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1.
Int J Mol Sci ; 20(18)2019 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-31514326

RESUMO

In mammals, leptin and tumor-necrosis factor (TNF) are prominent interacting adipokines mediating appetite control and insulin sensitivity. While TNF pleiotropically functions in immune defense and cell survival, leptin is largely confined to signaling energy stores in adipocytes. Knowledge about the function of avian leptin and TNF is limited and they are absent or lowly expressed in adipose, respectively. Employing radiation-hybrid mapping and FISH-TSA, we mapped TNF and its syntenic genes to chicken chromosome 16 within the major histocompatibility complex (MHC) region. This mapping position suggests that avian TNF has a role in regulating immune response. To test its possible interaction with leptin within the immune system and beyond, we compared the transcription patterns of TNF, leptin and their cognate receptors obtained by meta-analysis of GenBank RNA-seq data. While expression of leptin and its receptor (LEPR) were detected in the brain and digestive tract, TNF and its receptor mRNAs were primarily found in viral-infected and LPS-treated leukocytes. We confirmed leptin expression in the duodenum by immunohistochemistry staining. Altogether, we suggest that whereas leptin and TNF interact as adipokines in mammals, in birds, they have distinct roles. Thus, the interaction between leptin and TNF may be unique to mammals.


Assuntos
Galinhas/genética , Mapeamento Cromossômico , Digestão , Regulação da Expressão Gênica , Leptina/genética , Mamíferos/genética , Transdução de Sinais , Fator de Necrose Tumoral alfa/metabolismo , Animais , Linhagem Celular , Galinhas/metabolismo , Duodeno/metabolismo , Feminino , Leptina/metabolismo , Metáfase/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Mapeamento de Híbridos Radioativos , Receptores para Leptina/metabolismo , Receptores do Fator de Necrose Tumoral/genética , Receptores do Fator de Necrose Tumoral/metabolismo , Sintenia/genética , Fator de Necrose Tumoral alfa/genética
2.
Rev. esp. med. nucl. imagen mol. (Ed. impr.) ; 37(2): 94-102, mar.-abr. 2018. tab, graf
Artigo em Espanhol | IBECS | ID: ibc-171453

RESUMO

Objetivos. La precisión cuantitativa en PET requiere una adecuada aplicación de la corrección de atenuación, lo cual representa uno de los mayores retos que aún están por resolver en la técnica PET/RM. El propósito de este estudio es evaluar el efecto de utilizar mapas de atenuación basados en RM y el uso de antenas flexibles sobre la precisión cuantitativa en PET con especial hincapié en grandes arterias. Materiales y métodos. Se utilizaron datos PET/TC de 8 pacientes oncológicos. Los datos PET fueron reconstruidos utilizando mapas de atenuación con diferente nivel de detalle emulando las distintas aproximaciones utilizadas actualmente por lo equipos PET/RM. Las imágenes PET obtenidas con mapas de atenuación basados en TC y RM fueron comparadas para evaluar las desviaciones cuantitativas obtenidas. El efecto producido por las antenas flexibles fue también estudiado. Resultados. El uso de mapas de atenuación más simplificados da lugar a un incremento en las desviaciones cuantitativas en grasa, tejido blando y hueso. Las desviaciones en pulmón son altas debido a su heterogeneidad y a la variabilidad entre pacientes. La cuantificación en grandes arterias muestra pequeñas desviaciones excepto en el caso de utilizar antenas flexibles. La cuantificación mediante TBR proporciona menores desviaciones al cancelarse las desviaciones medidas en arterias y las venas utilizadas como referencia. Conclusiones. Los mapas de atenuación simplificados que se utilizan en PET/RM producen un incremento significativo de variabilidad cuantitativa especialmente en pulmones y huesos. La cuantificación aplicada al estudio de la aterosclerosis produce pequeñas desviaciones, especialmente cuando se utiliza el TBR (AU)


