Chromosome 5BS Dotaz Zobrazit nápovědu
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.
- Klíčová slova
- Chromosome 5BS, Genetic markers, Hexaploid wheat, Physical mapping, Sequencing, Synteny, Triticum aestivum,
- MeSH
- chléb * MeSH
- chromozomy rostlin genetika MeSH
- fyzikální mapování chromozomů * MeSH
- polymerázová řetězová reakce MeSH
- pšenice genetika MeSH
- umělé bakteriální chromozomy genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
- Klíčová slova
- Aegilops biuncialis, bread wheat, chromosome flow sorting, homoeologous recombination, in situ hybridization, meiotic chromosome pairing, ph1b mutant,
- Publikační typ
- časopisecké články MeSH
Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.
- MeSH
- chromozomy rostlin genetika MeSH
- mikro RNA genetika MeSH
- molekulární evoluce * MeSH
- pšenice genetika MeSH
- RNA rostlin genetika MeSH
- RNA transferová genetika MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- mikro RNA MeSH
- RNA rostlin MeSH
- RNA transferová MeSH
Dynamics of cold tolerance and crown proteome composition has been analysed in a set of two winter wheat cultivars Mironovskaya 808 and Bezostaya 1 and four reciprocal substitution lines with interchanged chromosomes 5A and 5B during a long-term cold-acclimation (CA) treatment. Proteome analysis has revealed 298 differently abundant spots during experiment. Most of them (260) were changed due to CA process and only 52 spots displayed differences between genotypes. Two hundred and seven protein spots were successfully identified by tandem mass spectrometry. Comparison of samples before and after vernalization fulfillment by a combination of ANOVA and Student' T-test displayed ten differentially abundant protein spots (e.g. chopper chaperones). However, differences in the accumulation of these spots did not reflect differences in vernalization requirement of genotypes. Therefore, our results indicate that vernalization process has not influenced total proteome of CA wheat crowns. A few protein spots (14 spots; e.g. malate dehydrogenase) revealed differential accumulation levels between the individual genotypes or their groups possessing chromosome 5A or 5B from Mironovskaya 808 versus Bezostaya 1. The study has shown the effect of chromosome 5A on physiological traits and also proteome in winter wheat. Putative candidate protein markers for cold tolerance in wheat are discussed.
- MeSH
- analýza hlavních komponent MeSH
- chromozomy rostlin * MeSH
- dvourozměrná diferenční gelová elektroforéza MeSH
- fenotyp MeSH
- fyziologická adaptace genetika MeSH
- metabolické sítě a dráhy MeSH
- nízká teplota MeSH
- proteom genetika metabolismus MeSH
- pšenice genetika metabolismus fyziologie MeSH
- regulace genové exprese u rostlin MeSH
- rostlinné proteiny genetika metabolismus MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- proteom MeSH
- rostlinné proteiny MeSH
Flowering time variation was identified within a mapping population of doubled haploid lines developed from a cross between the introgressive line 8.1 and spring bread wheat cv. Tähti. The line 8.1 carried introgressions from tetraploid Triticum militinae in the cv. Tähti genetic background on chromosomes 1A, 2A, 4A, 5A, 7A, 1B and 5B. The most significant QTL for the flowering time variation was identified within the introgressed region on chromosome 5A and its largest effect was associated with the VRN-A1 locus, accounting for up to 70% of phenotypic variance. The allele of T. militinae origin was designated as VRN-A1f-like. The effect of the VRN-A1f-like allele was verified in two other mapping populations. QTL analysis identified that in cv. Tähti and cv. Mooni genetic background, VRN-A1f-like allele incurred a delay of 1.9-18.6 days in flowering time, depending on growing conditions. Sequence comparison of the VRN-A1f-like and VRN-A1a alleles from the parental lines of the mapping populations revealed major mutations in the promoter region as well as in the first intron, including insertion of a MITE element and a large deletion. The sequence variation allowed construction of specific diagnostic PCR markers for VRN-A1f-like allele determination. Identification and quantification of the effect of the VRN-A1f-like allele offers a useful tool for wheat breeding and for studying fine-scale regulation of flowering pathways in wheat.
