Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA^mA^m), is central to wheat evolution, domestication and genetic improvement¹. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu², which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome³) and Ae. tauschii (the donor of the D genome⁴), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.

Summary: Considerable progress has been made in understanding the function of receptor‐like kinase (RLK) genes in model plants. However, much less is known about these genes in crop species. Here we report the characterization of three new wheat RLK genes (TaRLK‐R1, 2 and 3). The primary structure of the putative proteins TaRLK‐R1, 2 and 3 contained a signal peptide, a cysteine‐rich extracellular domain, a transmembrane domain, and a predicted intracellular kinase domain. The fusions between TaRLK‐R1, 2 or 3 and the green fluorescence protein (GFP) were targeted to the plasma membrane; such targeting required the signal peptide, extracellular domain and transmembrane domain. Transcription of TaRLK‐R1, 2 and 3 was found mainly in the green organs, and was regulated by light. Transcript levels of TaRLK‐R1, 2 and 3 increased during the hypersensitive reaction (HR) to stripe rust fungus. In addition, the TaRLK‐R3 transcript level was also upregulated by abiotic stresses. Further experiments revealed that the recombinant kinase domain of TaRLK‐R3 exhibited auto‐phosphorylation activity in vitro. Knocking down the transcript levels of TaRLK‐R1, 2 or 3 individually or all together by virus‐induced gene silencing compromised the wheat HR to stripe rust fungus. The demonstration of TaRLK‐R1, 2 and 3 as positive contributors in the wheat HR to stripe rust fungus suggests a new direction for further functional studies of this important family of RLK genes, and may facilitate the breeding of wheat varieties resistant to stripe rust disease.

MADS-box genes are important transcription factors for plant development, especially floral organogenesis. Brachypodium distachyon is a model for biofuel plants and temperate grasses such as wheat and barley, but a comprehensive analysis of MADS-box family proteins in Brachypodium is still missing. We report here a genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. We identified 57 MADS-box genes and classified them into 32 MIKC^c-type, 7 MIKC*-type, 9 Mα, 7 Mβ and 2 Mγ MADS-box genes according to their phylogenetic relationships to the Arabidopsis and rice MADS-box genes. Detailed gene structure and motif distribution were then studied. Investigation of their chromosomal localizations revealed that Brachypodium MADS-box genes distributed evenly across five chromosomes. In addition, five pairs of type II MADS-box genes were found on synteny blocks derived from whole genome duplication blocks. We then performed a systematic expression analysis of Brachypodium MADS-box genes in various tissues, particular floral organs. Further detection under salt, drought, and low-temperature conditions showed that some MADS-box genes may also be involved in abiotic stress responses, including type I genes. Comparative studies of MADS-box genes among Brachypodium, rice and Arabidopsis showed that Brachypodium had fewer gene duplication events. Taken together, this work provides useful data for further functional studies of MADS-box genes in Brachypodium distachyon.

Low-molecular-weight glutenin subunits (LMW-GS) strongly influence the bread-making quality of bread wheat. These proteins are encoded by a multi-gene family located at the Glu-A3, Glu-B3 and Glu-D3 loci on the short arms of homoeologous group 1 chromosomes, and show high allelic variation. To characterize the genetic and protein compositions of LMW-GS alleles, we investigated 16 Aroona near-isogenic lines (NILs) using SDS-PAGE, 2D-PAGE and the LMW-GS gene marker system. Moreover, the composition of glutenin macro-polymers, dough properties and pan bread quality parameters were determined for functional analysis of LMW-GS alleles in the NILs.