Construction of a map-based reference genome sequence for barley, Hordeum vulgare L

Yellow Dwarf Virus Resistance in Barley: Phenotyping, Remote Imagery, and Virus-Vector Characterization

Yellow dwarf viruses (YDVs) spread by aphids are some of the most economically important barley (Hordeum vulgare) virus-vector complexes worldwide. Detection and control of these viruses are critical components in the production of barley, wheat, and numerous other grasses of agricultural importance. Genetic control of plant diseases is often preferable to chemical control to reduce the environmental and economic cost of foliar insecticides. Accordingly, the objectives of this work were to (i) screen a barley population for resistance to YDVs under natural infection using phenotypic assessment of disease symptoms, (ii) implement drone imagery to further assess resistance and test its utility as a disease screening tool, (iii) identify the prevailing virus and vector types in the experimental environment, and (iv) perform a genome-wide association study to identify genomic regions associated with measured traits. Significant genetic differences were found in a population of 192 barley inbred lines regarding their YDV symptom severity, and symptoms were moderately to highly correlated with grain yield. The YDV severity measured with aerial imaging was highly correlated with on-the-ground estimates (r = 0.65). Three aphid species vectoring three YDV species were identified with no apparent genotypic influence on their distribution. A quantitative trait locus impacting YDV resistance was detected on chromosome 2H, albeit undetected using aerial imaging. However, quantitative trait loci for canopy cover and mean normalized difference vegetation index were successfully mapped using the drone. This work provides a framework for utilizing drone imagery in future resistance breeding efforts for YDVs in cereals and grasses, as well as in other virus-vector disease complexes.

Unlocking plant genetics with telomere-to-telomere genome assemblies

Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.

Global identification of LIM genes in response to different heat stress regimes in Lactuca sativa

BACKGROUND

LIM (Lineage-11 (LIN-11), Insulin-1 (ISL-1), and Mechanotransduction-3 (MEC-3)) genes belong to a family that hold ubiquitous properties contributing to organ, seed, and pollen development as well as developmental and cellular responses to biotic and abiotic stresses. Lettuce (Lactuca sativa) is a highly consumed vegetable crop susceptible heat stress. High temperatures limit lettuce's overall yield, quality and marketability. Lettuce LIM genes have not been identified and their role in response to high temperatures is not known. Aiming to identify potential new targets for thermoresilience, we searched for LIM genes in lettuce and compared them with orthologous of several dicotyledons and monocotyledons plant species.

RESULTS

We identified fourteen lettuce LIM genes distributed into eight different subgroups using a genome-wide analysis strategy. Three belonging to DAR (DA means "large" in Chinese) class I, two DAR class II, one in the WLIM1, two in the WLIM2, one in the PLIM1, two in the PLIM2 class, one ßLIM and two δLIMs. No DAR-like were identified in any of the species analyzed including lettuce. Interestingly, unlike other gene families in lettuce which underwent large genome tandem duplications, LIM genes did not increase in number compared to other plant species. The response to heat stress induced a dynamic transcriptional response on LsLIM genes. All heat stress regimes, including night stress, day stress and day and night stress were largely responsible for changes in LIM transcriptional expression.

CONCLUSIONS

Our global analysis at the genome level provides a detailed identification of LIM genes in lettuce and other dicotyledonous and monocotyledonous plant species. Gene structure, physical and chemical properties as well as chromosomal location and Cis-regulatory element analysis together with our gene expression analysis under different temperature regimes identified LsWLIM1, LsWLIM2b, LsDAR3 and LsDAR5 as candidate genes that could be used by breeding programs aiming to produce lettuce varieties able to withstand high temperatures.

Hordedane diterpenoid phytoalexins restrict Fusarium graminearum infection but enhance Bipolaris sorokiniana colonization of barley roots

Plant immunity is a multilayered process that includes recognition of patterns or effectors from pathogens to elicit defense responses. These include the induction of a cocktail of defense metabolites that typically restrict pathogen virulence. Here, we investigate the interaction between barley roots and the fungal pathogens Bipolaris sorokiniana (Bs) and Fusarium graminearum (Fg) at the metabolite level. We identify hordedanes, a previously undescribed set of labdane-related diterpenoids with antimicrobial properties, as critical players in these interactions. Infection of barley roots by Bs and Fg elicits hordedane synthesis from a 600-kb gene cluster. Heterologous reconstruction of the biosynthesis pathway in yeast and Nicotiana benthamiana produced several hordedanes, including one of the most functionally decorated products 19-β-hydroxy-hordetrienoic acid (19-OH-HTA). Barley mutants in the diterpene synthase genes of this cluster are unable to produce hordedanes but, unexpectedly, show reduced Bs colonization. By contrast, colonization by Fusarium graminearum, another fungal pathogen of barley and wheat, is 4-fold higher in the mutants completely lacking hordedanes. Accordingly, 19-OH-HTA enhances both germination and growth of Bs, whereas it inhibits other pathogenic fungi, including Fg. Analysis of microscopy and transcriptomics data suggest that hordedanes delay the necrotrophic phase of Bs. Taken together, these results show that adapted pathogens such as Bs can subvert plant metabolic defenses to facilitate root colonization.

Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages

BACKGROUND

Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation.

METHODS

We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination.

RESULTS

In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties.

CONCLUSIONS

We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.

The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A

Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including "Golden Promise," a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.