Objectives. Accuracy on quantitative PET image analysis relies on the correct application of attenuation correction which is one of the major challenges for PET/MRI that remains to be solved. The purpose of this study is to evaluate the effect of MRI-based attenuation maps and the use of flexible coils on the quantitative accuracy of PET images with a special focus on large arteries. Materials and methods. PET/CT data from eight oncologic patients was used. PET data was reconstructed using attenuation maps with different level of detail emulating several approaches available on current PET/MRI scanners. PET images obtained with CT-based and MRI-based attenuation maps were compared to evaluate the quantitative biases obtained. The quantitative effect produced by flexible MRI receiver coils on the attenuation maps was also studied. Results. The use of simpler attenuation maps produced increased biases between PET data reconstructed with CT-based and MRI-based attenuation maps for fat, non-fat soft-tissues and bone. Biases in lung were very high due to the large heterogeneity and inter-patient variability of the lung. The quantification on large arteries had small deviations except for the case when flexible coils were used. The TBR provided smaller biases in all cases as it cancelled out the similar deviations obtained for arteries and reference veins. Conclusions. Simplified attenuation maps used on PET/MRI significantly increase the quantitative variability of PET images especially on lungs and bones. The quantification of PET images acquired with PET/MRI scanners applied to studies of atherosclerosis has small deviations, especially when the TBR is considered (AU)


Assuntos
Humanos , Tomografia por Emissão de Pósitrons/métodos , Aterosclerose/diagnóstico por imagem , Placa Aterosclerótica/diagnóstico por imagem , Mapeamento de Híbridos Radioativos , Absorciometria de Fóton/métodos
3.
Sci Rep ; 8(1): 1982, 2018 01 31.
Artigo em Inglês | MEDLINE | ID: mdl-29386528

RESUMO

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.


Assuntos
Camelus/genética , Genoma , Mapeamento de Híbridos Radioativos , Animais , Cricetinae , DNA/genética , Feminino
4.
BMC Genet ; 18(1): 77, 2017 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-28793857

RESUMO

BACKGROUND: Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly. RESULTS: A radiation hybrid panel of chicken-hamster Wg3hCl2 cells was used to map the genome location of the chicken leptin gene. Contrary to our expectations, based on comparative genome mapping and sequence characteristics, the chicken leptin was not located on a microchromosome, which are known to contain GC-rich and repetitive regions, but at the distal tip of the largest chromosome (1p). Following conserved synteny with other vertebrates, we also mapped five additional genes to this genomic region (ARF5, SND1, LRRC4, RBM28, and FLNC), bridging the genomic gap in the current Galgal5 build for this chromosome region. All of the short scaffolds containing these genes were found to consist of GC-rich (54 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1. In this syntenic group, the RNA-binding protein 28 (RBM28) was in closest proximity to leptin. We deduced the full-length of the RBM28 cDNA sequence and profiled its expression patterns detecting a negative correlation (R = - 0.7) between the expression of leptin and of RBM28 across tissues that expressed at least one of the genes above the average level. This observation suggested a local regulatory interaction between these genes. In adipose tissues, we observed a significant increase in RBM28 mRNA expression in breeds with lean phenotypes. CONCLUSION: Mapping chicken leptin together with a cluster of five syntenic genes provided the final proof for its identification as the true chicken ortholog. The high GC-content observed for the chicken leptin syntenic group suggests that other similar clusters of genes in GC-rich genomic regions are missing from the current genome assembly (Galgal5), which should be resolved in future assemblies of the chicken genome.


Assuntos
Proteínas Aviárias/genética , Galinhas/genética , Leptina/genética , Mapeamento de Híbridos Radioativos/métodos , Sequência de Aminoácidos , Animais , Células Cultivadas , Cromossomos , Cricetinae , Marcadores Genéticos , Genoma , Genômica , Sequências Repetitivas de Ácido Nucleico , Homologia de Sequência , Sintenia
5.
Methods Mol Biol ; 1429: 91-101, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27511169

RESUMO

Radiation treatment of genomes is used to generate chromosome breaks for numerous applications. This protocol describes the preparation of seeds and the determination of the optimal level of irradiation dosage for the creation of a radiation hybrid (RH) population. These RH lines can be used to generate high-resolution physical maps for the assembly of sequenced genomes as well as the fine mapping of genes. This procedure can also be used for mutation breeding and forward/reverse genetics.


Assuntos
Cromossomos de Plantas/efeitos da radiação , Genoma de Planta , Mapeamento de Híbridos Radioativos/métodos , Radiação Ionizante , Triticum/genética , Triticum/efeitos da radiação
6.
Plant J ; 86(2): 195-207, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26945524

RESUMO

Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.


