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‣ An integrated molecular map of yellow passion fruit based on simultaneous maximum-likelihood estimation of linkage and linkage phases

OLIVEIRA, Eder J.; VIEIRA, Maria Lucia C.; GARCIA, Antonio Augusto F.; MUNHOZ, Carla F.; MARGARIDO, Gabriel R. A.; CONSOLI, Luciano; MATTA, Frederico P.; MORAES, Michel C.; ZUCCHI, Maria I.; FUNGARO, Maria Helena P.
Fonte: AMER SOC HORTICULTURAL SCIENCE Publicador: AMER SOC HORTICULTURAL SCIENCE
Tipo: Artigo de Revista Científica
Português
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The development of genetic maps for auto-incompatible species, such as the yellow passion fruit (Passiflora edulis Sims f.flavicarpa Deg.) is restricted due to the unfeasibility of obtaining traditional mapping populations based on inbred lines. For this reason, yellow passion fruit linkage maps were generally constructed using a strategy known as two-way pseudo-testeross, based on monoparental dominant markers segregating in a 1:1 fashion. Due to the lack of information from these markers in one of the parents, two individual (parental) maps were obtained. However, integration of these maps is essential, and biparental markers can be used for such an operation. The objective of our study was to construct an integrated molecular map for a full-sib population of yellow passion fruit combining different loci configuration generated from amplified fragment length polymorphisms (AFLPs) and microsatellite markers and using a novel approach based on simultaneous maximum-likelihood estimation of linkage and linkage phases, specially designed for outcrossing species. Of the total number of loci, approximate to 76%, 21%, 0.7%, and 2.3% did segregate in 1:1, 3:1, 1:2:1, and 1:1:1:1 ratios, respectively. Ten linkage groups (LGs) were established with a logarithm of the odds (LOD) score >= 5.0 assuming a recombination fraction : <= 0.35. On average...

‣ A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Palhares, Alessandra C; Rodrigues-Morais, Taislene B; Van Sluys, Marie-Anne; Domingues, Douglas S; Maccheroni, Walter; Jordão, Hamilton; Souza, Anete P; Marconi, Thiago G; Mollinari, Marcelo; Gazaffi, Rodrigo; Garcia, Antonio A F; Vieira, Maria L C
Fonte: BioMed Central; London Publicador: BioMed Central; London
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
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Abstract Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM...

‣ Mapeamento genético de marcadores AFLP e de retrotransposons em cana-de-açúcar (Saccharum spp.); Genetic mapping of AFLP and retrotransposon-derived markers in sugarcane (Saccharum spp.)

Palhares, Alessandra Carolina
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 17/05/2010 Português
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No presente trabalho, AFLPs e marcadores baseados em retrotransposons foram utilizados para a construção de um mapa de ligação integrado em cana-de-açúcar. Dois retrotransposons encontrados no genoma da cana-de-açúcar, denominados SURE e Garapa, foram estudados. Os princípios da técnica NBS-profiling foram usados para gerar marcadores direcionados às sequências desses retrotransposons. Os marcadores foram analisados numa população F1 de cana-de-açúcar, composta por 188 indivíduos, oriunda do cruzamento entre os genitores IAC66-6 e TUC71-7. O mapa integrado foi construído usando-se o software OneMap, especialmente desenvolvido para mapear espécies não endogâmicas. Excelentes padrões de AFLP e de marcas direcionadas ao retrotransposon SURE foram obtidos; entretanto, para o Garapa, ainda são necessários ajustes na técnica. Um total de 600 marcadores de dose única foi obtido a partir de 22 combinações de enzimas de restrição/primers de AFLP e seis combinações otimizadas para amplificar marcas direcionadas ao retrotransposon SURE. Construiu-se um mapa com 107 grupos de ligação, com tamanho de 4.316,5 cM e densidade de 8,74 cM/marcador. O mapeamento dos marcadores derivados do retrotransposon SURE revelou que esse elemento não está uniformemente distribuído nos grupos de ligação e confirmou o seu baixo número de cópias no genoma da cana...

