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Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

In this Stage 2 Registered Report, Buchanan et al. show evidence confirming the phenomenon of semantic priming across speakers of 19 diverse languages.

Analysing camera-trap data of 163 mammal species before and after the onset of COVID-19 lockdowns, the authors show that responses to human activity are dependent on the degree to which the landscape is modified by humans, with carnivores being especially sensitive.

European rivers have over a million barriers hindering aquatic species migration and altering freshwater habitats. This study quantifies the spatial extent of upstream fish habitat alteration caused by physical blockage and shows that impoundments have altered 10% or 200,000 km of free-flowing river habitat in Europe.

Validated barrier inventories and modelling indicate that Europe’s rivers are fragmented by more than one million barriers, such as dams, weirs and fords, causing major impacts on biodiversity.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

Synthetic apparel is a major contributor to global plastic leakage driven by mismanaged apparel waste.

Around 1% of the A subgenome of modern bread wheat (Triticum aestivum) originates from einkorn (Triticum monococcum), the first domesticated wheat species.

The genome is folded in 3-dimensions, though the lack of robust ultra-resolution imaging makes this difficult to visualise. Here, the authors present 3D-EMISH that combines serial block-face scanning electron microscopy with in situ hybridization.

Familial dysautonomia is a rare genetic disease caused in part by neurodegeneration. Here, the authors show that the gut-metabolism axis is altered in both patients and transgenic mice and that disease pathology is ameliorated by controlling microbiome divergence.

Geospatial estimates of the prevalence of anemia in women of reproductive age across 82 low-income and middle-income countries reveals considerable heterogeneity and inequality at national and subnational levels, with few countries on track to meet the WHO Global Nutrition Targets by 2030.

A chromosome-scale genome assembly of rye inbred line ‘Lo7’ provides insights into its incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution and the yield benefits of rye–wheat introgressions.

Exploring the diversity of the wild progenitor of the wheat D subgenome allows for rapid trait discovery.

Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.

The Aegilops tauschii-derived leaf rust resistance gene Lr42 has been widely used for breeding resistance wheat cultivars, but the molecular basis is unknown. Here, the authors show that Lr42 encodes an NLR-type of disease resistance gene by bulked segregant mapping in Ae. tauschii and confirm its function in common wheat.

Large-scale genomic analyses in wheat identify regions associated with 50 agronomic traits evaluated in South Asia, Africa and the Americas. This genotype–phenotype map can be used to enhance wheat productivity and stress resilience.

Exposure to ultraviolet light is responsible for a large proportion of melanomas but the molecular mechanisms are unknown. In this study, melanoma is found to be induced in mice by UVA and UVB light in a pigment-dependent and -independent manner, respectively, resulting in different types of DNA damage.

The International Barley Genome Sequencing Consortium reports sequencing and assembly of a reference genome for barley, Hordeum vulgare.

Genome-wide analysis identifies 32 loci associated with breast cancer susceptibility, accounting for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade.

The treasure trove of disease resistance genes present in wild relatives of domesticated crops is rapidly discovered using association genetics and enrichment sequencing.

The resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata, encodes an unusual tandem kinase fusion protein that confers wheat leaf rust resistance.

The resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum, encodes an unusual protein kinase fusion protein that confers wheat stem rust resistance.

An integrated high-resolution genetic, physical and shotgun sequence assembly of the barley genome, one of the earliest domesticated and most important crops, is described; it will provide a platform for genome-assisted research and future crop improvement.

The nucleotide diversity present in maize exceeds that in humans by an order of magnitude, and it has been challenging to characterize the high levels of diversity in this important crop. Doreen Ware and colleagues have identified 55 million SNPs in 103 domesticated and pre-domestication Zea mays varieties, as well as in a representative from the sister genus Tripsacum.

Integration of skim sequencing data for a recombinant inbred line population derived from a cross between wild and domesticated einkorn wheat accessions with a reference genome assembly enables high-resolution mapping of agronomic traits.

Delorean et al., along with colleagues from the Open Wild Wheat Consortium, present an analysis of Aegilops tauschii genomes to investigate the origins of the Glu-D1 gene in modern wheats. They discover an abundance of novel Glu-D1 gene alleles that could serve as a reservoir for generating higher quality wheat varieties. This is a companion to the Consortium paper which is available in Nature Biotechnology.

Krattinger, Abrouk et al. use genome wide association study and haplotype analyses to investigate the genetics of glume colour in ten reference grade wheat genomes. Haplotype comparison identifies a MYB transcription factor as a candidate gene for red glume colour.

de Sousa et al. present a data-driven decentralized crop breeding approach called 3D-breeding that is geared toward improving yields for smallholder farmers. 3D-breeding is applied to a case study of durum wheat in Ethiopia, which demonstrates higher prediction accuracies for grain yield than the existing model.