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A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes

Goldammer, T.; Weikard, R.; Miziara, M. N.; Brunner, R. M.; Agarwala, R.; Schaeffer, A. A.; Womack, E.; Amaral, M. E. J.
Fonte: Karger Publicador: Karger
Tipo: Artigo de Revista Científica Formato: 235-241
ENG
Relevância na Pesquisa
46.08%
A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR(5,000). Comparative analysis of the BBU7 RH 5,000 map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH 5,000 map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence. Copyright (c) 2008 S. Karger AG...

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize

Guimarães, Claudia T.; Sills, Gavin R.; Sobral, Bruno W. S.
Fonte: The National Academy of Sciences of the USA Publicador: The National Academy of Sciences of the USA
Tipo: Artigo de Revista Científica
Publicado em 23/12/1997 EN
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46.08%
Comparative genetic maps of Papuan Saccharum officinarum L. (2n = 80) and S. robustum (2n = 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum ‘SES 208’ (2n = 64, x = 8), thus permitting relations to homology groups (“chromosomes”) of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n = 20)...

Comparative mapping of the human 22q11 chromosomal region and the orthologous region in mice reveals complex changes in gene organization

Puech, Anne; Saint-Jore, Bruno; Funke, Birgit; Gilbert, Debra J.; Sirotkin, Howard; Copeland, Neal G.; Jenkins, Nancy A.; Kucherlapati, Raju; Morrow, Bernice; Skoultchi, Arthur I.
Fonte: The National Academy of Sciences of the USA Publicador: The National Academy of Sciences of the USA
Tipo: Artigo de Revista Científica
Publicado em 23/12/1997 EN
Relevância na Pesquisa
46.04%
The region of human chromosome 22q11 is prone to rearrangements. The resulting chromosomal abnormalities are involved in Velo-cardio-facial and DiGeorge syndromes (VCFS and DGS) (deletions), “cat eye” syndrome (duplications), and certain types of tumors (translocations). As a prelude to the development of mouse models for VCFS/DGS by generating targeted deletions in the mouse genome, we examined the organization of genes from human chromosome 22q11 in the mouse. Using genetic linkage analysis and detailed physical mapping, we show that genes from a relatively small region of human 22q11 are distributed on three mouse chromosomes (MMU6, MMU10, and MMU16). Furthermore, although the region corresponding to about 2.5 megabases of the VCFS/DGS critical region is located on mouse chromosome 16, the relative organization of the region is quite different from that in humans. Our results show that the instability of the 22q11 region is not restricted to humans but may have been present throughout evolution. The results also underscore the importance of detailed comparative mapping of genes in mice and humans as a prerequisite for the development of mouse models of human diseases involving chromosomal rearrangements.

Comparative organization of cattle chromosome 5 revealed by comparative mapping by annotation and sequence similarity and radiation hybrid mapping

Ozawa, Akihito; Band, Mark R.; Larson, Joshua H.; Donovan, Jena; Green, Cheryl A.; Womack, James E.; Lewin, Harris A.
Fonte: The National Academy of Sciences Publicador: The National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.15%
A whole genome cattle-hamster radiation hybrid cell panel was used to construct a map of 54 markers located on bovine chromosome 5 (BTA5). Of the 54 markers, 34 are microsatellites selected from the cattle linkage map and 20 are genes. Among the 20 mapped genes, 10 are new assignments that were made by using the comparative mapping by annotation and sequence similarity strategy. A LOD-3 radiation hybrid framework map consisting of 21 markers was constructed. The relatively low retention frequency of markers on this chromosome (19%) prevented unambiguous ordering of the other 33 markers. The length of the map is 398.7 cR, corresponding to a ratio of ≈2.8 cR5,000/cM. Type I genes were binned for comparison of gene order among cattle, humans, and mice. Multiple internal rearrangements within conserved syntenic groups were apparent upon comparison of gene order on BTA5 and HSA12 and HSA22. A similarly high number of rearrangements were observed between BTA5 and MMU6, MMU10, and MMU15. The detailed comparative map of BTA5 should facilitate identification of genes affecting economically important traits that have been mapped to this chromosome and should contribute to our understanding of mammalian chromosome evolution.