Assuntos
Triticum/genética , Mapeamento Cromossômico , Mapeamento de Sequências Contíguas , Sequenciamento de Nucleotídeos em Larga Escala , Polimorfismo de Nucleotídeo Único , Mapeamento de Híbridos Radioativos , Análise de Sequência de DNA
7.
Plant Biotechnol J ; 14(8): 1716-26, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-26915753

RESUMO

The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat.


Assuntos
Citoplasma/genética , Mapeamento de Híbridos Radioativos/métodos , Triticum/genética , Alelos , Núcleo Celular/genética , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Variação Genética , Mapeamento Físico do Cromossomo
8.
Genet Mol Res ; 14(4): 13096-104, 2015 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-26535622

RESUMO

River buffalo chromosome 1 (BBU1) is a sub-metacentric chromosome homologous to bovine chromosomes 1 and 27. In this study, we constructed a new framework radiation hybrid (RH) map from BBU1 using BBURH5000 panel adding nine new genes (ADRB3, ATP2C1, COPB2, CRYGS, P2RY1, SLC5A3, SLC20A2, SST, and ZDHHC2) and one microsatellite (CSSM043) to the set of markers previously mapped on BBU1. The new framework RH map of BBU1 contained 141 markers (55 genes, 2 ESTs, 10 microsatellites, and 74 SNPs) distributed within one linkage group spanning 2832.62 centirays. Comparison of the RH map to sequences from bovine chromosomes 1 and 27 revealed an inversion close to the telomeric region. In addition, we ordered a set of 34 scaffolds from the buffalo genome assembly UMD_CASPUR_WB_2.0. The RH map could provide a valuable tool to order scaffolds from the buffalo genome sequence, contributing to its annotation.


Assuntos
Búfalos/genética , Cromossomos de Mamíferos , Genoma , Genômica , Mapeamento de Híbridos Radioativos , Animais , Bovinos , Marcadores Genéticos , Genômica/métodos
9.
BMC Genomics ; 16: 800, 2015 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-26475137

RESUMO

BACKGROUND: The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. METHODS: In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. RESULTS: A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. CONCLUSION: This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.


Assuntos
Genoma de Planta , Poaceae/genética , Mapeamento de Híbridos Radioativos/métodos , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genótipo
10.
BMC Genomics ; 16: 406, 2015 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-26003112

RESUMO

BACKGROUND: Physical and linkage maps are important aids for the assembly of genome sequences, comparative analyses of synteny, and to search for candidate genes by quantitative trait locus analysis. Yellowtail, Seriola quinqueradiata, is an economically important species in Japanese aquaculture, and genetic information will be useful for DNA-assisted breeding. We report the construction of a second generation radiation hybrid map, its synteny analysis, and a second generation linkage map containing SNPs (single nucleotide polymorphisms) in yellowtail. RESULTS: Approximately 1.4 million reads were obtained from transcriptome sequence analysis derived from 11 tissues of one individual. To identify SNPs, cDNA libraries were generated from a pool of 500 whole juveniles, and the gills and kidneys of 100 adults. 9,356 putative SNPs were detected in 6,025 contigs, with a minor allele frequency ≥ 25%. The linkage and radiation hybrid maps were constructed based on these contig sequences. 2,081 markers, including 601 SNPs markers, were mapped onto the linkage map, and 1,532 markers were mapped in the radiation hybrid map. CONCLUSIONS: The second generation linkage and physical maps were constructed using 6,025 contigs having SNP markers. These maps will aid the de novo assembly of sequencing reads, linkage studies and the identification of candidate genes related to important traits. The comparison of marker contigs in the radiation hybrid map indicated that yellowtail is evolutionarily closer to medaka than to green-spotted pufferfish, three-spined stickleback or zebrafish. The synteny analysis may aid studies of chromosomal evolution in yellowtail compared with model fish.


