The cereals are of enormous importance to mankind. Many of the major cereal species - specifically, wheat, barley, oat, rye, and maize - have large genomes. Early cytogenetics, genome analysis and genetic mapping in the cereals benefited greatly from their large chromosomes, and the allopolyploidy of wheat and oats that has allowed for the development of many precise cytogenetic stocks. In the genomics era, however, large genomes are disadvantageous. Sequencing large and complex genomes is expensive, and the assembly of genome sequence is hampered by a significant content of repetitive DNA and, in allopolyploids, by the presence of homoeologous genomes. Dissection of the genome into its component chromosomes and chromosome arms provides an elegant solution to these problems. In this review we illustrate how this can be achieved by flow cytometric sorting. We describe the development of methods for the preparation of intact chromosome suspensions from the major cereals, and their analysis and sorting using flow cytometry. We explain how difficulties in the discrimination of specific chromosomes and their arms can be overcome by exploiting extant cytogenetic stocks of polyploid wheat and oats, in particular chromosome deletion and alien addition lines. Finally, we discuss some of the applications of flow-sorted chromosomes, and present some examples demonstrating that a chromosome-based approach is advantageous for the analysis of the complex genomes of cereals, and that it can offer significant potential for the delivery of genome sequencing and gene cloning in these crops.

• MeSH
• chromozomy rostlin genetika   MeSH
• cytogenetika MeSH
• genomika metody   MeSH
• genová knihovna MeSH
• jedlá semena cytologie   genetika   MeSH
• průtoková cytometrie metody   MeSH
• sekvenční analýza DNA MeSH
• umělé bakteriální chromozomy genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of ecological environments during domestication, it is yet to be determined whether they have a common genetic basis for flowering time. In this study, we show, through map-based cloning, that flowering time in sorghum is controlled by a major quantitative trait locus (QTL) Heading Date 1 (HD1), located on chromosome 10. The causal gene encodes the CONSTANS gene family which contains a CCT domain. A 5-bp deletion of a minor allele present in the coding sequence leads to a gene frameshift that delays flowering in sorghum. In contrast, in foxtail millet, association mapping of HD1 showed a common causal site with a splicing variant from "GT" to "AT" that was highly correlated with flowering time. In addition, the rice HD1 gene is known to harbor several causal variants controlling flowering time. These data indicate that the major flowering time QTL HD1 was under parallel domestication in sorghum, foxtail millet, and rice. The pattern of common mixed minor, or even rare, causal alleles in HD1 across different species may be representative of the genetic basis of the domestication syndrome. Furthermore, large DNA sequence analysis of HD1 revealed multiple origins for domesticated sorghum and a single origin for domesticated foxtail millet.

• Klíčová slova
• comparative mapping, flowering time, parallel domestication,
• MeSH
• DNA rostlinná genetika   MeSH
• genetická variace MeSH
• genetické lokusy MeSH
• jedlá semena genetika   MeSH
• klonování DNA MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• párování bází genetika   MeSH
• rostlinné geny * MeSH
• rostlinné proteiny chemie   genetika   MeSH
• rýže (rod) genetika   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA MeSH
• sekvenční delece MeSH
• sekvenční seřazení MeSH
• selekce (genetika) MeSH
• Setaria (rostlina) genetika   MeSH
• Sorghum genetika   MeSH
• terciární struktura proteinů MeSH
• zemědělství * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• rostlinné proteiny MeSH

BACKGROUND: Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. RESULTS: We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. CONCLUSION: We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.

• MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   izolace a purifikace   MeSH
• genom rostlinný MeSH
• genomová knihovna MeSH
• hybridizace in situ fluorescenční MeSH
• karyotypizace MeSH
• nemoci rostlin genetika   MeSH
• průtoková cytometrie MeSH
• pšenice genetika   MeSH
• translokace genetická MeSH
• umělé bakteriální chromozomy genetika   MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

BACKGROUND: Rye (Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding. RESULTS: Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers. CONCLUSION: This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.

• MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   MeSH
• fyzikální mapování chromozomů MeSH
• genetické markery MeSH
• genom rostlinný * MeSH
• genová knihovna MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární sekvence - údaje MeSH
• repetitivní sekvence nukleových kyselin MeSH
• rostlinné geny MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• umělé bakteriální chromozomy MeSH
• výpočetní biologie MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• genetické markery MeSH

Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.

• MeSH
• biotechnologie MeSH
• genetická vazba MeSH
• jedlá semena genetika   MeSH
• klonování DNA metody   MeSH
• pšenice genetika   MeSH
• rostlinné geny genetika   MeSH
• Publikační typ
• časopisecké články MeSH

Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE, CONSTITUTIVE PHOTOMORPHOGENIC DWARF, and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROID-INSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroid-related genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars.