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)

Karsenty, Emmanuelle; Barillot, Emmanuel; Tosser-Klopp, Gwenola; Lahbib-Mansais, Yvette; Milan, Denis; Hatey, François; Cirera, Susanna; Sawera, Milena; Jørgensen, Claus B.; Chowdhary, Bhanu; Fredholm, Merete; Wimmers, Klaus; Ponsuksili, Siriluck; Davol
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/01/2003 EN
Relevância na Pesquisa
46.08%
The GENETPIG database has been established for storing and disseminating the results of the European project: ‘GENETPIG: identification of genes controlling economic traits in pig’. The partners of this project have mapped about 630 porcine and human ESTs onto the pig genome. The database collects the mapping results and links them to other sources of mapping data; this includes pig maps as well as available comparative mapping information. Functional annotation of the mapped ESTs is also given when a significant similarity to cognate genes was established. The database is accessible for consultation via the Internet at http://www.infobiogen.fr/services/Genetpig/.

Comparative Mapping in the Pinaceae

Krutovsky, Konstantin V.; Troggio, Michela; Brown, Garth R.; Jermstad, Kathleen D.; Neale, David B.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /09/2004 EN
Relevância na Pesquisa
46.11%
A comparative genetic map was constructed between two important genera of the family Pinaceae. Ten homologous linkage groups in loblolly pine (Pinus taeda L.) and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco) were identified using orthologous expressed sequence tag polymorphism (ESTP) and restriction fragment length polymorphism (RFLP) markers. The comparative mapping revealed extensive synteny and colinearity between genomes of the Pinaceae, consistent with the hypothesis of conservative chromosomal evolution in this important plant family. This study reports the first comparative map in forest trees at the family taxonomic level and establishes a framework for comparative genomics in Pinaceae.

Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements.

Lagercrantz, U
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /11/1998 EN
Relevância na Pesquisa
46.19%
Chromosome organization and evolution in the Brassicaceae family was studied using comparative linkage mapping. A total of 160 mapped Arabidopsis thaliana DNA fragments identified 284 homologous loci covering 751 cM in Brassica nigra. The data support that modern diploid Brassica species are descended from a hexaploid ancestor, and that the A. thaliana genome is similar in structure and complexity to those of each of the hypothetical diploid progenitors of the proposed hexaploid. Thus, the Brassica lineage probably went through a triplication after the divergence of the lineages leading to A. thaliana and B. nigra. These duplications were also accompanied by an exceptionally high rate of chromosomal rearrangements. The average length of conserved segments between A. thaliana and B. nigra was estimated at 8 cM. This estimate corresponds to approximately 90 rearrangements since the divergence of the two species. The estimated rate of chromosomal rearrangements is higher than any previously reported data based on comparative mapping. Despite the large number of rearrangements, fine-scale comparative mapping between model plant A. thaliana and Brassica crops is likely to result in the identification of a large number of genes that affect important traits in Brassica crops.

Comparative mapping of the barley Ppd-H1 photoperiod response gene region, which lies close to a junction between two rice linkage segments.

Dunford, Roy P; Yano, Masahiro; Kurata, Nori; Sasaki, Takuji; Huestis, Gordon; Rocheford, Torbert; Laurie, David A
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/2002 EN
Relevância na Pesquisa
46.25%
Comparative mapping of cereals has shown that chromosomes of barley, wheat, and maize can be described in terms of rice "linkage segments." However, little is known about marker order in the junctions between linkage blocks or whether this will impair comparative analysis of major genes that lie in such regions. We used genetic and physical mapping to investigate the relationship between the distal part of rice chromosome 7L, which contains the Hd2 heading date gene, and the region of barley chromosome 2HS containing the Ppd-H1 photoperiod response gene, which lies near the junction between rice 7 and rice 4 linkage segments. RFLP markers were mapped in maize to identify regions that might contain Hd2 or Ppd-H1 orthologs. Rice provided useful markers for the Ppd-H1 region but comparative mapping was complicated by loss of colinearity and sequence duplications that predated the divergence of rice, maize, and barley. The sequences of cDNA markers were used to search for homologs in the Arabidopsis genome. Homologous sequences were found for 13 out of 16 markers but they were dispersed in Arabidopsis and did not identify any candidate equivalent region. The implications of the results for comparative trait mapping in junction regions are discussed.

Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

Kumari, Kajal; Muthamilarasan, Mehanathan; Misra, Gopal; Gupta, Sarika; Subramanian, Alagesan; Parida, Swarup Kumar; Chattopadhyay, Debasis; Prasad, Manoj
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 21/06/2013 EN
Relevância na Pesquisa
46.19%
Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02–0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%)...

A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes

Goldammer, T.; Weikard, R.; Miziara, M.N.; Brunner, R.M.; Agarwala, R.; Schäffer, A.A.; Womack, J.E.; Amaral, M.E.J.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.08%
A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR5,000. Comparative analysis of the BBU7 RH5,000 map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH5,000 map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionary conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence.

Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping

Książkiewicz, Michał; Zielezinski, Andrzej; Wyrwa, Katarzyna; Szczepaniak, Anna; Rychel, Sandra; Karlowski, Wojciech; Wolko, Bogdan; Naganowska, Barbara
Fonte: Springer US Publicador: Springer US
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.11%
The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula...

Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice

Varshney, R.; Sigmund, R.; Borner, A.; Korzun, V.; Stein, N.; Sorrells, M.; Langridge, P.; Graner, A.
Fonte: Elsevier Sci Ireland Ltd Publicador: Elsevier Sci Ireland Ltd
Tipo: Artigo de Revista Científica
Publicado em //2005 EN
Relevância na Pesquisa
66.15%
Recent increase in the availability of expressed sequence tag (EST) data has facilitated the development of microsatellite or simple sequence repeat (SSR) markers in a number of plant species groups, including cereals. As these SSRs are derived from ESTs/genes (EST-SSRs), they exhibit a higher potential for transfer through cross-amplification in related species than SSR markers generated from genomic DNA libraries. In this study, a sub-set of 165 EST-SSR markers from a total of 185 assigned to the genetic map of barley was examined for transferability to wheat, rye and rice. A higher proportion, i.e., 78.2% of barley markers showed amplification in wheat followed by 75.2% in rye and 42.4% in rice. Furthermore, in silico comparison of SSR-ESTs (ESTs containing SSRs) corresponding to 185 mapped barley EST-SSR loci against 1,369,182 publicly available cereal ESTs showed significant homology with ESTs of wheat (93.5%), rye (37.3%), rice (57.3%), sorghum (51.9%) and maize (51.9%). Sequence similarity of the barley ESTs with 379,944 ESTs of the two model dicot species, Arabidopsis and Medicago suggested theoretical transferability of barley markers into dicot species although at low frequency (9.7% in Arabidopsis and 8.6% in Medicago). In silico comparative mapping (sequence comparison) of mapped barley SSR-ESTs against the mapping data of rye...

Precise mapping of breakpoints in conserved synteny between human chromosome 1 and pig chromosomes 4, 6 and 9

Sun, H. S.; Tuggle, C. K.; Goureau, A.; Fitzsimmons, Carolyn Jean; Pinton, P.; Chardon, P.; Yerle, M.
Fonte: Blackwell Publicador: Blackwell
Tipo: Artigo de Revista Científica
Publicado em //2002 EN
Relevância na Pesquisa
56.11%
Previous comparative mapping suggested that at least five pig chromosomes (Sscr4, 6, 9, 10 and 14) share homology with human chromosome 1 (Hsap1). A significant quantitative trait loci (QTL) for fat deposition has been identified on Sscr4 that appears to be near the junction region between Sscr4 and Sscr9 relative to Hsap1. It is of interest to define the boundaries of conserved synteny between pig chromosomes and Hsap1 to use human map information to identify putative comparative positional candidates for this QTL. Eleven genes, including Janus kinase 1 (JAK1), Prostaglandin E receptor3 (PTGER3), urate oxidase (UOX), coagulation factor 3 (F3), vascular cell adhesion molecule 1 (VCAM1), ribosomal protein L5 (RPL5), POU domain, class 2, transcription factor 1 (POU2F1), coagulation factor 5 (F5), Prostaglandin endoperoxide synthase-2 (PTGS2), myosin binding protein H (MYBPH) and Antithrombin III (SERPINC1), were selected to refine the boundaries of the blocks of conserved synteny between Hsap1 and pig chromosomes. Pig sequence tagged sites (STSs) were developed and used to physically map these 11 genes using a somatic cell hybrid panel. Eight loci have been mapped by using fluorescent in situ hybridization (FISH) to improve map resolution. Heterologous FISH was used to refine the location of VCAM1 on human chromosomes. In addition...

Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order

Shi, X.-W.; Fitzsimmons, Carolyn Jean; Genet, C.; Prather, R.; Whitworth, K.; Green, J. A.; Tuggle, C. K.
Fonte: Blackwell Publicador: Blackwell
Tipo: Artigo de Revista Científica
Publicado em //2001 EN
Relevância na Pesquisa
46.19%
A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N/RBP56), α-2-plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi-directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-NPEPPS-TAF2N-SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.; The definitive version is available at www.blackwell-synergy.com

An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts

Bouza, Carmen; Hermida, Miguel; Pardo, Bel??n G.; Vera, Manuel; Fern??ndez, Carlos; Herr??n Moreno, Roberto de la; Navajas-P??rez, Rafael; ??lvarez-Dios, Jos?? Antonio; G??mez-Tato, Antonio; Mart??nez, Paulino
Fonte: Biomed Central Publicador: Biomed Central
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
56.27%
[Background] The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. [Results] A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7???cM with low average intermarker distance (3.7???cM; ~2???Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed...

EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human

Tuggle, Christopher K.; Green, Jon A.; Fitzsimmons, Carolyn Jean; Woods, Rami; Prather, Randall S.; Malchenko, Sergei; Soares, Bento M.; Kucaba, Tamara; Crouch, Keith; Smith, Christina; Tack, Dylan; Robinson, Natalie; O'Leary, Brian; Scheetz, Todd; Casava
Fonte: Springer Publicador: Springer
Tipo: Artigo de Revista Científica
Publicado em //2003 EN
Relevância na Pesquisa
46.04%
A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3’ end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.; The original publication can be found at www.springerlink.com

Comparative mapping of Cucurbita moschata and C. pepo using SSR markers

Gong, L.; Lelley, T.
Fonte: INRA. Centre de Recherche d'Avignon. Unité Génétique et Amélioration des Fruits et Légumes, Montfavet (France) Publicador: INRA. Centre de Recherche d'Avignon. Unité Génétique et Amélioration des Fruits et Légumes, Montfavet (France)
Tipo: Poster
EN; ENG
Relevância na Pesquisa
56.04%
The first SSR-based genetic linkage map of C. moschata was created by integrating the maps of two F2 populations with one common parent developed from the crosses Waltham Butternut (WB) × Nigerian Local (NL) and ZHOU (a hull-less type) × WB. This integrated C. moschata map comprises 205 SSR markers and 2 morphological traits (Gr and n). The map is composed of 27 linkage groups with a marker density of 7 cM. Comparison of the C. moschata map and the published C. pepo map revealed a high level of macro-synteny. Seventy-one common SSR markers between C. moschata and C. pepo are located in homologous linkage groups. These markers representing orthologous loci in general have conserved orders and similar genetic distances. Four SSR markers were mapped in non-homologous linkage groups. They may represent different members of multi-gene families, chromosomal rearrangements and paralogs. The comparative mapping of C. moschata and C. pepo reported here will be useful for further studies on Cucurbit evolution, gene isolation, and breeding.; Cucurbitaceae 2008. IX EUCARPIA Meeting. Avignon (France), May 21-24th, 2008

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S.; Liang, Chun
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 24/06/2014 EN
Relevância na Pesquisa
46.11%
Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory).

Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry)

Vilanova, Santiago; Sargent, Daniel J.; Arús, Pere; Monfort, Amparo
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artículo Formato: 502559 bytes; 22098 bytes; application/pdf; application/pdf
ENG
Relevância na Pesquisa
46.08%
12 páginas.-- Incluye el archivo suplementario Synteny_conservation_s1.pdf: FV×FN reference map. The diploid Fragaria reference map constructed using MapMaker from the data of Sargent et al. (2006) and the novel markers (boldface and red) added in this paper.; [Background] The Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera are x = 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison between Malus (subfamily Maloideae) and Prunus (subfamily Prunoideae); however no data has been published to date comparing Malus or Prunus to a member of the subfamily Rosoideae. In this paper we compare the genome of Fragaria, a member of the Rosoideae, to Prunus, a member of the Prunoideae.; [Result] The diploid genomes of Prunus (2n = 2x = 16) and Fragaria (2n = 2x = 14) were compared through the mapping of 71 anchor markers – 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) – on the reference maps of both genera. These markers provided good coverage of the Prunus (78%) and Fragaria (78%) genomes...

Characterizing the chromosomes of the Australian model marsupial Macropus eugenii (Tammar wallaby)

Alsop, Amber; Miethke, Patricia; Rofe, Ruth; Koina, Edda; Sankovic, Natasha; Deakin, Janine; Haines, Helen; Rapkins, Robert; Graves, Jennifer
Fonte: Kluwer Academic Publishers Publicador: Kluwer Academic Publishers
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.11%
Marsupials occupy a phylogenetic middle ground that is very valuable in genome comparisons of mammal and other vertebrate species. For this reason, whole genome sequencing is being undertaken for two distantly related marsupial species, including the model kangaroo species Macropus eugenii (the tammar wallaby). As a first step towards the molecular characterization of the tammar genome, we present a detailed description of the tammar karyotype, report the development of a set of molecular anchor markers and summarize the comparative mapping data for this species.