Assuntos
Oryzias/genética , Perciformes/genética , Mapeamento de Híbridos Radioativos/métodos , Sintenia , Tetraodontiformes/genética , Peixe-Zebra/genética , Animais , Evolução Molecular , Perfilação da Expressão Gênica , Ligação Genética , Genoma , Modelos Animais , Filogenia , Polimorfismo de Nucleotídeo Único
11.
J Appl Genet ; 56(1): 85-95, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25081836

RESUMO

The identification of genetic markers associated with important economic traits is fundamental to improving the productivity and quality of livestock. In this investigation, we searched for 177 expressed sequence tags (ESTs) putatively involved in meat quality from the available pig EST database, and detected eight single nucleotide polymorphisms (SNPs) in eight ESTs. We investigated the associations of these SNPs with 18 carcass and meat quality traits in a Landrace × Lantang F2 resource population (n = 257). Association analysis revealed that seven SNPs (except E42) were associated with some of the carcass- and meat quality-related traits. Particularly, significant associations of three SNPs (E53, E82, and E36) with backfat thickness traits were observed. Further, the genetic effects of E53 on four live backfat thickness traits were validated in an independent population (n = 221). More investigations about E53 sequence characteristics were performed, i.e., radiation hybrid (RH) mapping, 3'-RACE, and screening analysis of the positive BAC clones. Our research identified the genetic effects of eight EST-derived SNPs on carcass and meat quality traits, and suggested that E53 may be a useful marker for live backfat thickness traits in pig breeding programs.


Assuntos
Etiquetas de Sequências Expressas , Carne/análise , Polimorfismo de Nucleotídeo Único , Sus scrofa/genética , Adiposidade/genética , Animais , Feminino , Genótipo , Masculino , Fenótipo , Mapeamento de Híbridos Radioativos
13.
BMC Genomics ; 15: 625, 2014 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-25052253

RESUMO

BACKGROUND: The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements on a small scale in ruminants remain speculative. Recently completed goat genome sequence was released but is still in a draft stage. The draft sequence used a variety of assembly packages, as well as a radiation hybrid (RH) map of chromosome 1 as part of its validation. RESULTS: Using an improved RH mapping pipeline, whole-genome dense maps of 45,953 SNP markers were constructed with statistical confidence measures and the saturated maps provided a fine map resolution of approximate 65 kb. Linking RH maps to the goat sequences showed that the assemblies of scaffolds/super-scaffolds were globally accurate. However, we observed certain flaws linked to the process of anchoring chromosome using conserved synteny with cattle. Chromosome assignments, long-range order, and orientation of the scaffolds were reassessed in an updated genome sequence version. We also present new results exploiting the updated goat genome sequence to understand genomic rearrangements and chromosome evolution between mammals during species radiations. The sequence architecture of rearrangement sites between the goat and cattle genomes presented abundant segmental duplication on regions of goat chromosome 9 and 14, as well as new insertions in homologous cattle genome regions. This complex interplay between duplicated sequences and Robertsonian translocations highlights the rearrangement mechanism of centromeric nonallelic homologous recombination (NAHR) in mammals. We observed that species-specific shifts in ANKRD26 gene duplication are coincident with breakpoint reuse in divergent lineages and this gene family may play a role in chromosome stabilization in chromosome evolution. CONCLUSIONS: We generated dense maps of the complete whole goat genome. The chromosomal maps allowed us to anchor and orientate assembled genome scaffolds along the chromosomes, annotate chromosome rearrangements and thereby get a better understanding of the genome evolution of ruminants and other mammals.


Assuntos
Evolução Molecular , Rearranjo Gênico/genética , Genômica/métodos , Cabras/genética , Mapeamento de Híbridos Radioativos/métodos , Animais , Bovinos , Cromossomos de Mamíferos/genética , Família Multigênica/genética , Proteínas Nucleares/genética , Polimorfismo de Nucleotídeo Único/genética , Reprodutibilidade dos Testes
14.
BMC Genomics ; 15: 165, 2014 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-24571093

