News & Updates

Recently, Shen et al. published the paper " Chromosome-scale assembly of the wild cereal relative Elymus sibiricus." on the Sci Data. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Liu et al. published the paper "Chromosome-level assembly of the synthetic hexaploid wheat-derived cultivar Chuanmai 104" on the Sci Data. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Surbhi et al. published the paper "Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii" on the bioRxiv. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Jia et al. published the paper "Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement" on the Molecular Plant. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, We published the paper "Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States" on the Plant Cell. You can access these resources from JBorwse. In this study, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, eight showed convergent changes between the two countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these two regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.The raw data and sequencing data have been deposited in the National Genomics Data Center (NGDC) database under project CRA005878. The genotype data in variant call formats (VCF) are available in the NGDC database under accession number GVM000315.

Recently, Ahmed et al. published the paper "Einkorn genomics sheds light on history of the oldest domesticated wheat" on the Nature. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse. In this study, they generated two high-quality genome assemblies including a wild einkorn accession TA299 and a domesticated einkorn landrace TA10622. They found einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent.

Recently, Ahmed et al. published the paper "Einkorn genomics sheds light on history of the oldest domesticated wheat" on the Nature. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Yang et al. published the paper "Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat" on the Plant Commun. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Zhang et al. published the paper "A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement" on the Molecular Plant. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Shi et al. published the paper "Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen use efficiency in the wheat cultivar Kenong 9204" on the Molecular Plant. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse. In this study, they generated a high-quality genome assembly for a high-NUE wheat cultivar Kenong 9204 and systematically analyzed the genes related to nitrogen uptake and metabolism. By comparative analysis, we found that the high-affinity nitrate transporter gene family expanded in Triticeae.

Recently, Coombes et al. published the paper "Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines" on the Plant Biotechnology Journal. You can access these resources from BLAST and GetSequence. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, they have precisely pinpointed the borders of introgressed segments, most of which occur within genes and also report a genome assembly and annotation of Am. muticum that has facilitated the identification of Am. muticum resistance genes commonly introgressed in lines resistant to stripe rust.

Recently, Kale et al. published the paper "A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat" on the Plant Biotechnology Journal. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Aury et al. published the paper "Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding" on the GigaScience. They produced a chromosome-scale assembly of the 14.26-gigabase Renan genome. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Athiyannan et al. published the paper "Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning" on the Nat Genet. They enerate a 14.7 gigabase chromosome-scale assembly of the South African bread wheat (Triticum aestivum) cultivar Kariega by combining high-fidelity long reads, optical mapping and chromosome conformation capture.They also identified the race-specific disease resistance gene Yr27, which encodes an intracellular immune receptor, to be a major contributor to this resistance. Yr27 is allelic to the leaf rust resistance gene Lr13; the Yr27 and Lr13 proteins show 97% sequence identity.
You can access genome resources from BLAST, GetSequence, JBrowse and PrimerServer.

Recently, Li et al. published the paper "Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield" on the Mol Plant. They exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified 6.7% of the wheat genome that fell in selection sweeps between landraces and cultivars with genes known for yield improvement. These sweeps were asymmetrically distributed on the A- and B-sub-genomes with regulatory genes being favorably selected.
We mapped these data to genome of Chinese Spring v2.1 and you can access variant resources including 10,672,823 SNPs and 842,369 InDels from JBrowse for Chinese Spring v2.1.

Recently, Li et al. published the paper "Genome sequences of the five Sitopsis species of Aegilops and the origin of polyploid wheat B-subgenome" on the Mol Plant. They report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Ae. bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides. Their results support that the donor of common wheat B-subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B-lineage to which the still extant Ae. speltoides and Am. muticum belong.
You can access genome resources from BLAST, GetSequence, JBrowse and PrimerServer.

Recently, Avni et al. published the paper "Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement" on the plant journal. They produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome.
You can access genome resources from BLAST, GetSequence, JBrowse and PrimerServer.

Recently, Wang et al. published the paper "Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation" on the G3 Genes|Genomes|Genetics. They updated genome of Ae. tauschii acc. AL8/78 to Aet5.0. You can access genome resources from BLAST, GetSequence and PrimerServer. To easily access these data, they also built a JBrowse.

Recently, our paper about this website was published in Molecular Plant. "WheatOmics: a platform combining multiple omics data to accelerate functional genomics studies in wheat".

Recently, Zhang et al. published the paper "Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements" on the Genome Research. They created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. You can access these resources from Triticum urartu JBorwse track GSE167229.To easily access these data, they also built a website.

Recently, Rabanus-Wallace et al. published the paper "Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential" on the Nature Genetics. They produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, He et al. published the paper "CRISPR-Cereal: A Guide RNA Design Tool Integrating Regulome and Genomic Variation for Wheat, Maize and Rice" on the Plant Biotechnology Journal.They developed a fast and precise sgRNA design tool, named CRISPR-Cereal for wheat, maize and rice. Compared to other sgRNA design tools,CRISPR-Ceral has several advantages. You can search your gene ID (IWGSCv1.1) on their website "CRISPR-Cereal".

Recently, Sato et al. published the paper "Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’" on the DNA Research.They established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. You can access these resources from BLAST, GetSequence, PrimerServer and JBorwse.

Recently, Wang et al. published the paper "An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses" on the Plant Cell.They provided a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat. We added these data to JBorwse track(GSE139019). To easily access these data, they also built a website Chinese Spring Chromatin State Database.

Recently, Zhou et al. published the paper "Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement" on Nature Plants.They de novo assembled four new reference genomes. Now, these four Aegilops tauschii genomes (AY17, AY61, T093, XJ02) and their's genes and proteins were added to our website. You can access these resources from BLAST, GetSequences, PrimerServer and JBorwse.

Recently, Zhu et al. published Chinese Spring genome v2.1 on Plant Journal. You can access these resources from BLAST, GetSequences, PrimerServer and JBorwse.