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  • Stein, Nils  (19)
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  • 1
    Language: English
    In: Genome biology, 12 June 2013, Vol.14(6), pp.R58
    Description: 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. A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.
    Keywords: Chromosomes, Plant ; DNA Copy Number Variations ; Genome, Plant ; Hordeum -- Genetics
    ISSN: 14656906
    E-ISSN: 1474-760X
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  • 2
    In: Plant Journal, November 2013, Vol.76(4), pp.718-727
    Description: Next‐generation whole‐genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence‐based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost‐efficient establishment of powerful genomic information for many species.
    Keywords: Next‐Generation Sequencing ; Genome Assembly ; Genetic Mapping ; Barley ; Hordeum Vulgare ; Population Sequencing ; Technical Advance
    ISSN: 0960-7412
    E-ISSN: 1365-313X
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  • 3
    In: Plant Journal, November 2013, Vol.76(3), pp.494-505
    Description: Advanced resources for genome‐assisted research in barley () including a whole‐genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole‐genome resequencing and variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the m‐coding exome reduces barley genomic complexity more than 50‐fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in‐solution hybridization‐based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar orex as well as publicly available full‐length cs and assembled RNA‐Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the m‐coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping‐by‐sequencing and genetic diversity analyzes.
    Keywords: Barley ; Genomics ; Genetic Diversity ; Hordeum Bulbosum ; Hordeum Pubiflorum ; Hordeum Vulgare ; Targeted Resequencing ; Riticeae
    ISSN: 0960-7412
    E-ISSN: 1365-313X
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  • 4
    Language: English
    In: Plant physiology, January 2014, Vol.164(1), pp.412-23
    Description: Barley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
    Keywords: Physical Chromosome Mapping ; Polymorphism, Single Nucleotide ; Hordeum -- Genetics
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 5
    Language: English
    In: Plant physiology, June 2016, Vol.171(2), pp.1113-27
    Description: Inflorescence architecture in small-grain cereals has a direct effect on yield and is an important selection target in breeding for yield improvement. We analyzed the recessive mutation laxatum-a (lax-a) in barley (Hordeum vulgare), which causes pleiotropic changes in spike development, resulting in (1) extended rachis internodes conferring a more relaxed inflorescence, (2) broadened base of the lemma awns, (3) thinner grains that are largely exposed due to reduced marginal growth of the palea and lemma, and (4) and homeotic conversion of lodicules into two stamenoid structures. Map-based cloning enforced by mapping-by-sequencing of the mutant lax-a locus enabled the identification of a homolog of BLADE-ON-PETIOLE1 (BOP1) and BOP2 as the causal gene. Interestingly, the recently identified barley uniculme4 gene also is a BOP1/2 homolog and has been shown to regulate tillering and leaf sheath development. While the Arabidopsis (Arabidopsis thaliana) BOP1 and BOP2 genes act redundantly, the barley genes contribute independent effects in specifying the developmental growth of vegetative and reproductive organs, respectively. Analysis of natural genetic diversity revealed strikingly different haplotype diversity for the two paralogous barley genes, likely affected by the respective genomic environments, since no indication for an active selection process was detected.
    Keywords: Genes, Homeobox ; Genes, Plant ; Sequence Homology, Amino Acid ; Arabidopsis Proteins -- Chemistry ; Hordeum -- Anatomy & Histology ; Inflorescence -- Anatomy & Histology
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 6
    Language: English
    In: BMC Plant Biology, Sept 28, 2011, Vol.11, p.131
    Description: Background The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. Results More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. Conclusions The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
    Keywords: Base Sequence -- Research ; Single Nucleotide Polymorphisms -- Research ; Rye -- Genetic Aspects ; Rye -- Research
    ISSN: 1471-2229
    Source: Cengage Learning, Inc.
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  • 7
    Language: English
    In: BMC Plant Biology, Sept 28, 2011, Vol.11, p.131
    Description: Background The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. Results More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. Conclusions The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
    Keywords: Base Sequence -- Research ; Single Nucleotide Polymorphisms -- Research ; Rye -- Genetic Aspects ; Rye -- Research
    ISSN: 1471-2229
    Source: Cengage Learning, Inc.
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  • 8
    In: Nature, 2017, Vol.544(7651), p.427
    Description: 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.
    Keywords: Gene ; Barley ; Chromosome ; Carbohydrate ; Genome ; Recombination ; Agricultural-Industry ; Chromatin ; Nutrient ; Gen ; Gerste ; Chromosom ; Kohlehydrat ; Genom ; Rekombination ; Agrikultur ; Chromatin ; Nährstoff ; Sciences (General) ; Physics;
    ISSN: 0028-0836
    E-ISSN: 1476-4687
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  • 9
    In: Plant Biotechnology Journal, October 2014, Vol.12(8), pp.1122-1131
    Description: Crop wild relatives () provide an important source of allelic diversity for any given crop plant species for counteracting the erosion of genetic diversity caused by domestication and elite breeding bottlenecks. L. is representing the secondary gene pool of the genus . It has been used as a source of genetic introgressions for improving elite barley germplasm ( L.). However, genetic introgressions from .  have yet not been broadly applied, due to a lack of suitable molecular tools for locating, characterizing, and decreasing by recombination and marker‐assisted backcrossing the size of introgressed segments. We applied next‐generation sequencing () based strategies for unlocking genetic diversity of three diploid introgression lines of cultivated barley containing chromosomal segments of its close relative . Firstly, exome capture‐based (re)‐sequencing revealed large numbers of single nucleotide polymorphisms (s) enabling the precise allocation of introgressions. This resource was further exploited by designing a custom multiplex genotyping assay. Secondly, two‐enzyme‐based genotyping‐by‐sequencing () was employed to allocate the introgressed segments and to genotype a mapping population. Both methods provided fast and reliable detection and mapping of the introgressed segments and enabled the identification of recombinant plants. Thus, the utilization of as a resource of natural genetic diversity in barley crop improvement will be greatly facilitated by these tools in the future.
    Keywords: Hordeum Bulbosum ; Crop Wild Relatives ; Introgression Line ; Genotyping‐By‐Sequencing ; Exome Capture ; Next‐Generation Sequencing
    ISSN: 1467-7644
    E-ISSN: 1467-7652
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  • 10
    Language: English
    In: BMC Plant Biology, 01 September 2011, Vol.11(1), p.131
    Description: Abstract Background The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. Results More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. Conclusions The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
    Keywords: EST Resource ; Next Generation Sequencing ; Secale Cereale L ; Rye5k Snp Array ; Single Nucleotide Polymorphisms ; Botany
    ISSN: 1471-2229
    E-ISSN: 1471-2229
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