RESUMO

BACKGROUND: Yellowtail (Seriola quinqueradiata) are an economically important species in Japan. However, there are currently no methods for captive breeding and early rearing for yellowtail. Thus, the commercial cultivation of this species is reliant upon the capture of wild immature fish. Given this, there is a need to develop captive breeding techniques to reduce pressure on wild stocks and facilitate the sustainable development of yellowtail aquaculture. We constructed a whole genome radiation hybrid (RH) panel for yellowtail gene mapping and developed a framework physical map using a nanofluidic dynamic array to use SNPs (single nucleotide polymorphisms) in ESTs (expressed sequence tags) for the DNA-assisted breeding of yellowtail. RESULTS: Clonal RH cell lines were obtained after ionizing radiation; specifically, 78, 64, 129, 55, 42, and 53 clones were isolated after treatment with 3,000, 4,000, 5,000, 6,000, 8,000, or 10,000 rads, respectively. A total of 421 hybrid cell lines were obtained by fusion with mouse B78 cells. Ninety-four microsatellite markers used in the genetic linkage map were genotyped using the 421 hybrid cell lines. Based upon marker retention and genome coverage, we selected 93 hybrid cell lines to form an RH panel. Importantly, we performed the first genotyping of yellowtail markers in an RH panel using a nanofluidic dynamic array (Fluidigm, CA, USA). Then, 580 markers containing ESTs and SNPs were mapped in the first yellowtail RH map. CONCLUSIONS: We successfully developed a yellowtail RH panel to facilitate the localization of markers. Using this, a framework RH map was constructed with 580 markers. This high-density physical map will serve as a useful tool for the identification of genes related to important breeding traits using genetic structural information, such as conserved synteny. Moreover, in a comparison of 30 sequences in the RH group 1 (SQ1), yellowtail appeared to be evolutionarily closer to medaka and the green-spotted pufferfish than to zebrafish. We suggest that synteny analysis may be potentially useful as a tool to investigate chromosomal evolution by comparison with model fish.


Assuntos
Peixes/genética , Mapeamento de Híbridos Radioativos , Animais , Cruzamento , Linhagem Celular , Cromossomos , Etiquetas de Sequências Expressas , Feminino , Fibroblastos , Ligação Genética , Genoma , Masculino , Técnicas Analíticas Microfluídicas , Nanotecnologia , Polimorfismo de Nucleotídeo Único , Sintenia
15.
Artigo em Inglês | MEDLINE | ID: mdl-26356853

RESUMO

The process of mapping markers from radiation hybrid mapping (RHM) experiments is equivalent to the traveling salesman problem and, thereby, has combinatorial complexity. As an additional problem, experiments typically result in some unreliable markers that reduce the overall quality of the map. We propose a clustering approach for addressing both problems efficiently by eliminating unreliable markers without the need for mapping the complete set of markers. Traditional approaches for eliminating markers use resampling of the full data set, which has an even higher computational complexity than the original mapping problem. In contrast, the proposed approach uses a divide-and-conquer strategy to construct framework maps based on clusters that exclude unreliable markers. Clusters are ordered using parallel processing and are then combined to form the complete map. We present three algorithms that explore the trade-off between the number of markers included in the map and placement accuracy. Using an RHM data set of the human genome, we compare the framework maps from our proposed approaches with published physical maps and with the results of using the Carthagene tool. Overall, our approaches have a very low computational complexity and produce solid framework maps with good chromosome coverage and high agreement with the physical map marker order.


Assuntos
Análise por Conglomerados , Biologia Computacional/métodos , Mapeamento de Híbridos Radioativos/métodos , Algoritmos , Bases de Dados Genéticas , Genoma Humano , Humanos
16.
Theor Appl Genet ; 126(8): 1977-90, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23715938

RESUMO

Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.


Assuntos
Infertilidade das Plantas/genética , Infertilidade das Plantas/efeitos da radiação , Mapeamento de Híbridos Radioativos , Triticum/genética , Triticum/efeitos da radiação , Cromossomos de Plantas/genética , Variação Genética/efeitos da radiação , Genótipo , Meiose/genética , Plantas Geneticamente Modificadas/efeitos da radiação , Sementes/genética , Sementes/efeitos da radiação , Deleção de Sequência/genética , Deleção de Sequência/efeitos da radiação
17.
Funct Integr Genomics ; 13(1): 19-32, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23479086