‣ Estudo de uma população segregante (F1) de maracujá-doce: enriquecimento do mapa de ligação e mapeamento de QTL para produção e qualidade de frutos; A study of a sweet passion fruit segregating population (F1): enrichment of the linkage map and QTL mapping for yield and fruit quality

Laperuta, Larissa Di Cássia
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 10/06/2011 Português
Relevância na Pesquisa
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A cultura do maracujá-doce (Passiflora alata Curtis, 2n = 18) não apresenta expressão comercial como à do maracujá-amarelo. No entanto, por se tratar de uma frutífera relativamente nova nos mercados, com grande potencial de expansão devido ao seu valor agregado, há necessidade de se realizarem estudos genéticos e de melhoramento visando a sua expansão comercial, que deve vir acompanhada pela geração de conhecimento científico. Assim, o objetivo deste estudo foi enriquecer o mapa genético integrado da espécie com marcadores funcionais e mapear QTL relacionados à produção e qualidade de fruto. Para tal, foi utilizada uma população F1 composta por 180 indivíduos, provenientes do cruzamento simples entre dois acessos de maracujá-doce. Para a construção do mapa de ligação, utilizou-se um algoritmo que estima, por verossimilhança, simultaneamente, a fase de ligação e a frequência de recombinação, especialmente desenhado para espécies não endogâmicas. Em paralelo, 100 genótipos dessa mesma população foram avaliados fenotipicamente em dois locais, durante dois anos, para caracteres de interesse agronômico. As análises de QTL foram feitas pelo método de mapeamento por intervalo composto e marcadores com diferentes padrões de segregação. Os dados fenotípicos mostraram que existe variabilidade genética na população F1 para ser explorada com fins de melhoramento. Um novo mapa de ligação integrado foi gerado com 1786...

‣ Construction of a functional map for rubber tree (Hevea brasiliensis) = : Construção de um mapa funcional em seringueira (Hevea brasiliensis); Construção de um mapa funcional em seringueira (Hevea brasiliensis)

Carla Cristina da Silva
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 18/06/2014 Português
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A seringueira (Hevea brasiliensis), espécie nativa da Amazônia, é a maior fonte de borracha natural do mundo. Programas de melhoramento genético da seringueira têm sido cruciais para a obtenção de caracteres desejáveis. Entretanto, o ciclo de melhoramento da seringueira é muito longo (cerca de 30 anos), tornando-se essencial o desenvolvimento de novas técnicas de avaliação precoce. As bibliotecas de cDNA e Expressed Sequence Tags (ESTs) são ferramentas muito importantes em biologia molecular: possibilitam identificar genes preferencialmente expressos em tecidos ou tipos celulares e também são valiosas fontes de marcadores polimórficos, instrumentos poderosos para genotipagem e mapeamento molecular. O uso de marcadores derivados de ESTs permite construir mapas funcionais, nos quais são posicionados genes transcritos ou regiões próximas aos genes. Este tipo de mapeamento é importante para estudos de associação gene-característica, e identificação de genes candidatos. Este trabalho objetivou a construção de bibliotecas de cDNA de diferentes tecidos (painel, látex e folha) e tratamentos (exposição ao frio e infecção controlada por Microcyclus ulei) de seringueira para desenvolver sequências EST e marcadores moleculares gene-direcionados a partir destas sequências...

‣ Integrated Genomic Map from Uropathogenic Escherichia coli J96

Melkerson-Watson, Lyla J.; Rode, Christopher K.; Zhang, Lixin; Foxman, Betsy; Bloch, Craig A.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /10/2000 Português
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Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10 insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis in NotI digests. However...

