physical mapping
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Methods in molecular biology ; vol. 255-256
1st ed. xx, 360 s.
BACKGROUND: The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. RESULTS: A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides. Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200-999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000-3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach. CONCLUSION: The high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the BAC scaffold length when compared with the published physical maps for other wheat chromosomes. The genetic and bioinformatics resources developed in this study provide new possibilities for exploring chromosome organization and for breeding applications.
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
- MeSH
- biotechnologie metody MeSH
- chromozomy rostlin genetika MeSH
- genom rostlinný * MeSH
- mapování chromozomů metody MeSH
- pšenice genetika MeSH
- sekvenční analýza DNA metody MeSH
- tandemové repetitivní sekvence MeSH
- umělé bakteriální chromozomy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cíl: Cílem je zhodnotit využití tlakové mapy (Pressure Mapping System; PMS) při komplexním vyšetření spinálních pacientů s mobilitou na vozíku. Soubor a metodika: Zpracován byl soubor 29 pacientů, kteří byli vyšetřeni v rámci spinální ambulance celoživotní péče FN Brno v roce 2015 (podrobná anamnéza, klinické vyšetření sedu ve vozíku a vleže a vsedě na lehátku, vyšetření PMS, fotodokumentace sedu ve vozíku). Výsledky: Z celkového počtu 21 mužů a osmi žen utrpělo lézi míšní 26 pacientů úrazem. U jednoho muže a dvou žen se jednalo o neúrazovou etiologii. Všichni se pohybovali na mechanickém vozíku. Rozložení tlaku na sedacím polštáři u jednotlivých pacientů ukázalo, že u 10 byl tlak pod hrboly sedacích kostí pod 100 mm Hg (průměr 80 ? 24 mm Hg vlevo, 91 ? 24 mm Hg vpravo). U 12 pacientů byla jednostranná patologie tlaku nad 100 mm Hg pod hrbolem sedací kosti (průměr 93 ? 21 mm Hg vlevo, průměr 103 ? 36 mm Hg vpravo). U sedmi byla oboustranná patologie nad 100 mm Hg pod hrbolem sedací kosti (průměr 128 ? 19 mm Hg vlevo, 117 ? 21 mm Hg vpravo). Rozdíly byly ověřeny jako významné u tlaku pod hrbolem sedací kosti vlevo. Závěr: Ověřili jsme, že vyšetření pomocí PMS vhodně doplňuje komplexní posouzení pacienta s mobilitou na vozíku.
Aim: The aim of the study was to evaluate the use of the Pressure Mapping System (PMS) to comprehensively evaluate spinal cord-injured (SCI) patients with wheelchair mobility. Materials and methods: A cohort of 29 patients with both traumatic and non-traumatic aetiology was analysed. The patients were examined at the spinal outpatient clinic for life-long care at the University Hospital Brno in 2015. The examination included detailed medical history, clinical evaluation while sitting in a wheelchair, laying and sitting on an examination couch, clinical evaluation of pressure on a seating cushion using PMS, photo documentation of sitting in a wheelchair. Results: Of the total of 21 men and eight women with SCI, 26 had a traumatic lesion (20 men and six women). Three (one man and two women) had non-traumatic aetiology. All were mobile on a mechanical wheelchair. The distribution of pressure on a seating cushion showed that the pressure under ischial tuberosities was lower than 100 mm Hg in 10 patients (mean 80 ? 24 mm Hg left, 91 ?? 24 mm Hg right). Unilateral pathology of pressure above 100 mm Hg under an ischial tuberosity was found in 12 patients (mean 93 ? 21 mm Hg left, 103 ? 36 mm Hg right). We found bilateral pathology of pressure over 100 mm Hg under both ischial tuberosities in seven patients (mean 128 ?? 19 mm Hg left and 117 ? 21 mm Hg right). Statistically significant differences in pressure were only found under the left ischial tuberosity. Conclusion: We verified that examination with PMS is an appropriate element of comprehensive assessment of patients with wheelchair mobility.
- Klíčová slova
- pressure mapping system Conformat,
- MeSH
- bolesti zad etiologie prevence a kontrola MeSH
- dekubity * epidemiologie etiologie prevence a kontrola MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- nemoci míchy MeSH
- paraplegie MeSH
- poranění míchy * MeSH
- postižení MeSH
- postura těla MeSH
- posturální rovnováha MeSH
- předškolní dítě MeSH
- senioři MeSH
- tlak MeSH
- vozíky pro invalidy * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- hodnotící studie MeSH
Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development, the locus for which has been chromosomally localized to 5q31-34. We have isolated four hypervariable microsatellite markers (heterozygosity values range from 0.70 to 0.89) which have been mapped to distal 5q. Fifteen unrelated TCOF1 families have been analyzed for linkage to these markers. There is strong evidence demonstrating linkage to all of these markers; the strongest support for positive linkage being provided by the marker IG52, with a maximum pairwise lod score of 9.77 at a recombination fraction of 0.055. Analysis of recombinant individuals, physical mapping by fluorescence in situ hybridization and genetic linkage analysis demonstrated that the TCOF1 locus was flanked proximally by the loci 2C7 and 2D10, and distally by the loci IG26 and IG52 with a maximum lod score of 14.4, as assessed by multipoint linkage analysis. The refinement of the localization of the TCOF1 locus to 5q32-33.2, with flanking markers, represents an important step towards the identification of the mutated gene itself.
- MeSH
- dospělí MeSH
- elektromyografie metody MeSH
- fyzioterapie (obor) MeSH
- lidé MeSH
- muskuloskeletální nemoci diagnóza MeSH
- techniky fyzikální terapie MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- Publikační typ
- srovnávací studie MeSH
BACKGROUND: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. RESULTS: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. CONCLUSIONS: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
- MeSH
- centromera metabolismus MeSH
- chromozomy rostlin genetika MeSH
- fruktany analýza MeSH
- fyzikální mapování chromozomů metody MeSH
- genom rostlinný * MeSH
- optické jevy * MeSH
- pšenice genetika MeSH
- semena rostlinná genetika MeSH
- umělé bakteriální chromozomy genetika MeSH
- zemědělství * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