The Utilization of Reference-Guided Assembly and In Silico Libraries Improves the Draft Genome of Clarias batrachus and Culter alburnus

Long-read sequencing technologies can generate highly contiguous genome assemblies compared to short-read methods. However, their higher cost often poses a significant barrier. To address this, we explore the utilization of mapping-based genome assembly and reference-guided assembly as cost-effective alternative approaches. We assess the efficacy of these approaches in improving the contiguity of Clarias batrachus and Culter alburnus draft genomes. Our findings demonstrate that employing an iterative mapping strategy leads to a reduction in assembly errors. Specifically, after three iterations, the Mismatches per 100 kbp value for the C. batrachus genome decreased from 2447.20 to 2432.67, reaching a minimum of 2422.67 after two iterations. Additionally, the N50 value for the C. batrachus genome increased from 362,143 to 1,315,126 bp, with a maximum of 1,315,403 bp after two iterations. Furthermore, we achieved Mismatches per 100 kbp values of 3.70 for the reference-guided assembly of C. batrachus and 0.34 for C. alburnus. Correspondingly, the N50 value for the C. batrachus and C. alburnus genomes increased from 362,143 bp and 3,686,385 bp to 2,026,888 bp and 43,735,735 bp, respectively. Finally, we successfully utilized the improved C. batrachus and C. alburnus genomes to compare genome studies using the combined approach of Ragout and Ragtag. Through a comprehensive comparative analysis of mapping-based and reference-guided genome assembly methods, we shed light on the specific contributions of reference-guided assembly in reducing assembly errors and improving assembly continuity and integrity. These advancements establish reference-guided assembly and the utilization of in silico libraries as a promising and suitable approach for comparative genomics studies.

Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet

Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate.

N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence

Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.

A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes

BACKGROUND

As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects.

RESULTS

We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive.

CONCLUSION

Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly .

Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley

Faced with terrestrial threats, land plants seal their aerial surfaces with a lipid-rich cuticle. To breathe, plants interrupt their cuticles with adjustable epidermal pores, called stomata, that regulate gas exchange, and develop other specialised epidermal cells such as defensive hairs. Mechanisms coordinating epidermal features remain poorly understood. Addressing this, we studied two loci whose allelic variation causes both cuticular wax-deficiency and misarranged stomata in barley, identifying the underlying genes, Cer-g/ HvYDA1, encoding a YODA-like (YDA) MAPKKK, and Cer-s/ HvBRX-Solo, encoding a single BREVIS-RADIX (BRX) domain protein. Both genes control cuticular integrity, the spacing and identity of epidermal cells, and barley's distinctive epicuticular wax blooms, as well as stomatal patterning in elevated CO₂ conditions. Genetic analyses revealed epistatic and modifying relationships between HvYDA1 and HvBRX-Solo, intimating that their products participate in interacting pathway(s) linking epidermal patterning with cuticular properties in barley. This may represent a mechanism for coordinating multiple adaptive features of the land plant epidermis in a cultivated cereal.

Unraveling the genetics of polyamine metabolism in barley for senescence-related crop improvement

We explored the polyamine (PA) metabolic pathway genes in barley (Hv) to understand plant development and stress adaptation in Gramineae crops with emphasis on leaf senescence. Bioinformatics and functional genomics tools were utilized for genome-wide identification, comprehensive gene features, evolution, development and stress effects on the expression of the polyamine metabolic pathway gene families (PMGs). Three S-adenosylmethionine decarboxylases (HvSAMDCs), two ornithine decarboxylases (HvODCs), one arginine decarboxylase (HvADC), one spermidine synthase (HvSPDS), two spermine synthases (HvSPMSs), five copper amine oxidases (HvCuAOs) and seven polyamine oxidases (HvPAOs) members of PMGs were identified and characterized in barley. All the HvPMG genes were found to be distributed on all chromosomes of barley. The phylogenetic and comparative assessment revealed that PA metabolic pathway is highly conserved in plants and the prediction of nine H. vulgare miRNAs (hvu-miR) target sites, 18 protein-protein interactions and 961 putative CREs in the promoter region were discerned. Gene expression of HvSAMDC3, HvCuAO7, HvPAO4 and HvSPMS1 was apparent at every developmental stage. SPDS/SPMS gene family was found to be the most responsive to induced leaf senescence. This study provides a reference for the functional investigation of the molecular mechanism(s) that regulate polyamine metabolism in plants as a tool for future breeding decision management systems.

The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication

The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.

Perennials as Future Grain Crops: Opportunities and Challenges

Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.

GrainGenes: a data-rich repository for small grains genetics and genomics

As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.

The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei

Leaf rust, caused by Puccinia hordei, is an economically significant disease of barley, but only a few major resistance genes to P. hordei (Rph) have been cloned. In this study, gene Rph3 was isolated by positional cloning and confirmed by mutational analysis and transgenic complementation. The Rph3 gene, which originated from wild barley and was first introgressed into cultivated Egyptian germplasm, encodes a unique predicted transmembrane resistance protein that differs from all known plant disease resistance proteins at the amino acid sequence level. Genetic profiles of diverse accessions indicated limited genetic diversity in Rph3 in domesticated germplasm, and higher diversity in wild barley from the Eastern Mediterranean region. The Rph3 gene was expressed only in interactions with Rph3-avirulent P. hordei isolates, a phenomenon also observed for transcription activator-like effector-dependent genes known as executors conferring resistance to Xanthomonas spp. Like known transmembrane executors such as Bs3 and Xa7, heterologous expression of Rph3 in N. benthamiana induced a cell death response. The isolation of Rph3 highlights convergent evolutionary processes in diverse plant-pathogen interaction systems, where similar defence mechanisms evolved independently in monocots and dicots.

Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.

Genome sequences of three Aegilops species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Aegilops longissima and Aegilops speltoides. Whole-genome comparative analysis, along with the recently sequenced Aegilops sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and are most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides genome is closest to the wheat B subgenome, and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

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.

GreeNC 2.0: a comprehensive database of plant long non-coding RNAs

The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.

A high-resolution consensus linkage map for barley based on GBS-derived genotypes

As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregating progenies. We adopted a uniform set of SNP-calling and filtering conditions to identify 50 875 distinct SNPs segregating in at least one population. These SNPs were grouped into 18 580 non-redundant SNPs (bins). The resulting consensus linkage map spanned 1050.1 cM, providing an average density of 17.7 bins and 48.4 SNPs per cM. The consensus map is characterized by the absence of large intervals devoid of marker coverage (significant gaps), the largest interval between bins was only 3.7 cM and the mean distance between adjacent bins was 0.06 cM. This high-resolution linkage map will contribute to several applications in genomic research, such as providing useful information on the recombination landscape for QTLs/genes identified via GWAS or ensuring a uniform distribution of SNPs when developing low-cost genotyping tools offering a limited number of markers.

Proteins, Small Peptides and Other Signaling Molecules Identified as Inconspicuous but Possibly Important Players in Microspores Reprogramming Toward Embryogenesis

In this review, we describe and integrate the latest knowledge on the signaling role of proteins and peptides in the stress-induced microspore embryogenesis (ME) in some crop plants with agricultural importance (i.e., oilseed rape, tobacco, barley, wheat, rice, triticale, rye). Based on the results received from the most advanced omix analyses, we have selected some inconspicuous but possibly important players in microspores reprogramming toward embryogenic development. We provide an overview of the roles and downstream effect of stress-related proteins (e.g., β-1,3-glucanases, chitinases) and small signaling peptides, especially cysteine—(e.g., glutathione, γ-thionins, rapid alkalinization factor, lipid transfer, phytosulfokine) and glycine-rich peptides and other proteins (e.g., fasciclin-like arabinogalactan protein) on acclimation ability of microspores and the cell wall reconstruction in a context of ME induction and haploids/doubled haploids (DHs) production. Application of these molecules, stimulating the induction and proper development of embryo-like structures and green plant regeneration, brings significant improvement of the effectiveness of DHs procedures and could result in its wider incorporation on a commercial scale. Recent advances in the design and construction of synthetic peptides–mainly cysteine-rich peptides and their derivatives–have accelerated the development of new DNA-free genome-editing techniques. These new systems are evolving incredibly fast and soon will find application in many areas of plant science and breeding.

Genome-wide association mapping of Pyrenophora teres f. maculata and Pyrenophora teres f. teres resistance loci utilizing natural Turkish wild and landrace barley populations

Unimproved landraces and wild relatives of crops are sources of genetic diversity that were lost post domestication in modern breeding programs. To tap into this rich resource, genome-wide association studies in large plant genomes have enabled the rapid genetic characterization of desired traits from natural landrace and wild populations. Wild barley (Hordeum spontaneum), the progenitor of domesticated barley (Hordeum vulgare), is dispersed across Asia and North Africa, and has co-evolved with the ascomycetous fungal pathogens Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of the diseases net form of net blotch and spot form of net blotch, respectively. Thus, these wild and local adapted barley landraces from the region of origin of both the host and pathogen represent a diverse gene pool to identify new sources of resistance, due to millions of years of co-evolution. The barley—P. teres pathosystem is governed by complex genetic interactions with dominant, recessive, and incomplete resistances and susceptibilities, with many isolate-specific interactions. Here, we provide the first genome-wide association study of wild and landrace barley from the Fertile Crescent for resistance to both forms of P. teres. A total of 14 loci, four against P. teres f. maculata and 10 against P. teres f. teres, were identified in both wild and landrace populations, showing that both are genetic reservoirs for novel sources of resistance. We also highlight the importance of using multiple algorithms to both identify and validate additional loci.

Genetic and molecular characterization of determinant of six-rowed spike of barley carrying vrs1.a4

Decisive role of reduced vrs1 transcript abundance in six-rowed spike of barley carrying vrs1.a4 was genetically proved and its potential causes were preliminarily analyzed. Six-rowed spike 1 (vrs1) is the major determinant of the six-rowed spike phenotype of barley (Hordeum vulgare L.). Alleles of Vrs1 have been extensively investigated. Allele vrs1.a4 in six-rowed barley is unique in that it has the same coding sequence as Vrs1.b4 in two-rowed barley. The determinant of row-type in vrs1.a4 carriers has not been experimentally identified. Here, we identified Vrs1.b4 in two-rowed accessions and vrs1.a4 in six-rowed accessions from the Qinghai-Tibet Plateau at high frequency. Genetic analyses revealed a single nuclear gene accounting for row-type alteration in these accessions. Physical mapping identified a 0.08-cM (~ 554-kb) target interval on chromosome 2H, wherein Vrs1 was the most likely candidate gene. Further analysis of Vrs1 expression in offspring of the mapping populations or different Vrs1.b4 and vrs1.a4 lines confirmed that downregulated expression of vrs1.a4 causes six-rowed spike. Regulatory sequence analysis found a single 'TA' dinucleotide deletion in vrs1.a4 carriers within a 'TA' tandem-repeat-enriched region ~ 1 kb upstream of the coding region. DNA methylation levels did not correspond to the expression difference and therefore did not affect Vrs1 expression. More evidence is needed to verify the causal link between the 'TA' deletion and the downregulated Vrs1 expression and hence the six-rowed spike phenotype.