• MeSH
• alely MeSH
• aminokyseliny MeSH
• brassinosteroidy metabolismus   MeSH
• fenotyp MeSH
• ječmen (rod) genetika   růst a vývoj   metabolismus   MeSH
• jedlá semena MeSH
• mapování chromozomů MeSH
• modely strukturální MeSH
• molekulární sekvence - údaje MeSH
• mutace MeSH
• počasí MeSH
• počítačová simulace MeSH
• regulace genové exprese u rostlin * MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• signální transdukce MeSH
• teplota MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• aminokyseliny MeSH
• brassinosteroidy MeSH

BACKGROUND: A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS: Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION: The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.

• Klíčová slova
• 1RS BAC library, 454 sequences, DNA motifs, Rye, Secale cereale, Subtelomeric heterochromatin, TE–tandem junctions, Tandem repeats, Transposable elements,
• MeSH
• amplifikace genu * MeSH
• chromozomy rostlin genetika   MeSH
• fylogeneze MeSH
• genová knihovna MeSH
• heterochromatin genetika   MeSH
• hybridizace in situ fluorescenční MeSH
• komponenty genomu MeSH
• sekvenční analýza DNA MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• tandemové repetitivní sekvence * MeSH
• transpozibilní elementy DNA * MeSH
• umělé bakteriální chromozomy MeSH
• žito genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• heterochromatin MeSH
• transpozibilní elementy DNA * MeSH

Laccases constitute a multi-gene family of multi-copper glycoproteins. The barley laccase-like multicopper oxidase (LMCO) gene structure, the DNA sequence polymorphism and putative protein have not yet been described. As part of the study of LMCO in cereals, we have characterized the genomic structure of the putative LMCO gene HvLac1 from the barley variety 'Morex' and mapped HvLac1 on chromosome 4H. The genomic sequence of the HvLac1 gene is 2646 bp long and covers 100% of the coding region. It contains four exons and three introns. In this study, we have described the HvLac1 gene nucleotide polymorphisms (In/Del) in 134 barley varieties. Initial characterization of the barley and rice LMCO and the phylogeny analysis indicate that a monocot LMCO family is composed of five members. There are two high pI isoforms of putative HvLac1 protein derived from two in frame translation start codons with 602aa or 592aa residues. Isoforms differ in their predicted subcellular localization and both isoforms are characterized on C-terminus by the presence of the KDEL-like motif, which contributes to the accumulation of soluble proteins in the endoplasmic reticulum. Our results suggest that this unique feature of HvLac1 could be important for their role in physiological processes.

• MeSH
• DNA rostlinná analýza   genetika   MeSH
• fylogeneze MeSH
• ječmen (rod) enzymologie   genetika   MeSH
• konformace proteinů MeSH
• lakasa chemie   genetika   MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• polymorfismus genetický MeSH
• rostlinné proteiny chemie   genetika   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH
• lakasa MeSH
• rostlinné proteiny MeSH

B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.

• Klíčová slova
• Argonaute, B chromosomes, B-located genes, Secale cereale, gene erosion, gene expression, pseudogenization,
• MeSH
• amplifikace genu MeSH
• Argonaut proteiny metabolismus   MeSH
• buněčné jádro metabolismus   MeSH
• chromatin metabolismus   MeSH
• chromozomy rostlin genetika   MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• genetická transkripce MeSH
• genová dávka MeSH
• genová ontologie MeSH
• messenger RNA genetika   metabolismus   MeSH
• počítačová simulace MeSH
• regulace genové exprese u rostlin MeSH
• rostlinné geny MeSH
• rostlinné proteiny metabolismus   MeSH
• sekvence nukleotidů MeSH
• žito enzymologie   genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Argonaut proteiny MeSH
• chromatin MeSH
• DNA řízené RNA-polymerasy MeSH
• messenger RNA MeSH
• rostlinné proteiny MeSH

Barley alpha-amylase variability influences the quality of barley grain in the brewing, feed and food industries. alpha-Amylase proteins are encoded by multigene families in cereals, and this study focused on the barley Amy32b gene. We identified coding region single nucleotide polymorphism (cSNP) and insertion/deletion variation in DNA sequences, which resulted in amino acid substitution and stop codon formation, respectively. The substitution affected the beta1 strand in domain C, whereas the stop codon removed the beta5 strand. Possible effects of these changes on the protein are discussed. A cSNP in the coding region of the Amy32b gene was used as a specific marker to map Amy32b loci on chromosome 7H.

• MeSH
• alfa-amylasy genetika   MeSH
• DNA primery MeSH
• genetická variace * MeSH
• genotyp MeSH
• ječmen (rod) genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• mapování chromozomů * MeSH
• molekulární sekvence - údaje MeSH
• rostlinné geny genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sekvenční seřazení MeSH
• substituce aminokyselin genetika   MeSH
• terminační kodon genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• alfa-amylasy MeSH
• DNA primery MeSH
• terminační kodon MeSH