An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

SummaryBread wheat (Triticum aestivum) is a globally important crop, accounting for 20% of the calories consumed by mankind. We sequenced its large and challenging 17 Gb hexaploid genome using 454 pyrosequencing and compared this with the sequences of diploid ancestral and progenitor genomes. Between 94,000-96,000 genes were identified, and two-thirds were assigned to the A, B and D genomes. High-resolution synteny maps identified many small disruptions to conserved gene order. We show the hexaploid genome is highly dynamic, with significant loss of gene family members upon polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a new resource for accelerating gene discovery and improving this major crop.

Wild relatives of common wheat, Triticum aestivum, and related species are an important source of disease and pest resistance and several useful traits have been transferred from these species to wheat. C-banding and in situ hybridization analyses are powerful cytological techniques allowing the detection of alien chromatin in wheat. Cbanding permits identification of the wheat and alien chromosomes involved in wheat-alien translocations, whereas genomic in situ hybridization analysis allows determination of their size and breakpoint positions. The present review summarizes the available data on wheat-alien transfers conferring resistance to diseases and pests. Ten of the 57 spontaneous and induced wheat-alien translocations were identified as whole arm translocations with the breakpoints within the centromeric regions. The majority of transfers (45) were identified as terminal translocations with distal alien segments translocated to wheat chromosome arms. Only two intercalary wheat-alien transloctions were identified, one induced by radiation treatment with a small segment of rye chromosome 6RL (H25) inserted into the long arm of wheat chromosome 4A, and the other probably induced by homoeologous recombination with a segment derived from the long arm of a group 7 Agropyron elongatum chromosome with Lrl9 inserted into the long arm of 7D. The presented information should be useful for further directed chromosome engineering aimed at producing superior germplasm.

The Q gene is largely responsible for the widespread cultivation of wheat because it confers the freethreshing character. It also pleiotropically influences many other domestication-related traits such as glume shape and tenacity, rachis fragility, spike length, plant height, and spike emergence time. We isolated the Q gene and verified its identity by analysis of knockout mutants and transformation. The Q gene has a high degree of similarity to members of the AP2 family of transcription factors. The Q allele is more abundantly transcribed than q, and the two alleles differ for a single amino acid. An isoleucine at position 329 in the Q protein leads to an abundance of homodimer formation in yeast cells, whereas a valine in the q protein appears to limit homodimer formation. Ectopic expression analysis allowed us to observe both silencing and overexpression effects of Q. Rachis fragility, glume shape, and glume tenacity mimicked the q phenotype in transgenic plants exhibiting post-transcriptional silencing of the transgene and the endogenous Q gene. Variation in spike compactness and plant height were associated with the level of transgene transcription due to the dosage effects of Q. The q allele is the more primitive, and the mutation that gave rise to Q occurred only once leading to the world's cultivated wheats. W HEAT, rice, and maize are the three major cereal crops that provide most of the calories consumed by humans. Bread (common) wheat (Triticum aestivum L., 2n ¼ 6x ¼ 42, AABBDD genomes) arose 8000-10,000 years ago (for review see Nesbitt and Samuel 1996;Feldman 2001) from the spontaneous hybridization of the tetraploid wheat T. turgidum L. (2n ¼ 4x ¼ 28, AABB genomes) with the diploid goatgrass Aegilops tauschii Coss. (2n ¼ 2x ¼ 14, DD genomes) (Kihara 1944;McFadden and Sears 1946). Domestication of wheat resulted from mutations that gave rise to traits such as soft glumes, a nonfragile rachis, and the free-threshing character.The Q gene governs the free-threshing character and square spike phenotype. In addition, Q pleiotropically affects a repertoire of other characters important for domestication such as rachis fragility (Leighty and

The classic wheat evolutionary history is one of adaptive radiation of the diploid Triticum͞Aegilops species (A, S, D), genome convergence and divergence of the tetraploid (Triticum turgidum AABB, and Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine phylogenetic relationships among Triticum and Aegilops species of the wheat lineage and to establish the timeline of wheat evolution based on gene sequence comparisons.

Virus-induced gene silencing (VIGS) is an important tool for the analysis of gene function in plants. In VIGS, viruses engineered to carry sequences derived from plant gene transcripts activate the host's sequence-specific RNA degradation system. This mechanism targets the RNAs of the viral genome for degradation, and as the virus contains transcribed plant sequence, homologous host mRNAs are also targeted for destruction. While routinely used in some dicots, no VIGS system was known for monocot plants until the recent report of silencing in barley (Hordeum vulgare) by barley stripe mosaic virus (BSMV). Here, we report development of protocols for use of BSMV to efficiently silence genes in hexaploid wheat (Triticum aestivum). The VIGS system was first optimized in studies silencing phytoene desaturase expression. Next, we used it to assay genes functioning in leaf rust resistance mediated by Lr21, which encodes a nucleotide binding site-leucine-rich repeat class resistance gene product. We demonstrated that infection with BSMV constructs carrying a 150-bp fragment of Lr21 caused conversion of incompatible interactions to compatible, whereas infection with a control construct or one that silences phytoene desaturase had no effect on resistance or susceptibility. Additionally, silencing the RAR1, SGT1, and HSP90 genes, known to be required in many but not all nucleotide binding site-leucine-rich repeat resistance pathways in diverse plant species, resulted in conversion to compatibility, indicating that these genes are essential in Lr21-mediated resistance. These studies indicate that BSMV-VIGS is a powerful tool for dissecting the genetic pathways of disease resistance in hexaploid wheat.Wheat is one of the most important sources of protein in the human diet. It is a staple for 35% of the human population and supplies approximately 20% of the calories consumed worldwide (http://www.cymmt. org/). Losses from pathogens and pests greatly impact wheat production. One of the most pervasive of these diseases is leaf rust, caused by Puccinia triticina, which over the course of human history has caused famines and ruined the economies of entire countries (Agrios, 1988). Currently, worldwide annual losses from leaf rust are estimated to be the equivalent of U.S. $2 billion (National Agricultural Statistics Service, http://www. usda.gov/nass).Plants have evolved potent surveillance and response systems that provide resistance to a diverse set of pathogens, including fungi, bacteria, viruses, nematodes, and insects. Despite this broad range of intruders, in most cases examined, the resistance pathways (R-pathways) that counter them are based on very similar molecular architecture. One of the bestcharacterized modes of disease resistance is known as gene-for-gene resistance (Flor, 1971), whereby resistance to a specific pathogen requires the presence of a particular allele of a plant resistance gene (R-gene) and a gene encoding its cognate elicitor in the pathogen. The vast majority of R-genes that have been isolated are kn...

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