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Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.

Cultivation of common hop (Humulus lupulusL.) has increased dramatically during the past decade, with the primary growth occurring in the Pacific Northwest of the United States. A major limitation to hop production is hop powdery mildew [caused by Podosphaera macularis(Wallr.) Braun & Takam]. To date, a comprehensive evaluation of wild hop germplasm resources for resistance to hop powdery mildew has yet to be conducted. Herein, we report the first extensive powdery mildew resistance screening of 244 wild H. lupuluspopulations (6,732 individuals) collected from North America and Eurasia. We used an elimination screening approach by sequentially inoculating four P. macularisisolates containing virulence on all previously described Rgenes. We detected the presence of powdery mildew resistance to isolates representing extant pathogenic diversity in seven germplasms (UMN‐PMR‐002 Male [Reg. no. GP‐38, PI 699936], UMN‐PMR‐005 [Reg. no. GP‐39, PI 699937], UMN‐PMR‐006 Female [GP‐40, PI 699938], UMN‐PMR‐007 Male [Reg. no. GP‐41, PI 699939], UMN‐PMR‐008 [Reg. no. GP‐042, PI 699940], UMN‐PMR‐010 Male [Reg. no. GP‐43, OU 699941], UMN‐PMR‐013 Female [Reg. no. GP‐44, PI 699942]). Based upon genotypic profiling, the seven germplasms were identified in H. lupulusvar. lupulusoriginating from Eurasia. These accessions could be used to introgress broad‐spectrum powdery mildew resistance in hop breeding programs worldwide. New hop powdery mildew resistant sources were identified from wild Eurasian hops.Rootstocks of powdery mildew resistant sources were deposited in the National Plant Germplasm System.Biological sex of powdery mildew resistant germplasm was determined to aid in future breeding and genetic studies.

Improving grain protein content and flour quality is an important goal for wheat (Triticum aestivumL.) breeding programs. Identification of genomic regions and markers associated with quality traits can help enrich wheat breeding germplasm with favorable alleles. This study was carried out to identify genetic loci controlling bread‐making quality traits in a nested association mapping population of 230 lines. Lines were evaluated for grain protein content and three gluten aggregation traits from the Brabender GlutoPeak instrument: peak maximum time (PMT), maximum torque (MT), and aggregation energy (AE). The strongest positive correlation was observed between AE and MT (r= .87), whereas the strongest negative correlation was between PMT and MT (r= −.46). We identified 25 quantitative trait loci (QTL) associated with these traits on 14 chromosomes, of which three QTL were common between MT and AE. Quantitative trait loci explaining the largest variations were observed for grain protein content and AE, with QTL that explained 13% of the observed variation for each trait. Nearly 62% of the discovered QTL were of medium effect, as the median percentage of observed phenotypic variation explained by the detected QTL was 7% (range of 4–13%). Based on QTL analysis and marker screening results, the populations discussed in this study are segregating for the known alleles of the high‐molecular‐weight glutenin gene Glu‐D1. As some lines have better phenotypic performance relative to the elite common parent RB07, crossing these lines with elite breeding lines can help increase the frequency of alleles contributing to improve flour quality traits.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticumspp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. 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 stresses4,5. 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 Sm16, 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.

The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis.Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.

Crop improvement relies on the ability to utilize novel genetic variation. Six‐rowed malting barley (Hordeum vulgareL. subsp. vulgare) developed in the US Midwest has an especially narrow genetic base. Therefore, developing strategies to widen the genetic base in barley is important for continued crop improvement. A wild barley [Hordeum vulgareL. subsp. spontaneum(K. Koch) Thell.] advanced backcross–nested association mapping (AB‐NAM) population was developed to assess wild‐barley‐derived alleles in an elite spring six‐rowed malting barley background. The 796 BC2F4:6lines in the AB‐NAM were derived from 25 wild barley accessions backcrossed to the cultivar Rasmusson. Because the AB‐NAM design minimizes the deleterious and unadapted traits of the wild barley parents, the population was screened in five field environments for the agronomic traits: days to heading, height, productive tiller number (PTN), test weight, and yield. The number of loci identified ranged from two (PTN, the trait with the lowest heritability) to 19 (height). Domestication‐related genes were identified for each trait, particularly the photoperiod gene Ppd‐H1for days to heading, height, and PTN and the nonbrittle Btr1/Btr2loci for test weight and yield. Only a single variant showed beneficial variation for yield from a wild barley allele, but positive effects were identified for the other traits examined, including positive variants for test weight on chromosomes 1H and 3H. The AB‐NAM population is a novel resource to map agronomically important traits associated with wild barley alleles.

Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.

The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown. By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis-than by trans-genetic factors. We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping.

Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgareL.), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six‐row and two‐row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model‐based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two‐row spring, two six‐row spring, and two six‐row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long‐range LD suggestive of admixture. Genetic distance (allele‐sharing) between populations varied from 0.11 (six‐row spring vs. six‐row spring) to 0.45 (two‐row spring vs. six‐row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele‐sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable.

Restoration of native plant communities requires adapted germplasm; thus, information is needed to guide native seed collection and production. Analysis of genetic variation has potential to provide insight into diversity and relatedness of natural populations. Our objectives were to examine genetic diversity of native species in Minnesota to discover if variation is related to biomes or distance, and possibly to develop seed collection zones. Our study included prairie cordgrass (Spartina pectinata), purple prairie clover (Dalea purpurea), and spotted joe‐pye weed (Eupatorium maculatum). Using amplified fragment length polymorphisms, we analyzed 100 samples from eight populations for prairie cordgrass, 152 samples from nine populations for purple prairie clover, and 127 samples from 10 populations for spotted joe‐pye weed. We found moderate to high levels of genetic diversity within each species. Small populations were not necessarily lower in diversity than larger ones. Analysis of molecular variance results indicate clear population differentiation. However, rather than displaying geographic or ecological associations, the variation had discontinuous patterns. Therefore, we were not able to develop unambiguous recommendations for seed collection. We discuss the applicability of molecular markers in detecting adaptive potential.

Leaf rust, stem rust, and stripe rust are among the most important diseases of wheat and barley worldwide and are best controlled using genetic resistance. To increase the diversity of rust resistance in wheat and barley, a project was initiated to identify and characterise rust resistance genes from the wild species of Aegilops sharonensis (Sharon goatgrass) and Hordeum vulgare ssp. spontaneum (wild barley), respectively. One hundred and two accessions of Sharon goatgrass from Israel and 318 Wild Barley Diversity Collection (WBDC) accessions from the Fertile Crescent, Central Asia, North Africa, and the Caucasus region were evaluated for resistance to leaf rust, stem rust, and/or stripe rust. Sharon goatgrass exhibited a wide range of infection types (ITs) in response to leaf rust, stem rust, and stripe rust. The percentage of resistant accessions in Sharon goatgrass was 58.8?78.4% for leaf rust, 11.8?69.6% for stem rust, and 46.1% for stripe rust, depending on the race used and the plant growth stage. Genetic studies with Sharon goatgrass revealed oligogenic resistance to leaf rust and stem rust. Wild barley also exhibited a wide range of ITs to leaf rust and stem rust; however, the overall frequency of resistance was lower than for Sharon goatgrass. The percentage of resistant accessions in wild barley was 25.8% for leaf rust and 5.7?20.1% for stem rust, depending on the race used. Resistance to the new virulent stem rust race TTKS (i.e. Ug99), present in eastern Africa, was found in both Sharon goatgrass (70% of accessions) and wild barley (25% of 20 accessions tested). Association mapping for stem rust resistance was applied in the WBDC using Diversity Arrays Technology (DArT) markers. Using the highly conservative P value threshold of 0.001, 14 and 15 significant marker associations were detected when the number of subpopulations (K value) was set for 10 and 8, respectively. These significant associations were in 9 and 8 unique chromosome bins, respectively. Two significant marker associations were detected for resistance to the wheat stem rust race MCCF in the same bin as the rpg4/Rpg5 complex on chromosome 7(5H). The presence of a major stem rust resistance gene in this bin on chromosome 7(5H) was validated in a bi-parental mapping population (WBDC accession Damon cv. Harrington) constructed with DArT markers. The results from this study indicate that Sharon goatgrass and wild barley are rich sources of rust resistance genes for cultivated wheat and barley improvement, respectively, and that association mapping may be useful for positioning disease resistance genes in wild barley.

Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam(hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No garyhomologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted garyprotein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Garyis expressed in wheat and barley spikes and garycDNA sequences are also found in rice, oat, rye, maize, sorghum and sugarcane. The short inverted terminal repeats, flanked by an eight-nucleotide host sequence duplication, which are characteristic of a hATtransposon are absent. Genetic mapping in barley shows that garyis located on the distal end of the long arm of chromosome 2H. Wheat homologues of garymap to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garysmaps to the syntenic location near the bottom of rice chromosome 4. These data suggest that garyhas resided in a single genomic location for at least 60 Myr and has lost the ability to transpose, yet expresses a transposase-related protein that is being conserved under host selection. We propose that the garytransposase-like gene has been recruited by the cereal grasses for an unknown function.Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam(hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No garyhomologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted garyprotein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Garyis expressed in wheat and barley spikes and garycDNA sequences are also found in rice, oat, rye, maize, sorghum and sugarcane. The short inverted terminal repeats, flanked by an eight-nucleotide host sequence duplication, which are characteristic of a hATtransposon are absent. Genetic mapping in barley shows that garyis located on the distal end of the long arm of chromosome 2H. Wheat homologues of garymap to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garysmaps to the syntenic location near the bottom of rice chromosome 4. These data suggest that garyhas resided in a single genomic location for at least 60 Myr and has lost the ability to transpose, yet expresses a transposase-related protein that is being conserved under host selection. We propose that the garytransposase-like gene has been recruited by the cereal grasses for an unknown function.

Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is a major disease problem in wheat (Triticum aestivum). Genetic engineering holds significant potential to enhance FHB resistance in wheat. Due to the requirement of screening for FHB resistance on flowers at anthesis, the number of screens carried out in a year is limited. Our objective was to evaluate the feasibility of using the rapid-maturing dwarf wheat cultivar Apogee as an alternative genotype for transgenic FHB resistance research. Our transformation efficiency (number of transgenic plants/number of embryos) for Apogee was 1.33%. Apogee was also found to exhibit high FHB susceptibility and reached anthesis within 4 weeks. Interestingly, microsatellite marker haplotype analysis of the chromosome 3BS FHB resistant quantitative trait locus (QTL) region indicated that this region maybe deleted in Apogee. Our results indicate that Apogee is particularly well suited for accelerating transgenic FHB resistance research and transgenic wheat research in general.Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is a major disease problem in wheat (Triticum aestivum). Genetic engineering holds significant potential to enhance FHB resistance in wheat. Due to the requirement of screening for FHB resistance on flowers at anthesis, the number of screens carried out in a year is limited. Our objective was to evaluate the feasibility of using the rapid-maturing dwarf wheat cultivar Apogee as an alternative genotype for transgenic FHB resistance research. Our transformation efficiency (number of transgenic plants/number of embryos) for Apogee was 1.33%. Apogee was also found to exhibit high FHB susceptibility and reached anthesis within 4 weeks. Interestingly, microsatellite marker haplotype analysis of the chromosome 3BS FHB resistant quantitative trait locus (QTL) region indicated that this region maybe deleted in Apogee. Our results indicate that Apogee is particularly well suited for accelerating transgenic FHB resistance research and transgenic wheat research in general.

Wheat–barley chromosome addition lines are useful genetic resources for a variety of studies. In this study, transcript accumulation patterns in Betzes barley, Chinese Spring wheat, and Chinese Spring–Betzes chromosome addition lines were examined with the Barley1 Affymetrix GeneChip probe array. Of the 4014 transcripts detected in Betzes but not in Chinese Spring, 365, 271, 265, 323, 194, and 369 were detected in wheat–barley disomic chromosome addition lines 2(2H), 3(3H), 4(4H), 7(5H), 6(6H), and 1(7H), respectively. Thus, 1787 barley transcripts were detected in a wheat genetic background and, by virtue of the addition line in which they were detected, were physically mapped to barley chromosomes. We validated and extended our approach to physically map barley genes to the long and short arms of chromosome 6(6H). Our physical map data exhibited a high level of synteny with homologous sequences on the wheat and/or rice syntenous chromosomes, indicating that our barley physical maps are robust. Our results show that barley transcript detection in wheat–barley chromosome addition lines is an efficient approach for large-scale physical mapping of genes.