‣ A High-throughput AFLP-based Method for Constructing Integrated Genetic and Physical Maps: Progress Toward a Sorghum Genome Map

Klein, Patricia E.; Klein, Robert R.; Cartinhour, Samuel W.; Ulanch, Paul E.; Dong, Jianmin; Obert, Jacque A.; Morishige, Daryl T.; Schlueter, Shannon D.; Childs, Kevin L.; Ale, Melissa; Mullet, John E.
Fonte: Cold Spring Harbor Laboratory Press Publicador: Cold Spring Harbor Laboratory Press
Tipo: Artigo de Revista Científica
Publicado em /06/2000 Português
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Sorghum is an important target for plant genomic mapping because of its adaptation to harsh environments, diverse germplasm collection, and value for comparing the genomes of grass species such as corn and rice. The construction of an integrated genetic and physical map of the sorghum genome (750 Mbp) is a primary goal of our sorghum genome project. To help accomplish this task, we have developed a new high-throughput PCR-based method for building BAC contigs and locating BAC clones on the sorghum genetic map. This task involved pooling 24,576 sorghum BAC clones (∼4× genome equivalents) in six different matrices to create 184 pools of BAC DNA. DNA fragments from each pool were amplified using amplified fragment length polymorphism (AFLP) technology, resolved on a LI-COR dual-dye DNA sequencing system, and analyzed using Bionumerics software. On average, each set of AFLP primers amplified 28 single-copy DNA markers that were useful for identifying overlapping BAC clones. Data from 32 different AFLP primer combinations identified ∼2400 BACs and ordered ∼700 BAC contigs. Analysis of a sorghum RIL mapping population using the same primer pairs located ∼200 of the BAC contigs on the sorghum genetic map. Restriction endonuclease fingerprinting of the entire collection of sorghum BAC clones was applied to test and extend the contigs constructed using this PCR-based methodology. Analysis of the fingerprint data allowed for the identification of 3366 contigs each containing an average of 5 BACs. BACs in ∼65% of the contigs aligned by AFLP analysis had sufficient overlap to be confirmed by DNA fingerprint analysis. In addition...

‣ An Integrated Genetic Map of the African Human Malaria Vector Mosquito, Anopheles Gambiae

Zheng, L.; Benedict, M. Q.; Cornel, A. J.; Collins, F. H.; Kafatos, F. C.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1996 Português
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We present a genetic map based on microsatellite polymorphisms for the African human malaria vector, Anopheles gambiae. Polymorphisms in laboratory strains were detected for 89% of the tested microsatellite markers. Genotyping was performed for individual mosquitoes from 13 backcross families that included 679 progeny. Three linkage groups were identified, corresponding to the three chromosomes. We added 22 new markers to the existing X chromosome map, for a total of 46 microsatellite markers spanning a distance of 48.9 cM. The second chromosome has 57 and the third 28 microsatellite markers spanning a distance of 72.4 and 93.7 cM, respectively. The overall average distance between markers is 1.6 cM (or 1.1, 1.2, and 3.2 cM for the X, second, and third chromosomes, respectively). In addition to the 131 microsatellite markers, the current map also includes a biochemical selectable marker, Dieldrin resistance (Dl), on the second chromosome and five visible markers, pink-eye (p) and white (w) on the X, collarless (c) and lunate (lu) on the second, and red-eye (r) on the third. The cytogenetic locations on the nurse cell polytene chromosomes have been determined for 47 markers, making this map an integrated tool for cytogenetic, genetic...

‣ Integrated Genetic Map of Anopheles Gambiae: Use of Rapd Polymorphisms for Genetic, Cytogenetic and Sts Landmarks

Dimopoulos, G.; Zheng, L.; Kumar, V.; Torre, A. D.; Kafatos, F. C.; Louis, C.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /06/1996 Português
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Randomly amplified polymorphic DNA (RAPD) markers have been integrated in the genetic and cytogenetic maps of the malaria vector mosquito, Anopheles gambiae. Fifteen of these markers were mapped by recombination, relative to microsatellite markers that had been mapped previously. Thirty-four gel-purified RAPD bands were cloned and sequenced, generating sequence tagged sites (STSs) that can be used as entry points to the A. gambiae genome. Thirty one of these STSs were localized on nurse cell polytene chromosomes through their unique hybridization signal in in situ hybridization experiments. Five STSs map close to the breakpoints of polymorphic inversions, which are notable features of the Anopheles genome. The usefulness and limitations of this integrated mosquito map are discussed.