RESUMO

The species cytoplasm specific (scs) genes affect nuclear-cytoplasmic interactions in interspecific hybrids. A radiation hybrid (RH) mapping population of 188 individuals was employed to refine the location of the scs (ae) locus on Triticum aestivum chromosome 1D. "Wheat Zapper," a comparative genomics tool, was used to predict synteny between wheat chromosome 1D, Oryza sativa, Brachypodium distachyon, and Sorghum bicolor. A total of 57 markers were developed based on synteny or literature and genotyped to produce a RH map spanning 205.2 cR. A test-cross methodology was devised for phenotyping of RH progenies, and through forward genetic, the scs (ae) locus was pinpointed to a 1.1 Mb-segment containing eight genes. Further, the high resolution provided by RH mapping, combined with chromosome-wise synteny analysis, located the ancestral point of fusion between the telomeric and centromeric repeats of two paleochromosomes that originated chromosome 1D. Also, it indicated that the centromere of this chromosome is likely the result of a neocentromerization event, rather than the conservation of an ancestral centromere as previously believed. Interestingly, location of scs locus in the vicinity of paleofusion is not associated with the expected disruption of synteny, but rather with a good degree of conservation across grass species. Indeed, these observations advocate the evolutionary importance of this locus as suggested by "Maan's scs hypothesis."


Assuntos
Cromossomos de Plantas/genética , Mapeamento de Híbridos Radioativos , Sintenia , Triticum/genética , Centrômero/genética , Genes de Plantas , Loci Gênicos , Marcadores Genéticos , Telômero/genética
18.
Gene ; 515(1): 220-3, 2013 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-23219995

RESUMO

Solute-carrier family 27A molecules are integral transmembrane proteins that play a fundamental role in the uptake of long-chain fatty acids into mammalian cells. Our goal was to characterize this multigene family in pigs. Chromosomal location of the six porcine SLC27A genes was determined by radiation hybrid mapping and indicated that the six genes map to six different chromosomal locations. Moreover, we analyzed SLC27A mRNA expression in six pig tissues by quantitative RT-PCR. While SLC27A1, SLC27A3 and SLC27A4 were expressed in most, if not all, analyzed tissues, SLC27A2, SLC27A5 and SLC27A6 were predominantly expressed in the liver. In general, pig and human SLC27A mRNA expression profiles were remarkably concordant, although important differences were observed for SLC27A1 and SLC27A6 mRNAs. Discrepancies between mRNA expression profiles have been observed even in closely related primate species, and they might reflect the acquisition of regulatory changes promoting evolutionary adaptation.


Assuntos
Proteínas de Transporte de Ácido Graxo/genética , Perfilação da Expressão Gênica , Família Multigênica , Mapeamento de Híbridos Radioativos , Animais , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Suínos
19.
PLoS One ; 7(11): e48815, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23144983

RESUMO

Physical mapping and genome sequencing are underway for the ≈17 Gb wheat genome. Physical mapping methods independent of meiotic recombination, such as radiation hybrid (RH) mapping, will aid precise anchoring of BAC contigs in the large regions of suppressed recombination in Triticeae genomes. Reports of endosperm development following pollination with irradiated pollen at dosages that cause embryo abortion prompted us to investigate endosperm as a potential source of RH mapping germplasm. Here, we report a novel approach to construct RH based physical maps of all seven D-genome chromosomes of the hexaploid wheat 'Chinese Spring', simultaneously. An 81-member subset of endosperm samples derived from 20-Gy irradiated pollen was genotyped for deletions, and 737 markers were mapped on seven D-genome chromosomes. Analysis of well-defined regions of six chromosomes suggested a map resolution of ∼830 kb could be achieved; this estimate was validated with assays of markers from a sequenced contig. We estimate that the panel contains ∼6,000 deletion bins for D-genome chromosomes and will require ∼18,000 markers for high resolution mapping. Map-based deletion estimates revealed a majority of 1-20 Mb interstitial deletions suggesting mutagenic repair of double-strand breaks in pollen provides a useful resource for RH mapping and map based cloning studies.


Assuntos
Aneuploidia , Quebra Cromossômica , Cromossomos de Plantas/química , Endosperma/genética , Genoma de Planta , Triticum/genética , Raios gama , Marcadores Genéticos , Polinização , Mapeamento de Híbridos Radioativos
20.
BMC Genomics ; 13: 597, 2012 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-23127207

RESUMO

BACKGROUND: Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. RESULTS: Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome. CONCLUSIONS: The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.


Assuntos
Genoma de Planta/genética , Poaceae/genética , Mapeamento de Híbridos Radioativos/métodos , Cruzamentos Genéticos , Triticum/genética
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