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Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice Oryza sativa , sorghum Sorghum bicolor , and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21, barley genes in a putative linear order. We show that the barley H genome displays a mosaic of structural similarity to hexaploid bread wheat Triticum aestivum A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages.
We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding. A genome sequence is central to the development of true genomics-informed breeding strategies and for unlocking the full potential of natural genetic variation for future crop improvement. Given the combined challenges of food security and climate change, it is vital that this situation is resolved and resources are developed that, even if not meeting an optimal gold standard, in the interim provide a high value and high utility surrogate.
Genomic data both from sequenced BAC clones and the application of next-generation sequencing NGS methodologies are available at a limited scale Steuernagel et al. Given a close evolutionary relationship divergence 13 million years ago [MYA]; Gaut, that has resulted in extensive conservation of synteny Moore et al. This proposition is supported by agronomic traits such as flowering time and vernalization response being shared with wheat and the causal genes located at conserved genomic regions Fu et al.
Even race-specific disease resistance, a paradigm for species-specific genetic control in plants, shares conserved genetic elements in barley and wheat. Recently, a functional allele of the barley gene Mla, which confers resistance to the powdery mildew fungus Zhou et al. Indeed, an increasing body of information supports the notion of treating the Triticeae as a single genetic system. Barley is itself an important crop.
Historically, it also has been an important model for classical genetics where its diploid genome has facilitated genetic analysis, a position that extended into the genomics era where early EST sequences provided resources for microarray design that in turn established routine functional genomics Close et al. Subsequently, the same sequences were exploited to generate high-density gene maps using innovative marker technology Stein et al.
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The two TLR4 molecules are represented in purple and turquoise and the two MD-2 molecules in yellow and green. To answer these questions many mutagenesis, structural modeling and crytallisation studies have been performed. There was controversy as to whether TLR4 participates directly in ligand binding and discrimination. Lipid IVa is an agonist in the mouse, a partial agonist in the horse and is an antagonist for human cells Akashi et al.
Using chimeric constructs made from human and horse TLR4 and MD-2, sequences have been identified in both proteins that are required for lipid IVa to signal. A molecular model using this data predicted that interchain contacts occur between MD-2 and TLR4 and explain why two highly conserved residues in MD-2 F and H are critical for receptor dimerization in response to LPS Kobayashi et al. The model also predicted the presence of TLR4 receptor-receptor contacts. This fascinating structure shows the main dimerization face of TLR4 being between leucine-rich repeats 15— The mechanism for this is unclear, but the mutations could either affect the cooperative binding of lipid A or alter the conformational changes that occur during ligand-induced signal transduction.