Search

The predicted increase in frequency of droughts and rising temperatures in Europe will lead core populations of a temperate plant to an evolutionary dead-end unless they acquire genetic alleles that are present only in extreme edge Mediterranean, Scandinavian, or Siberian populations.

Here, a combination of forward genetics and genome-wide association analyses has been used to show that variation at a single genetic locus in Arabidopsis thaliana underlies phenotypic variation in vegetative growth as well as resistance to infection. The strong enhancement of resistance mediated by one of the alleles at this locus explains the allele's persistence in natural populations throughout the world, even though it drastically reduces the production of new leaves.

Detlef Weigel and colleagues report results from the first phase of the Arabidopsis 1001 Genomes Project, based on short-read sequencing of 80 geographically diverse strains. This collection of strains has been made available to the scientific community, and the authors show that the identified polymorphisms in these strains can be useful for imputation and genome-wide association studies.

To celebrate the first 10 years ofNature Reviews Genetics, we asked eight leading researchers for their views on the key developments in genetics and genomics in the past decade and the prospects for the future.

Closely related plant species can have drastically different abundances of transposable elements. Now it is shown that the genome of Arabis alpina has experienced a striking expansion of retrotransposons, probably shaped by reduced DNA methylation.

Stephen Wright, Detlef Weigel and colleagues report the whole-genome sequence of Capsella rubella, a highly selfing crucifer found throughout much of southern and western Europe. They compare mixed-stage flower bud transcriptomes from C. rubella and C. grandiflora, finding a shift in expression of genes associated with flowering phenotypes and providing insights into the transition to selfing.

Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata. In comparison with the much smaller genome of A. thaliana, from which A. lyrata diverged about 10 million years ago, they find that the reduction in genome size is attributed to a large number of deletions across the genome.

Sanwen Huang, Detlef Weigel, Roger Beachy and Jiayang Li propose a regulatory framework for precision breeding with genome-edited crops. They argue that society should benefit from the latest advances in plant genetics and genomics.

Here, the authors show that an inverted-repeat transposon located next to the pattern recognition receptor ELONGATION FACTOR-TU RECEPTOR (EFR)-encoding gene in Arabidopsis controls chromatin organization, EFR gene expression and plant immune response.

Genome assemblies of 13 domesticated and wild rice relatives reveal salient features of genome evolution across the genus Oryza, especially rapid species diversification and turnover of transposons. This study also releases a complete long-read assembly of IR 8 ‘Miracle Rice’.

With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field.

Data on de novo mutations in Arabidopsis thaliana reveal that mutations do not occur randomly; instead, epigenome-associated mutation bias reduces the occurrence of deleterious mutations.

The ability of a species to adapt to climate change depends on its genetic diversity. Here, based on the geographic distribution of genetic variants associated with drought resistance in Arabidopsis thaliana, the authors predict the future genetic maladaptation of Central European populations.

Massively parallel reporter assays in four plant species show that transcriptional regulatory elements are position dependent with enrichment downstream of the transcription start site, particularly GATC motifs with strong effects in vascular plants.

Analysis of genomic data from 25 distantly related plant species shows signatures of selection on the same gene families and functions that repeatedly contributed to local adaptation to climate.

Inter- and intra-species comparison of Arabidopsis centromere variation identifies rapid cycles of transposon invasion and purging through satellite homogenization that drive centromere evolution.

The authors conduct competition experiments with multiple strains of Pseudomonas (some pathogenic and some commensal) in the phylosphere microbiome of Arabidopsis plants, showing that both the host and the commensal strains interact to inhibit the pathogenic strains.

In plants and mammals, retrotransposons are transcriptionally silenced by DNA methylation, but activating transcription by mutating a gene involved in DNA methylation does not activate retrotransposition. Here it is shown that, after transcriptional reactivation, transposition remains suppressed due to the activity of a plant-specific RNA polymerase and a histone methyltransferase. This mechanism appears to be specific for a particular retrotransposon known as Évadé.

Interactions among plant hosts, bacteria and fungi are measured at high spatial resolution.

The leaf microbiome compositions of 267 Arabidopsis thaliana populations across Europe reveal associations with climate and plant genetics.

Pattern-triggered immunity is activated by recognition of microbe-derived structures by host pattern recognition receptors. Here the authors use a genotype-by sequencing approach to show that bacterial translation initiation factor 1 triggers PTI in Arabidopsis thaliana after recognition by the RLP32 receptor.

PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.

Phytochrome signaling in the nucleus can activate expression of photosynthesis-associated genes in plastids. Here Yang et al. show that NCP is a dual-targeted protein that promotes phytochrome B localization to photobodies in the nucleus while facilitating PEP polymerase assembly in the plastids.

Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.

Reduction in gene flow between varieties is part of the process of speciation. One underappreciated reason for such a reduction is hybrid necrosis — when the hybrid offspring have phenotypes that resemble the results of pathogen attack and environmental stress.

Arabidopsis thaliana, a member of the phenotypically diverse Brassicaceae family, has proved to be a key model organism for characterizing plant genome and morphological evolution. This Review outlines how recent comparative and functional genomic studies usingArabidopsisrelatives have further advanced our understanding of plant diversity and evolution.

The authors provide mechanistic insights into the crosstalk between signalling components of pattern-triggered immunity and effector-triggered immunity and their molecular linkers.

Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.

Light initiates chloroplast biogenesis by controlling gene expression in plastids. Here Yoo et al. show that nuclear phytochrome signaling triggers plastid gene expression via a novel dual-localized protein necessary for nuclear phytochrome signaling and subsequent anterograde signaling to the plastid.

A previously unknown way of reversing genome-wide sequence changes in DNA has been revealed by an analysis of plants carrying mutations in a gene called HOTHEAD. The mechanism remains a mystery.

Phloem is responsible for long-distance transport of molecules in plants and conducting phloem cells are joined by sieve areas that facilitate cell-to-cell transport. Here the authors identify mutations in the gene encoding CHOLINE TRANSPORTER-LIKE1 that cause abnormalities in sieve areas and impaired phloem conduction.