Conserved oligomeric Golgi (COG) complex genes functioning in defense are expressed in root cells undergoing a defense response to a pathogenic infection and exhibit regulation my MAPKs

The conserved oligomeric Golgi (COG) complex maintains correct Golgi structure and function during retrograde trafficking. Glycine max has 2 paralogs of each COG gene, with one paralog of each gene family having a defense function to the parasitic nematode Heterodera glycines. Experiments presented here show G. max COG paralogs functioning in defense are expressed specifically in the root cells (syncytia) undergoing the defense response. The expressed defense COG gene COG7-2-b is an alternate splice variant, indicating specific COG variants are important to defense. Transcriptomic experiments examining RNA isolated from COG overexpressing and RNAi roots show some COG genes co-regulate the expression of other COG complex genes. Examining signaling events responsible for COG expression, transcriptomic experiments probing MAPK overexpressing roots show their expression influences the relative transcript abundance of COG genes as compared to controls. COG complex paralogs are shown to be found in plants that are agriculturally relevant on a world-wide scale including Manihot esculenta, Zea mays, Oryza sativa, Triticum aestivum, Hordeum vulgare, Sorghum bicolor, Brassica rapa, Elaes guineensis and Saccharum officinalis and in additional crops significant to U.S. agriculture including Beta vulgaris, Solanum tuberosum, Solanum lycopersicum and Gossypium hirsutum. The analyses provide basic information on COG complex biology, including the coregulation of some COG genes and that MAPKs functioning in defense influence their expression. Furthermore, it appears in G. max and likely other crops that some level of neofunctionalization of the duplicated genes is occurring. The analysis has identified important avenues for future research broadly in plants.

A Comprehensive Phylogenetic Analysis of the MAP4K Family in the Green Lineage

The kinase-mediated phosphorylation impacts every basic cellular process. While mitogen-activated protein kinase technology kinase kinases (MAP4Ks) are evolutionarily conserved, there is no comprehensive overview of the MAP4K family in the green lineage (Viridiplantae). In this study, we identified putative MAP4K members from representative species of the two core groups in the green lineage: Chlorophyta, which is a diverse group of green algae, and Streptophyta, which is mostly freshwater green algae and land plants. From that, we inferred the evolutionary relationships of MAP4K proteins through a phylogenetic reconstruction. Furthermore, we provided a classification of the MAP4Ks in the green lineage into three distinct.

Potentiators of Disease During Barley Infection by Pyrenophora teres f. teres in a Susceptible Interaction

Pyrenophora teres f. teres is a necrotrophic fungal pathogen and causal agent of net form net blotch (NFNB), a significant disease of barley. RNA-seq data encompassing asymptomatic and subsequent necrotrophic phases of the pathogen was obtained for P. teres f. teres isolate W1-1 in NFNB-sensitive cultivar Baudin. Host genes notably regulated during infection included concerted induction of over half the repertoire of disease resistance genes, together with genes involved in oxidation-reduction processes, characteristic of a hypersensitive response. Several systemic acquired resistance response genes were suppressed and there was a complete absence of defense-related thionin gene expression. In P. teres f. teres, genes involved in hydrolase activities and cell-wall catabolic processes were induced during infection, while nitrate assimilation and response to oxidative stress processes were suppressed. Timecourse data allowed a number of predicted P. teres f. teres effector genes with differing expression profiles to be identified that may underlie barley sensitivity to NFNB. Candidate genes involved in the host-pathogen interaction provide a basis for functional characterization and control strategies based on fungicide or mutation targets, which will facilitate further research aimed at controlling NFNB disease.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genome-wide identification of bZIP transcription factor genes related to starch synthesis in barley (Hordeum vulgare L.)

The basic leucine zipper (bZIP) family of genes encode transcription factors that play key roles in plant growth and development. In this study, a total of 92 HvbZIP genes were identified and compared with previous studies using recently released barley genome data. Two novel genes were characterized in this study, and some misannotated and duplicated genes from previous studies have been corrected. Phylogenetic analysis results showed that 92 HvbZIP genes were classified into 10 groups and three unknown groups. The gene structure and motif distribution of the three unknown groups implied that the genes of the three groups may be functionally different. Expression profiling indicated that the HvbZIP genes exhibited different patterns of spatial and temporal expression. Using qRT-PCR, more than 10 HvbZIP genes were identified with expression patterns similar to those of starch synthase genes in barley. Yeast one-hybrid analysis revealed that two of the HvbZIP genes exhibited in vitro binding activity to the promoter of HvAGP-S. The two HvbZIP genes may be candidate genes for further study to explore the mechanism by which they regulate the synthesis of barley starch.

Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in Oryza sativa

Sulfate transporters (SULTRs), also known as H+/SO42- symporters, play a key role in sulfate transport, plant growth and stress responses. However, the evolutionary relationships and functional differentiation of SULTRs in Gramineae crops are rarely reported. Here, 111 SULTRs were retrieved from the genomes of 10 Gramineae species, including Brachypodium disachyon, Hordeum vulgare, Setaria italica, Sorghum bicolor, Zea mays, Oryza barthii, Oryza rufipogon, Oryza glabbermia and Oryza sativa (Oryza sativa ssp. indica and Oryza sativa ssp. japonica). The SULTRs were clustered into five clades based on a phylogenetic analysis. Syntheny analysis indicates that whole-genome duplication/segmental duplication and tandem duplication events were essential in the SULTRs family expansion. We further found that different clades and orthologous groups of SULTRs were under a strong purifying selective force. Expression analysis showed that rice SULTRs with high-affinity transporters are associated with the functions of sulfate uptake and transport during rice seedling development. Furthermore, using Oryza sativa ssp. indica as a model species, we found that OsiSULTR10 was significantly upregulated under salt stress, while OsiSULTR3 and OsiSULTR12 showed remarkable upregulation under high temperature, low-selenium and drought stresses. OsiSULTR3 and OsiSULTR9 were upregulated under both low-selenium and high-selenium stresses. This study illustrates the expression and evolutionary patterns of the SULTRs family in Gramineae species, which will facilitate further studies of SULTR in other Gramineae species.

Genetic analysis of the barley variegation mutant, grandpa1.a

BACKGROUND

Providing the photosynthesis factory for plants, chloroplasts are critical for crop biomass and economic yield. However, chloroplast development is a complicated process, coordinated by the cross-communication between the nucleus and plastids, and the underlying biogenesis mechanism has not been fully revealed. Variegation mutants have provided ideal models to identify genes or factors involved in chloroplast development. Well-developed chloroplasts are present in the green tissue areas, while the white areas contain undifferentiated plastids that are deficient in chlorophyll. Unlike albino plants, variegation mutants survive to maturity and enable investigation into the signaling pathways underlying chloroplast biogenesis. The allelic variegated mutants in barley, grandpa 1 (gpa1), have long been identified but have not been genetically characterized.

RESULTS

We characterized and genetically analyzed the grandpa1.a (gpa1.a) mutant. The chloroplast ultrastructure was evaluated using transmission electron microscopy (TEM), and it was confirmed that chloroplast biogenesis was disrupted in the white sections of gpa1.a. To determine the precise position of Gpa1, a high-resolution genetic map was constructed. Segregating individuals were genotyped with the barley 50 k iSelect SNP Array, and the linked SNPs were converted to PCR-based markers for genetic mapping. The Gpa1 gene was mapped to chromosome 2H within a gene cluster functionally related to photosynthesis or chloroplast differentiation. In the variegated gpa1.a mutant, we identified a large deletion in this gene cluster that eliminates a putative plastid terminal oxidase (PTOX).

CONCLUSIONS

Here we characterized and genetically mapped the gpa1.a mutation causing a variegation phenotype in barley. The PTOX-encoding gene in the delimited region is a promising candidate for Gpa1. Therefore, the present study provides a foundation for the cloning of Gpa1, which will elevate our understanding of the molecular mechanisms underlying chloroplast biogenesis, particularly in monocot plants.

Rpg7: A New Gene for Stem Rust Resistance from Hordeum vulgare ssp. spontaneum

Wheat stem rust (causal organism: Puccinia graminis f. sp. tritici) is an important fungal disease that causes significant yield losses in barley. The deployment of resistant cultivars is the most effective means of controlling this disease. Stem rust evaluations of a diverse collection of wild barley (Hordeum vulgare ssp. spontaneum) identified two Jordanian accessions (WBDC094 and WBDC238) with resistance to a virulent pathotype (P. graminis f. sp. tritici HKHJC) from the United States. To elucidate the genetics of stem rust resistance, both accessions were crossed to the susceptible landrace Hiproly. Segregation ratios of F₂ and F₃ progeny indicated that a single dominant gene confers resistance to P. graminis f. sp. tritici HKHJC. Molecular mapping of the resistance locus was performed in the Hiproly/WBDC238 F₂ population based on 3,329 single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Quantitative trait locus analysis positioned the resistance gene to the long arm of chromosome 3H between the physical/genetic positions of 683.8 Mbp/172.9 cM and 693.7 Mbp/176.0 cM. Because this resistance gene is novel, it was assigned the new gene locus symbol of Rpg7 with a corresponding allele symbol of Rpg7.i. At the seedling stage, Rpg7 confers resistance against a number of other important P. graminis f. sp. tritici pathotypes from the United States (MCCFC, QCCJB, and TTTTF) and Africa (TTKSK) as well as an isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis) from Minnesota. The resistance conferred by Rpg7 can be readily transferred into breeding programs because of its simple inheritance and clear phenotypic expression.

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding

KEY MESSAGE

The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, 'Jagger' and 'CDC Stanley,' and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

Combined effects of a glycine-rich RNA-binding protein and a NAC transcription factor extend grain fill duration and improve malt barley agronomic performance

