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.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

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.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum. Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2–13 million years ago.

/pdf/genome-sequence-of-the-cultivated-cotton-gossypium-arboreum-5d7xmfxbyj.pdf

Genome sequence of the cultivated cotton Gossypium arboreum

Editing plant genomes is technically challenging in hard-to-transform plants and usually involves transgenic intermediates, which causes regulatory concerns. Here we report two simple and efficient genome-editing methods in which plants are regenerated from callus cells transiently expressing CRISPR/Cas9 introduced as DNA or RNA. This transient expression-based genome-editing system is highly efficient and specific for producing transgene-free and homozygous wheat mutants in the T0 generation. We demonstrate our protocol to edit genes in hexaploid bread wheat and tetraploid durum wheat, and show that we are able to generate mutants with no detectable transgenes. Our methods may be applicable to other plant species, thus offering the potential to accelerate basic and applied plant genome-engineering research.

/pdf/efficient-and-transgene-free-genome-editing-in-wheat-through-4o09d84xkp.pdf

Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA.

The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.

https://science.sciencemag.org/content/sci/345/6194/1250092.full.pdf

Ancient hybridizations among the ancestral genomes of bread wheat

The genome sequence and its analysis of the diploid wild wheat Triticum urartu (progenitor of the wheat A genome) represent a tool for studying the complex, polyploid wheat genomes and should be a valuable resource for the genetic improvement of wheat. The hexaploid genome of bread wheat Triticum aestivum, designated AABBDD, evolved as a result of hybridization between three ancestral grasses. Two papers published in the issue of Nature present genome sequences and analysis of two of these wheat progenitors. First, the genome sequence of the diploid wild wheat T. urartu (ancestor of the A genome), which resembles cultivated wheat more strongly than either Aegilops speltoides (the B ancestor) or Ae. tauschii (the D donor). And second, the Ae. tauschii genome, together with an analysis of its transcriptome. These genomes and their analyses will be powerful tools for the study of complex, polyploid wheat genomes and a valuable resource for genetic improvement of wheat. 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 (AAGGAmAm), 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.

/pdf/draft-genome-of-the-wheat-a-genome-progenitor-triticum-4jtu60t41n.pdf

Draft genome of the wheat A-genome progenitor Triticum urartu

Optimizing the beneficial mineral elements in rice grains is of interest for rice breeders. To study the environmental effects on mineral accumulation in rice grains, we grew a double-haploid (DH) population derived from the cross between cultivars Chunjiang 06 (CJ06, a japonica rice) and TN1 (an indica rice) under two different ecological environments (Lingshui and Hangzhou, China) and determined the content of Ca, Fe, K, Mg, Mn, P, and Zn in brown rice. These contents show transgressive variation among the DH lines. Subsequently, the quantitative trait loci (QTLs) for mineral accumulation in rice grain were mapped on the chromosomes using CJ06/TN1 population. For the 7 mineral elements investigated, 23 and 9 QTLs were identified for Lingshui and Hangzhou, respectively. Of these, 24 QTLs were reported for the first time in this study and 8 QTLs are consistent with previous reports. Only 2 QTLs for Mg accumulation have been detected in both environments, indicating that mineral accumulation QTLs in rice grains are largely environment dependent. Additionally, co-localizations of QTLs for Mn and Zn, Mg and P, and Mg and Mn accumulation have been observed, implying that these loci might be involved in the accumulation of different elements. Furthermore, the QTLs for the accumulation of Fe, K, Mg, Mn, P, and Zn were mapped to a region close to each other on chromosomes 8 and 9, suggesting that clusters of genes exist on chromosomes 8 and 9. Further characterization of these QTLs will provide a better understanding of the molecular mechanism responsible for mineral accumulation in rice grains.

Biao Wang

Papers

Draft genome of the wheat A-genome progenitor Triticum urartu

Environmental effects on mineral accumulation in rice grains and identification of ecological specific QTLs

SlbHLH068 interacts with FER to regulate the iron-deficiency response in tomato.