OBJECTIVES: The extent and relevance of altered bone metabolism for statural growth in children with chronic kidney disease is controversial. We analyzed the impact of renal dysfunction and recombinant growth hormone therapy on a panel of serum markers of bone metabolism in a large pediatric chronic kidney disease cohort. METHODS: Bone alkaline phosphatase (BAP), tartrate-resistant acid phosphatase 5b (TRAP5b), sclerostin and C-terminal FGF-23 (cFGF23) normalized for age and sex were analyzed in 556 children aged 6-18 years with an estimated glomerular filtration rate (eGFR) of 10-60 ml/min/1.73 m2. 41 children receiving recombinant growth hormone therapy were compared to an untreated matched control group. RESULTS: Standardized levels of BAP, TRAP5b and cFGF-23 were increased whereas sclerostin was reduced. BAP was correlated positively and cFGF-23 inversely with eGFR. Intact serum parathormone was an independent positive predictor of BAP and TRAP5b and negatively associated with sclerostin. BAP and TRAP5B were negatively affected by increased C-reactive protein levels. In children receiving recombinant growth hormone, BAP was higher and TRAP5b lower than in untreated controls. Sclerostin levels were in the normal range and higher than in untreated controls. Serum sclerostin and cFGF-23 independently predicted height standard deviation score, and BAP and TRAP5b the prospective change in height standard deviation score. CONCLUSION: Markers of bone metabolism indicate a high-bone turnover state in children with chronic kidney disease. Growth hormone induces an osteoanabolic pattern and normalizes osteocyte activity. The osteocyte markers cFGF23 and sclerostin are associated with standardized height, and the markers of bone turnover predict height velocity.
- MeSH
- adaptorové proteiny signální transdukční MeSH
- alkalická fosfatasa krev MeSH
- biologické markery krev MeSH
- chronická renální insuficience * krev patofyziologie MeSH
- dítě MeSH
- fibroblastové růstové faktory krev MeSH
- fibroblastový růstový faktor 23 MeSH
- genetické markery MeSH
- izoenzymy krev MeSH
- kosti a kostní tkáň metabolismus MeSH
- kostní morfogenetické proteiny krev MeSH
- kyselá fosfatasa rezistentní k tartarátu MeSH
- kyselá fosfatasa krev MeSH
- lidé MeSH
- lidský růstový hormon aplikace a dávkování MeSH
- mladiství MeSH
- vyšetření funkce ledvin MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- klinické zkoušky MeSH
- multicentrická studie MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adaptorové proteiny signální transdukční MeSH
- alkalická fosfatasa MeSH
- biologické markery MeSH
- FGF23 protein, human MeSH Prohlížeč
- fibroblastové růstové faktory MeSH
- fibroblastový růstový faktor 23 MeSH
- genetické markery MeSH
- izoenzymy MeSH
- kostní morfogenetické proteiny MeSH
- kyselá fosfatasa rezistentní k tartarátu MeSH
- kyselá fosfatasa MeSH
- lidský růstový hormon MeSH
- SOST protein, human MeSH Prohlížeč
BACKGROUND: The new technologies that have the DNA laboratory over recent years and the general progress in knowledge of the human genome, have allowed the simultaneous observation of the activity of a large number of genes. Chronic myeloid leukemia is characterized with abnormal tyrosine kinase activity of the fused bcr/abl gene, which is most often product of translocation between chromosomes 9 an 22. It is as yet unknown whether this is the only and sufficient cause of the disease, or whether other supporting and co-active abnormalities exist. It is also not yet clear whether an increase of proliferating activity or reduced programmed cell death plays the dominant role. The aim of this study was to make further steps in resolving the question as to which of these hypotheses fits better. METHODS AND RESULTS: Membrane macroarrays (Clontech 7742-1: Human Cancer cDNA Expression Array with 588 gene probes) were used throughout the study, on which cDNA reverse-transcribed from total RNA in turn isolated from peripheral white blood cells and labelled with 32P was hybridized. Cells obtained from 5 patients with confirmed diagnoses by cytogenetic and molecular (bcr/abl) analyses, but who had not yet been treated by chemotherapy, were the source of the material. In some cases mononuclears and granulocytes were also isolated by Ficoll-Paque centrifugation. Radioactivity was detected by autoradiography or by a Phosphorimager (Fujifilm FLA-2000). Comparison with normal gene expression (healthy donor) was made by subtraction using Clontech AtlaImage 1.5 software. Although changes of expression of identical genes were not observed in all of patients examined, the majority of them were concordant. Values at least double those of the controls applied to the activity of c-jun N-terminal kinase, MMP-8, MMP-9, integrin alpha E, integrin beta and PDGF, whereas the expression of ZAP-70, IRF1, MCL-1, STAT 5B, RARA, CDC25B, RPSA, TNFR decreased. Increases of PCNA, MMP-17, CD59, rho G, CRAF1 and PIG7 or decreases of notch, caspase 8, caspase 4, interleukin 6 receptor, rho B and TIMP1 were observed only in some cell samples. CONCLUSIONS: It seems that some maturation processes and transmembrane signalling are blocked, as well as the effectors of apoptosis. On the other hand, the reduced activity of ZAP-70, IRF1 and MCL-1 also indicated that proliferation breaks were weakened. The involvement of both processes-released replication and ineffective apoptosis--was evident; the problem of bcr/abl gene fusion being the necessary first and sufficient step on the way towards developing chronic myeloid leukemia, however, remained unresolved.
- MeSH
- bcr-abl fúzové proteiny genetika MeSH
- chronická myeloidní leukemie genetika MeSH
- leukocyty * MeSH
- lidé MeSH
- regulace genové exprese u leukemie * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- anglický abstrakt MeSH
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- bcr-abl fúzové proteiny MeSH