Two key barley genes independently control anthesis and senescence timing, enabling the manipulation of grain fill duration, grain size/plumpness, and grain protein concentration. Plant developmental processes such as flowering and senescence have direct effects on cereal yield and quality. Previous work highlighted the importance of two tightly linked genes encoding a glycine-rich RNA-binding protein (HvGR-RBP1) and a NAC transcription factor (HvNAM1), controlling barley anthesis timing, senescence, and percent grain protein. Varieties that differ in HvGR-RBP1 expression, 'Karl'(low) and 'Lewis'(high), also differ in sequence 1 KB upstream of translation start site, including an ~ 400 bp G rich insertion in the 5'-flanking region of the 'Karl' allele, which could disrupt gene expression. To improve malt quality, the (low-grain protein, delayed-senescence) 'Karl' HvNAM1 allele was introgressed into Montana germplasm. After several seasons of selection, the resulting germplasm was screened for the allelic combinations of HvGR-RBP1 and HvNAM1, finding lines combining 'Karl' alleles for both genes (-/-), lines combining 'Lewis' (functional, expressed) HvGR-RBP1 with 'Karl' HvNAM1 alleles ( ±), and lines combining 'Lewis' alleles for both genes (+ / +). Field experiments indicate that the functional ('Lewis,'  +) HvGR-RBP1 allele is associated with earlier anthesis and with slightly shorter plants, while the 'Karl' (-) HvNAM1 allele delays maturation. Genotypes carrying the ± allele combination therefore had a significantly (3 days) extended grain fill duration, leading to a higher percentage of plump kernels, slightly enhanced test weight, and lower grain protein concentration when compared to the other allele combinations. Overall, our data suggest an important function for HvGR-RBP1 in the control of barley reproductive development and set the stage for a more detailed functional analysis of this gene.

Re-examination of the APETALA2/Ethylene-Responsive Factor Gene Family in Barley (Hordeum vulgare L.) Indicates a Role in the Regulation of Starch Synthesis

The APETALA2/Ethylene-Responsive factor (AP2/ERF) gene family is a large plant-specific transcription factor family, which plays important roles in regulating plant growth and development. A role in starch synthesis is among the multiple functions of this family of transcription factors. Barley (Hordeum vulgare L.) is one of the most important cereals for starch production. However, there are limited data on the contribution of AP2 transcription factors in barley. In this study, we used the recently published barley genome database (Morex) to identify 185 genes of the HvAP2/ERF family. Compared with previous work, we identified 64 new genes in the HvAP2/ERF gene family and corrected some previously misannotated and duplicated genes. After phylogenetic analysis, HvAP2/ERF genes were classified into four subfamilies and 18 subgroups. Expression profiling showed different patterns of spatial and temporal expression for HvAP2/ERF genes. Most of the 12 HvAP2/ERF genes analyzed using quantitative reverse transcription-polymerase chain reaction had similar expression patterns when compared with those of starch synthase genes in barley, except for HvAP2-18 and HvERF-73. HvAP2-18 is homologous to OsRSR1, which negatively regulates the synthesis of rice starch. Luciferase reporter gene, and yeast one-hybrid assays showed that HvAP2-18 bound the promoter of AGP-S and SBE1 in vitro. Thus, HvAP2-18 might be an interesting candidate gene to further explore the mechanisms involved in the regulation of starch synthesis in barley.

Cereal asparagine synthetase genes

Asparagine synthetase catalyses the transfer of an amino group from glutamine to aspartate to form glutamate and asparagine. The accumulation of free (nonprotein) asparagine in crops has implications for food safety because free asparagine is the precursor for acrylamide, a carcinogenic contaminant that forms during high-temperature cooking and processing. Here we review publicly available genome data for asparagine synthetase genes from species of the Pooideae subfamily, including bread wheat and related wheat species (Triticum and Aegilops spp.), barley (Hordeum vulgare) and rye (Secale cereale) of the Triticeae tribe. Also from the Pooideae subfamily: brachypodium (Brachypodium dIstachyon) of the Brachypodiae tribe. More diverse species are also included, comprising sorghum (Sorghum bicolor) and maize (Zea mays) of the Panicoideae subfamily and rice (Oryza sativa) of the Ehrhartoideae subfamily. The asparagine synthetase gene families of the Triticeae species each comprise five genes per genome, with the genes assigned to four groups: 1, 2, 3 (subdivided into 3.1 and 3.2) and 4. Each species has a single gene per genome in each group, except that some bread wheat varieties (genomes AABBDD) and emmer wheat (Triticum dicoccoides; genomes AABB) lack a group 2 gene in the B genome. This raises questions about the ancestry of cultivated pasta wheat and the B genome donor of bread wheat, suggesting that the hybridisation event that gave rise to hexaploid bread wheat occurred more than once. In phylogenetic analyses, genes from the other species cluster with the Triticeae genes, but brachypodium, sorghum and maize lack a group 2 gene, while rice has only two genes, one group 3 and one group 4. This means that TaASN2, the most highly expressed asparagine synthetase gene in wheat grain, has no equivalent in maize, rice, sorghum or brachypodium. An evolutionary pathway is proposed in which a series of gene duplications gave rise to the five genes found in modern Triticeae species.

Breeding Potentials of Bambara Groundnut for Food and Nutrition Security in the Face of Climate Change

Constant production of quality food should be a norm in any community, but climate change, increasing population, and unavailability of land for farming affect food production. As a result, food scarcity is affecting some communities, especially in the developing world. Finding a stable solution to this problem is a major cause of concern for researchers. Synergistic application of molecular marker techniques with next generation sequencing (NGS) technologies can unlock the potentials hidden in most crop genomes for improving yield and food availability. Most crops such as Bambara groundnut (BGN), Winged bean, and African yam bean are underutilized. These underutilized crops can compete with the major crops such as cowpea, soybean, maize, and rice, in areas of nutrition, ability to withstand drought stress, economic importance, and food production. One of these underutilized crops, BGN [Vigna subterranea (L.), Verdc.], is an indigenous African legume and can survive in tropical climates and marginal soils. In this review, we focus on the roles of BGN and the opportunities it possesses in tackling food insecurity and its benefits to local farmers. We will discuss BGN's potential impact on global food production and how the advances in NGS technologies can enhance its production.

Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley

Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific α-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.

Genome-wide diversity analysis of TCP transcription factors revealed cases of selection from wild to cultivated barley

Plant-specific TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1/2 (TCP) transcription factors have known roles in inflorescence architecture. In barley, there are two family members INTERMEDIUM-C (INT-c/HvTB1-1) and COMPOSITUM 1 (COM1/HvTCP24) which are involved in the manipulation of spike architecture, whereas the participation of TCP family genes in selection from wild (Hordeum vulgare subsp. spontaneum, Hs) to cultivated barley (Hordeum vulgare subsp. vulgare, Hv) remains poorly investigated. Here, by conducting a genome-wide survey for TCP-like sequences in publicly-released datasets, 22 HsTCP and 20 HvTCP genes encoded for mature proteins were identified and assigned into two classes (I and II) based on their functional domains and the phylogenetic analysis. Each counterpart of the orthologous gene in wild and cultivated barley usually represented a similarity on the transcriptional profile across the tissues. The diversity analysis of TCPs in 90 wild barley accessions and 137 landraces with geographically-referenced passport information revealed the detectable selection at three loci including INT-c/HvTB1-1, HvPCF2, and HvPCF8. Especially, the HvPCF8 haplotypes in cultivated barley were found correlating with their geographical collection sites. There was no difference observed in either transactivation activity in yeast or subcellular localization in Nicotiana benthamiana among these haplotypes. Nevertheless, the genome-wide diversity analysis of barley TCP genes in wild and cultivated populations provided insight for future functional characterization in plant development such as spike architecture.

A novel way to identify specific powdery mildew resistance genes in hybrid barley cultivars

Powdery mildew, a common cereal disease caused by the fungus Blumeria graminis, is a major limiting factor of barley production and genetic resistance is the most appropriate protection against it. To aid the breeding of new cultivars and their marketing, resistance genes can be postulated in homogeneous accessions. Although hybrid cultivars (F1) should be homogeneous, they are often not genetically uniform, especially if more than two genotypes are involved in their seed production or due to undesirable self-pollination, out-crossing and mechanical admixtures. To overcome these problems the accepted method of postulating specific resistance genes based on comparing response type arrays (RTAs) of genetically homogeneous cultivars with RTAs of standard genotypes was substituted by analysing the frequency of response types to clusters of pathogen isolates in segregating F2 generations. This method combines a genetic and phytopathological approach for identifying resistance genes. To assess its applicability six hybrid cultivars were screened and from three to seven with a total of 14 resistance genes were found. Two genes were newly located at the Mla locus and their heritability determined. In addition, three unknown dominant genes were detected. This novel, comprehensive and efficient method to identifying resistance genes in hybrid cultivars can also be applied in other cereals and crops.

Application of Genomic Big Data in Plant Breeding:Past, Present, and Future

Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.

Fast and accurate correction of optical mapping data via spaced seeds

Motivation

Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome.

Results

We create an efficient method for determining pairs of Rmaps that contain significant overlaps between them. Our method relies on the novel and nontrivial adaption and application of spaced seeds in the context of optical mapping, which allows for spurious and deleted cut sites to be accounted for. We apply our method to detecting and correcting these errors. The resulting error correction method, referred to as Elmeri, improves upon the results of state-of-the-art correction methods but in a fraction of the time. More specifically, cOMet required 9.9 CPU days to error correct Rmap data generated from the human genome, whereas Elmeri required less than 15 CPU hours and improved the quality of the Rmaps by more than four times compared to cOMet.

Availability and implementation

Elmeri is publicly available under GNU Affero General Public License at https://github.com/LeenaSalmela/Elmeri.

Supplementary information

Supplementary data are available at Bioinformatics online.

Optical map guided genome assembly

BACKGROUND

The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly.

RESULTS

We propose OPTICALKERMIT which directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler, OPTICALKERMIT produces an assembly with almost three times higher NGA50 with a lower number of misassemblies on real A. thaliana reads.

CONCLUSIONS

OPTICALKERMIT successfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.

Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.)

A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.

Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.)

A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.

Genome-wide characterization and expression analyses of the auxin/indole-3-acetic acid (Aux/IAA) gene family in barley (Hordeum vulgare L.)

Aux/IAA genes are early auxin-responsive genes and essential for auxin signaling transduction. There is little information about Aux/IAAs in the agriculturally important cereal, barley. Using in silico method, we identified and subsequently characterized 36 Aux/IAAs from the barley genome. Based on their genomic sequences and the phylogenic relationship with Arabidopsis and rice Aux/IAA, the 36 HvIAAs were categorized into two major groups and 14 subgroups. The indication of the presence or absence of these domains for the biological functions and acting mechanisms was discussed. The cis-element distributions in HvIAA promoters suggests that the HvIAAs expressions may not only regulated by auxin (the presence of AuxREs and TGA-element) but also by other hormones and developmental and environmental cues. We then studied the HvIAAs expression in response to NAA (1-Naphthaleneacetic acid) using quantitative real-time PCR (qRT-PCR). Like the promoter analysis, only 14 HvIAAs were upregulated by NAA over two-fold at 4 h. HvIAAs were clustered into three groups based on the spatiotemporal expression data. We confirmed by qRT-PCR that most HvIAAs, especially HvIAA3, HvIAA7, HvIAA8, HvIAA18, HvIAA24 and HvIAA34, are expressed in the developing barley spike compared within seedling, suggesting their roles in regulating spike development. Taken together, our data provide a foundation for further revealing the biological function of these HvIAAs.

