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Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2 , 3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4 , 5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. 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.

Resisting a dawn raid Circadian rhythms regulate a wide variety of developmental and metabolic processes resulting in enhanced fitness. This study of plant defence against the fungal pathogen Hyaloperonospora arabidopsidis , which causes downy mildew disease in Arabidopsis plants, reveals a link between the plant innate immune responses and the clock. The central circadian regulator CCA1 is shown to regulate a novel set of genes involved in R -gene-mediated defence. The mechanism allows plants to 'anticipate' infection at dawn when the pathogen normally disperses its spores. Circadian rhythms regulate a wide variety of developmental and metabolic processes resulting in enhanced fitness. In this study, a link is made between plant immune responses and the circadian clock. Plant defence against a fungal pathogen which causes downy mildew disease in Arabidopsis is studied, and it is shown that a novel set of defence genes are regulated by the circadian regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). The mechanism allows plants to 'anticipate' infection at dawn when the pathogen normally disperses its spores. Such a cross-talk mechanism reveals an important strategy for plants to time immune responses against pathogens. The principal immune mechanism against biotrophic pathogens in plants is the resistance ( R )-gene-mediated defence 1 . It was proposed to share components with the broad-spectrum basal defence machinery 2 . However, the underlying molecular mechanism is largely unknown. Here we report the identification of novel genes involved in R -gene-mediated resistance against downy mildew in Arabidopsis and their regulatory control by the circadian regulator, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). Numerical clustering based on phenotypes of these gene mutants revealed that programmed cell death (PCD) is the major contributor to resistance. Mutants compromised in the R -gene-mediated PCD were also defective in basal resistance, establishing an interconnection between these two distinct defence mechanisms. Surprisingly, we found that these new defence genes are under circadian control by CCA1, allowing plants to ‘anticipate’ infection at dawn when the pathogen normally disperses the spores and time immune responses according to the perception of different pathogenic signals upon infection. Temporal control of the defence genes by CCA1 differentiates their involvement in basal and R -gene-mediated defence. Our study has revealed a key functional link between the circadian clock and plant immunity.

Living organisms must acquire new biological functions to adapt to changing and hostile environments. Deepwater rice has evolved and adapted to flooding by acquiring the ability to significantly elongate its internodes, which have hollow structures and function as snorkels to allow gas exchange with the atmosphere, and thus prevent drowning. Many physiological studies have shown that the phytohormones ethylene, gibberellin and abscisic acid are involved in this response, but the gene(s) responsible for this trait has not been identified. Here we show the molecular mechanism of deepwater response through the identification of the genes SNORKEL1 and SNORKEL2, which trigger deepwater response by encoding ethylene response factors involved in ethylene signalling. Under deepwater conditions, ethylene accumulates in the plant and induces expression of these two genes. The products of SNORKEL1 and SNORKEL2 then trigger remarkable internode elongation via gibberellin. We also demonstrate that the introduction of three quantitative trait loci from deepwater rice into non-deepwater rice enabled the latter to become deepwater rice. This discovery will contribute to rice breeding in lowland areas that are frequently flooded during the rainy season.

Depending on the method of NaCl application, whether gradual or in a single step, plants may experience either salt stress or salt shock, respectively. The first phase of salt stress is osmotic stress. However, in the event of salt shock, plants suffer osmotic shock, leading to cell plasmolysis and leakage of osmolytes, phenomena that do not occur with osmotic stress. Patterns of gene expression are different in response to salt stress and salt shock. Salt stress initiates relatively smooth changes in gene expression in response to osmotic stress and a more pronounced change in expression of significant numbers of genes related to the ionic phase of salt stress. There is a considerable time delay between changes in expression of genes related to the osmotic and ionic phases of salt stress. In contrast, osmotic shock results in strong, rapid changes in the expression of genes with osmotic function, and fewer changes in ionicresponsive genes that occur earlier. There are very few studies in which the effects of salt stress and salt shock are described in parallel experiments. However, the patterns of changes in gene expression observed in these studies are consistently as described above, despite the use of diverse plant species. It is concluded that gene expression profiles are very different depending the method of salt application. Imposition of salt stress by gradual exposure to NaCl rather than salt shock with a single application of a high concentration of NaCl is recommended for genetic and molecular studies, because this more closely reflects natural incidences of salinity.