‣ Integrated genetic map and genetic analysis of a region associated with root traits on the short arm of rye chromosome 1 in bread wheat

Sharma, Sundrish; Bhat, Prasanna R.; Ehdaie, Bahman; Close, Timothy J.; Lukaszewski, Adam J.; Waines, J. Giles
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
Português
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58.161133%
A rye–wheat centric chromosome translocation 1RS.1BL has been widely used in wheat breeding programs around the world. Increased yield of translocation lines was probably a consequence of increased root biomass. In an effort to map loci-controlling root characteristics, homoeologous recombinants of 1RS with 1BS were used to generate a consensus genetic map comprised of 20 phenotypic and molecular markers, with an average spacing of 2.5 cM. Physically, all recombination events were located in the distal 40% of the arms. A total of 68 recombinants was used and recombination breakpoints were aligned and ordered over map intervals with all the markers, integrated together in a genetic map. This approach enabled dissection of genetic components of quantitative traits, such as root traits, present on 1S. To validate our hypothesis, phenotyping of 45-day-old wheat roots was performed in five lines including three recombinants representative of the entire short arm along with bread wheat parents ‘Pavon 76’ and Pavon 1RS.1BL. Individual root characteristics were ranked and the genotypic rank sums were subjected to Quade analysis to compare the overall rooting ability of the genotypes. It appears that the terminal 15% of the rye 1RS arm carries gene(s) for greater rooting ability in wheat.

‣ Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

Nayak, Spurthi N.; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jüngling, Ruth; Singh, Jagbir; Kavi Kishor, P. B.; Sivaramakrishnan, S.; Hoisington, Dave A.; Kahl, Günter; Winter, Peter; Cook, Douglas R.; Varshney, Rajeev
Fonte: Springer-Verlag Publicador: Springer-Verlag
Tipo: Artigo de Revista Científica
Português
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48.193613%
This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2...

‣ Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

Vipin, Cina Ann; Luckett, David J.; Harper, John D.I.; Ash, Gavin J.; Kilian, Andrzej; Ellwood, Simon R.; Phan, Huyen T.T.; Raman, Harsh
Fonte: Japanese Society of Breeding Publicador: Japanese Society of Breeding
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
48.184487%
We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.

‣ An Integrated Genetic and Cytogenetic Map for Zhikong Scallop, Chlamys farreri, Based on Microsatellite Markers

Feng, Liying; Hu, Liping; Fu, Xiaoteng; Liao, Huan; Li, Xuan; Zhan, Aibin; Zhang, Lingling; Wang, Shi; Huang, Xiaoting; Bao, Zhenmin
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 04/04/2014 Português
Relevância na Pesquisa
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The reliability of genome analysis and proficiency of genetic manipulation requires knowledge of the correspondence between the genetic and cytogenetic maps. In the present study, we integrated cytogenetic and microsatellite-based linkage maps for Zhikong scallop, Chlamys farreri. Thirty-eight marker-anchored BAC clones standing for the 19 linkage groups were used to be FISH probes. Of 38 BAC clones, 30 were successfully located on single chromosome by FISH and used to integrate the genetic and cytogenetic map. Among the 19 linkage groups, 12 linkage groups were physically anchored by 2 markers, 6 linkage groups were anchored by 1 marker, and one linkage group was not anchored any makers by FISH. In addition, using two-color FISH, six linkage groups were distinguished by different chromosomal location; linkage groups LG6 and LG16 were placed on chromosome 10, LG8 and LG18 on chromosome 14. As a result, 18 of 19 linkage groups were localized to 17 pairs of chromosomes of C. farreri. We first integrated genetic and cytogenetic map for C. farreri. These 30 chromosome specific BAC clones in the cytogenetic map could be used to identify chromosomes of C. farreri. The integrated map will greatly facilitate molecular genetic studies that will be helpful for breeding applications in C. farreri and the upcoming genome projects of this species.