Aligning optical maps to de Bruijn graphs

MOTIVATION

Optical maps are high-resolution restriction maps (Rmaps) that give a unique numeric representation to a genome. Used in concert with sequence reads, they provide a useful tool for genome assembly and for discovering structural variations and rearrangements. Although they have been a regular feature of modern genome assembly projects, optical maps have been mainly used in post-processing step and not in the genome assembly process itself. Several methods have been proposed for pairwise alignment of single molecule optical maps-called Rmaps, or for aligning optical maps to assembled reads. However, the problem of aligning an Rmap to a graph representing the sequence data of the same genome has not been studied before. Such an alignment provides a mapping between two sets of data: optical maps and sequence data which will facilitate the usage of optical maps in the sequence assembly step itself.

RESULTS

We define the problem of aligning an Rmap to a de Bruijn graph and present the first algorithm for solving this problem which is based on a seed-and-extend approach. We demonstrate that our method is capable of aligning 73% of Rmaps generated from the Escherichia coli genome to the de Bruijn graph constructed from short reads generated from the same genome. We validate the alignments and show that our method achieves an accuracy of 99.6%. We also show that our method scales to larger genomes. In particular, we show that 76% of Rmaps can be aligned to the de Bruijn graph in the case of human data.

AVAILABILITY AND IMPLEMENTATION

The software for aligning optical maps to de Bruijn graph, omGraph is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/omGraph.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Genome-Wide Analysis of the GRAS Gene Family in Barley (Hordeum vulgare L.)

The GRAS (named after first three identified proteins within this family, GAI, RGA, and SCR) family contains plant-specific genes encoding transcriptional regulators that play a key role in gibberellin (GA) signaling, which regulates plant growth and development. Even though GRAS genes have been characterized in some plant species, little research is known about the GRAS genes in barley (Hordeum vulgare L.). In this study, we observed 62 GRAS members from barley genome, which were grouped into 12 subgroups by using phylogenomic analysis together with the GRAS genes from Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). Chromosome localization and gene structure analysis suggested that duplication events and abundant presence of intronless genes might account for the massive expansion of GRAS gene family in barley. The analysis of RNA-seq data indicates the expression pattern of GRAS genes in various tissues at different stages in barley. Noteworthy, our qRT-PCR analysis showed the expression of 18 candidate GRAS genes abundantly in the developing inflorescence, indicating their potential roles in the barley inflorescence development and reproduction. Collectively, our evolutionary and expression analysis of GRAS family are useful for future functional characterization of GA signaling in barley and agricultural improvement.

Screening diversity and distribution of Copia retrotransposons reveals a specific amplification of BARE1 elements in genomes of the polyploid Hordeum murinum complex

We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.

Bymovirus-induced yellow mosaic diseases in barley and wheat: viruses, genetic resistances and functional aspects

Bymovirus-induced yellow mosaic diseases seriously threaten global production of autumn-sown barley and wheat, which are two of the presently most important crops around the world. Under natural field conditions, the diseases are caused by infection of soil-borne plasmodiophorid Polymyxa graminis-transmitted bymoviruses of the genus Bymovirus of the family Potyviridae. Focusing on barley and wheat, this article summarizes the achievements on taxonomy, geography and host specificity of these disease-conferring viruses, as well as the genetics of resistance in barley, wheat and wild relatives. Moreover, based on recent progress of barley and wheat genomics, germplasm resources and large-scale sequencing, the exploration and isolation of corresponding resistant genes from wheat and barley as well as relatives, no matter what a large and complicated genome is present, are becoming feasible and are discussed. Furthermore, the foreseen advances on cloning of the resistance or susceptibility-encoding genes, which will provide the possibility to explore the functional interaction between host plants and soil-borne viral pathogens, are discussed as well as the benefits for marker-assisted resistance breeding in barley and wheat.

Natural Genetic Variation Underlying Tiller Development in Barley (Hordeum vulgare L)

In barley (Hordeum vulgare L.), lateral branches called tillers contribute to grain yield and define shoot architecture, but genetic control of tiller number and developmental rate are not well characterized. The primary objectives of this work were to examine relationships between tiller number and other agronomic and morphological traits and identify natural genetic variation associated with tiller number and rate, and related traits. We grew 768 lines from the USDA National Small Grain Collection in the field and collected data over two years for tiller number and rate, and agronomic and morphological traits. Our results confirmed that spike row-type and days to heading are correlated with tiller number, and as much as 28% of tiller number variance was associated with these traits. In addition, negative correlations between tiller number and leaf width and stem diameter were observed, indicating trade-offs between tiller development and other vegetative growth. Thirty-three quantitative trait loci (QTL) were associated with tiller number or rate. Of these, 40% overlapped QTL associated with days to heading and 22% overlapped QTL associated with spike row-type, further supporting that tiller development is associated with these traits. Some QTL associated with tiller number or rate, including the major QTL on chromosome 3H, were not associated with other traits, suggesting that some QTL may be directly related to rate of tiller development or axillary bud number. These results enhance our knowledge of the genetic control of tiller development in barley, which is important for optimizing tiller number and rate for yield improvement.