Summary Due to their different lifestyles, effective defence against biotrophic pathogens normally leads to increased susceptibility to necrotrophs, and vice versa. Solving this trade‐off is a major challenge for obtaining broad‐spectrum resistance in crops and requires uncoupling the antagonism between the jasmonate (JA) and salicylate (SA) defence pathways. Pseudomonas syringae pv. tomato (Pto) DC3000, the causal agent of tomato bacterial speck disease, produces coronatine (COR) that stimulates stomata opening and facilitates bacterial leaf colonization. In Arabidopsis, stomata response to COR requires the COR co‐receptor AtJAZ2, and dominant AtJAZ2Δjas repressors resistant to proteasomal degradation prevent stomatal opening by COR. Here, we report the generation of a tomato variety resistant to the bacterial speck disease caused by PtoDC3000 without compromising resistance to necrotrophs. We identified the functional ortholog of AtJAZ2 in tomato, found that preferentially accumulates in stomata and proved that SlJAZ2 is a major co‐receptor of COR in stomatal guard cells. SlJAZ2 was edited using CRISPR/Cas9 to generate dominant JAZ2 repressors lacking the C‐terminal Jas domain (SlJAZ2Δjas). SlJAZ2Δjas prevented stomatal reopening by COR and provided resistance to PtoDC3000. Water transpiration rate and resistance to the necrotrophic fungal pathogen Botrytis cinerea, causal agent of the tomato gray mold, remained unaltered in Sljaz2Δjas plants. Our results solve the defence trade‐off in a crop, by spatially uncoupling the SA‐JA hormonal antagonism at the stomata, entry gates of specific microbes such as PtoDC3000. Moreover, our results also constitute a novel CRISPR/Cas‐based strategy for crop protection that could be readily implemented in the field.

Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat’s domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

Yusaku Uga and colleagues show that the gene underlying the rice quantitative trait locus DEEPER ROOTING 1 ( DRO1 ) influences root growth angle and allows plants to maintain high yield performance under drought conditions. They further show that DRO1 is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas 1 . Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 ( DRO1 ), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.

Makoto Matsuoka and colleagues use a whole-genome sequencing-based approach to perform genome-wide association analysis for important agronomic traits in rice. Using phenotypically diverse rice with low interrelationships, they rapidly identify novel genes associated with heading date, plant height and panicle number per plant, validating candidates with transgenic experiments. A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.

Two major genes for Na + exclusion in durum wheat, Nax1 and Nax2, that were previously identified as the Na + transporters TmHKT1;4-A2 and TmHKT1;5-A, were transferred into bread wheat in order to increase its capacity to restrict the accumulation of Na + in leaves. The genes were crossed from tetraploid durum wheat (Triticum turgidum ssp. durum) into hexaploid bread wheat (Triticum aestivum) by interspecific crossing and marker-assisted selection for hexaploid plants containing one or both genes. Nax1 decreased the leaf blade Na + concentration by 50%, Nax2 decreased it by 30%, and both genes together decreased it by 60%. The signature phenotype of Nax1, the retention of Na + in leaf sheaths resulting in a high Na + sheath:blade ratio, was found in the Nax1 lines. This conferred an extra advantage under a combination of waterlogged and saline conditions. The effect of Nax2 on lowering the Na + concentration in bread wheat was surprising as this gene is very similar to the TaHKT1;5-D Na + transporter already present in bread wheat, putatively at the Kna1 locus. The results indicate that both Nax genes have the potential to improve the salt tolerance of bread wheat.