Kernel color and grain protein concentration (GPC) are two of the most important attributes of barley (Hordeum vulgareL.) grain intended for use in malting and brewing. Grain with protein levels that are too low or high or that have dark kernel color, which may result from the disease complex of kernel discoloration (KD), is unacceptable for the malting and brewing industries. The purpose of this study was to use molecular markers to map quantitative trait loci (QTLs) for KD and GPC in two recombinant inbred line (RIL) populations. One population was created by means of the high GPC and KD resistant cultivar Chevron. The other population was created from a KD resistant cultivar MNBrite that was derived from Chevron through eight generations of crossing and selection for bright kernels. The traits KD and GPC were evaluated in four and three environments, respectively, using the Chevron population and six environments using the MNBrite population. GPC and KD score were negatively correlated in both populations. A revised genetic map for the Chevron/M69 population, with an additional 45 simple sequence repeat (SSR) markers, was used to identify nine QTLs associated with KD on chromosomes 1(7H), 2(2H), 4(4H), 6(6H), and 7(5H), including two major QTLs on chromosome 6(6H). A single QTL for GPC identified in the Chevron mapping population, accounting for over 55% of the phenotypic variation, was located on chromosome 6(6H) and was coincident with one of the two major QTLs for KD. In this region, the Chevron allele increased GPC and decreased KD score. In the MNBrite mapping population, the same region of chromosome 6(6H) was mapped with SSR markers, and QTL analysis verified that this region was associated with both KD and GPC, indicating that MNBrite inherited this region of chromosome 6(6H) from Chevron. The results of this study suggest that if GPC and KD are controlled by tightly linked genes, then it should be possible to use SSR markers to identify recombinants in this region of chromosome 6(6H) and break the linkage to allow selection for KD resistance without high GPC. Alternatively, if GPC and KD are conditioned by the same gene, then it should be possible to select for KD resistance from Chevron by means of SSR markers and to use phenotypic selection to introgress other genes to reduce GPC to acceptable levels.

Wheat spikes infected by Fusarium graminearumresult in Fusariumhead blight, a devastating disease of wheat. The spikes respond to infection by inducing a set of defense response genes in infected spikelets much as has been shown in other plant-pathogen interactions. To determine whether defense response genes are expressed systemically within F. graminearum-inoculated wheat spikes, we examined transcript accumulation of four defense response genes (peroxidase, PR-1, PR-3 and PR-5) in colonized and uncolonized portions of wheat spikes of resistant and susceptible genotypes. We determined whether sampled regions of point-inoculated wheat spikes were colonized or not using a Fusariumspp.-specific plate assay and an F. graminearumisolate expressing β-glucuronidase (GUS). The GUS-expressing F. graminearumisolate proved particularly useful for visualizing and following the spread of the fungus and for measuring the amount of fungal biomass in spike tissues. We found that transcripts of the four defense response genes accumulated in both colonized and uncolonized regions of spikes of resistant and susceptible genotypes at 48h after inoculation. These results demonstrate that direct contact with the pathogen is not required for induction of defense response genes and that these genes are activated in both susceptible and resistant genotypes.

The longitudinal axis of the maize leaf is composed of, in proximal to distal order, sheath, ligule, auricle and blade. The semidominant Liguleless3-O (Lg3-O) mutation disrupts leaf development at the ligular region of the leaf midrib by transforming blade to sheath. In a previous study, we showed that leaf sectors of Lg3 mutant activity are cell nonautonomous in the transverse dimension and can confer several alternative developmental fates (Fowler, Muehlbauer and Freeling (1996)Genetics 143, 489-503). In our present study we identify five Lg3 sector types in the leaf: sheath-like with displaced ligule (sheath-like), sheathlike with ectopic ligule (ectopic ligule), auricle-like, macrohairless blade and wild-type blade. The acquisition of a specific sector fate depends on the timing of Lg3 expression. Early Lg3 expression results in adoption of the sheath-like phenotype at the ligule position (a proximal cell fate), whereas later Lg3 expression at the same position results in one of the more distal cell fates. Furthermore, sheathlike Lg3 sectors exhibit a graded continuum of phenotypes in the transformed blade region from the most proximal (sheath) to the most distal (wild-type blade), suggesting that cell fate acquisition is a gradual process. We propose a model for leaf cell fate acquisition based on a timing mechanism whereby cells of the leaf primordium progress through a maturation schedule of competency stages which eventually specify the cell types along the proximal to distal axis of the leaf. In addition, the lateral borders between Lg3 ‘on’ sectors and wild-type leaf sometimes provide evidence of no spreading of the transformed phenotype. In these cases, competency stages are inherited somatically.

Molecular mapping led to the identification of two major Fusarium head blight (FHB) resistance QTL, Fhb1and Qfhs.ifa-5A. The actual function of the resistance genes is still unknown. The resistant line CM82036, the susceptible line Remus and six closely related lines were analyzed for differential gene expression after Fusarium attack. The related lines show contrasting levels of FHB resistance due to the possession of Fhb1and Qfhs.ifa-5A. At anthesis plants were challenged by Fusarium graminearumor water and at six time points after inoculation gene expression of specific wheat floral tissue was analyzed by cDNA-AFLPs and the Affymetrix Wheat GeneChip.

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effects should have been B73, rather than Mo17, due to the original coding of biallele SNPs as “0s” and “1s”. Going through the entire analysis procedure, it was determined that the mistake was made while tabulating the eQTL results from QTL Cartographer.

There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys.