There is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. The model plant Arabidopsis thaliana is in many ways an ideal candidate for such studies, because it is a highly selfing hermaphrodite. As a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. Furthermore, linkage disequilibrium in such a species will be much more extensive than in a comparable outcrossing species. We tested the feasibility of genome-wide association mapping in A. thaliana by searching for associations with flowering time and pathogen resistance in a sample of 95 accessions for which genome-wide polymorphism data were available. In spite of an extremely high rate of false positives due to population structure, we were able to identify known major genes for all phenotypes tested, thus demonstrating the potential of genome-wide association mapping in A. thaliana and other species with similar patterns of variation. The rate of false positives differed strongly between traits, with more clinal traits showing the highest rate. However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies.

The contribution of arms race dynamics to plant-pathogen coevolution has been called into question by the presence of balanced polymorphisms in resistance genes of Arabidopsis thaliana, but less is known about the pathogen side of the interaction. Here we investigate structural polymorphism in pathogenicity islands (PAIs) in Pseudomonas viridiflava, a prevalent bacterial pathogen of A. thaliana. PAIs encode the type III secretion system along with its effectors and are essential for pathogen recognition in plants. P. viridiflava harbors two structurally distinct and highly diverged PAI paralogs (T-and S-PAI) that are integrated in different chromosome locations in the P. viridiflava genome. Both PAIs are segregating as presence͞absence polymorphisms such that only one PAI ([T-PAI, ١S-PAI] and [١T-PAI, S-PAI]) is present in any individual cell. A worldwide population survey identified no isolate with neither or both PAI. T-PAI and S-PAI genotypes exhibit virulence differences and a host-specificity tradeoff. Orthologs of each PAI can be found in conserved syntenic locations in other Pseudomonas species, indicating vertical phylogenetic transmission in this genus.Molecular evolutionary analysis of PAI sequences also argues against ''recent'' horizontal transfer. Spikes in nucleotide divergence in flanking regions of PAI and ١-PAI alleles suggest that the dual PAI polymorphism has been maintained in this species under some form of balancing selection. Virulence differences and host specificities are hypothesized to be responsible for the maintenance of the dual PAI system in this bacterial pathogen.bacteria ͉ balancing selection ͉ plant-pathogen interaction ͉ arms race ͉ horizontal gene transfer

We report the isolation and identification of two natural pathogens of Arabidopsis thaliana, Pseudomonas viridiflava and Pseudomonas syringae, in the midwestern United States. P. viridiflava was found in six of seven surveyed Arabidopsis thaliana populations. We confirmed the presence in the isolates of the critical pathogenicity genes hrpS and hrpL. The pathogenicity of these isolates was verified by estimating in planta bacterial growth rates and by testing for disease symptoms and hypersensitive responses to A. thaliana. Infection of 21 A. thaliana ecotypes with six locally collected P. viridiflava isolates and with one P. syringae isolate showed both compatible (disease) and incompatible (resistance) responses. Significant variation in response to infection was evident among Arabidopsis ecotypes, both in terms of symptom development and in planta bacterial growth. The ability to grow and cause disease symptoms on particular ecotypes also varied for some P. viridiflava isolates. We believe that these pathogens will provide a powerful system for exploring coevolution in natural plant-pathogen interactions.

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C4 grasses are among the most productive plants and most promising cellulosic biofuel feedstocks. Successful implementation of cellulosic biofuel feedstocks will depend on the improvement of critical crop characteristics and subsequent conversion technologies. The content and composition of lignin, cellulose, and hemicellulose, their biomass yields, and their biotic and abiotic stress tolerances are critical factors which can be enhanced by molecular breeding methods, including marker-assisted selection and transgenic approaches. To maximize biomass yield, no flowering or late flowering and no grain set would be ideal for cellulosic biofuel crops. Reducing fecundity also reduces the risk of undesired gene transfer and invasiveness, thus accelerating deregulation processes and permitting faster implementation of highly improved genotypes in cellulosic feedstock production. Why Do We Need to Develop Cellulosic Biofuels?The hunt for carbon neutral energy sources has become one of the primary challenges of the twenty-first century. The use of ethanol is a proven concept for replacing gasoline and reducing CO 2 emission from fossil oil. Currently, ethanol is produced from sugar-and starch-rich crops, which are grown by labor-and machine-intensive agriculture and require high-nitrogen fertilization. These practices in turn negatively impact the overall energy and CO 2 balance for this particular production chain. Cellulosic biofuels are a promising component in a future mix of alternative renewable energy solutions. There are challenges which exist in the use of cellulosic biofuel crops; but with continuously developing plant breeding, crop development, and farming as well as conversion technologies, cellulosic biofuel crops will emerge as strong contenders in the race for sustainable energy sources. Among the many choices for cellulosic biofuels are trees and short rotation coppice, agricultural waste material, and by-products from crops and biomass grasses. This review will focus on the genetic improvement of selected C4 grasses including Sorghum bicolor, Miscanthus species, hybrids between these species, and hybrids between Miscanthus × sugarcane (Miscane), and Panicum virgatum (switchgrass) for the development of dedicated cellulosic biofuel crops. Characteristics of Sustainable Cellulosic Biofuel CropsThe transition from the Mesozoic to Neolithic period (around 10,000 BCE) is defined by the development of nascent agricultural practices and the selection and genetic manipulation of cereal grasses to meet the qualitative and quantitative requirements of food and feedstock. In this respect, the development of cellulosic biofuel feedstock will be similar. Tailoring crops for biofuel production is critical in improving the overall economy of ethanol production from cellulosic feedstock (Wyman 2007).