)

Caffeine is a secondary metabolite produced by a variety of plants including Coffea canephora (robusta) and there is growing evidence that caffeine is part of a chemical defence strategy protecting young leaves and seeds from potential predators. The genes encoding XMT and DXMT, the enzymes from Coffea canephora (robusta) that catalyse the three independent N-methyl transfer reactions in the caffeine-biosynthesis pathway, have been cloned and the proteins have been expressed in Escherichia coli. Both proteins have been crystallized in the presence of the demethylated cofactor S-adenosyl-L-cysteine (SAH) and substrate (xanthosine for XMT and theobromine for DXMT). The crystals are orthorhombic, with space group P2(1)2(1)2(1) for XMT and C222(1) for DXMT. X-ray diffraction to 2.8 A for XMT and to 2.5 A for DXMT have been collected on beamline ID23-1 at the ESRF.