‣ Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex; Liu, Zhanjiang
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
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Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits.

‣ Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

Khajuria, Yash Paul; Saxena, Maneesha S.; Gaur, Rashmi; Chattopadhyay, Debasis; Jain, Mukesh; Parida, Swarup K.; Bhatia, Sabhyata
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 14/05/2015 Português
Relevância na Pesquisa
48.07754%
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented...

‣ Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

Pootakham, Wirulda; Ruang-Areerate, Panthita; Jomchai, Nukoon; Sonthirod, Chutima; Sangsrakru, Duangjai; Yoocha, Thippawan; Theerawattanasuk, Kanikar; Nirapathpongporn, Kanlaya; Romruensukharom, Phayao; Tragoonrung, Somvong; Tangphatsornruang, Sithichoke
Fonte: Frontiers Media S.A. Publicador: Frontiers Media S.A.
Tipo: Artigo de Revista Científica
Publicado em 27/05/2015 Português
Relevância na Pesquisa
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Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23–1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28...

‣ An integrated physical map of human chromosome 16

Doggett, N.; Goodwin, L.; Tesmer, J.; Meincke, L.; Bruce, D.; Clark, L.; Altherr, M.; Ford, A.; Chi, H.C.; Marrone, B.; Longmire, J.; Lane, S.; Whitmore, S.; Lowenstein, N.; Sutherland, G.; Mundt, M.; Knill, E.; Bruno, W.; Macken, C.; Torney, D.; et al.
Fonte: Nature Publishing Publicador: Nature Publishing
Tipo: Artigo de Revista Científica
Publicado em //1995 Português
Relevância na Pesquisa
48.22594%
We describe an integrated physical, genetic and cytogenetic map of human chromosome 16 comprising both a low-resolution megaYAC map and a high-resolution cosmid contig/mlnlYAC map, which provides nearly complete coverage of the euchromatic arms of the chromosome. The physical map is anchored to a high-resolution cytogenetic breakpoint map and is Integrated with genetic and gene transcript maps of the chromosome by sequence-tagged sites and clone hybridizations.

‣ An integrated genetic linkage map for almond based on RAPD, ISSR, SSR and morphological markers

Gregory, D.; Sedgley, M.; Wirthensohn, M.; Arus, P.; Kaiser, B.; Collins, G.
Fonte: International Society for Horticultural Science Publicador: International Society for Horticultural Science
Tipo: Artigo de Revista Científica
Publicado em //2005 Português
Relevância na Pesquisa
48.36472%
An integrated genetic linkage map of almond (Prunus dulcis) based on RAPD, ISSR, SSR and morphological markers was constructed using a pseudo-testcross mapping format and Joinmap 3.0. A total of 93 individuals from a F₁ full-sib family produced from a cross between ‘Nonpareil’ and ‘Lauranne’ was genotyped with 120 molecular markers (60 RAPD, 23 ISSR, 1 SCAR, and 36 SSR) to produce two parental maps. Hybridity of the mapping population was confirmed by DNA fingerprinting and cluster analysis using RAPD and ISSR markers, and SSR inheritance. The two parental maps were aligned using 12 molecular markers (2 RAPD, 4 ISSR, and 5 SSR) that were segregating in both parents (intercross markers). Two distorted markers were observed at the distal region of two linkage groups. A map position was provided for the kernel taste loci, on linkage group B, 49.1 cM from the ISSR marker (AG)₈YC-1786. Six linkage groups were obtained for the integrated map with a marker density of 11.5 cM/marker, covering 161.9 cM (Kosambi), representing a 31% coverage of the T x E Prunus reference map. This map provides an initial step for producing a SSR saturated integrated genetic linkage map of the almond genome, including morphological markers. The use of both peach and cherry SSRs illustrates the use of interspecific derived primers as a source of polymorphism generation in the Prunus genus...

‣ A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Palhares, Alessandra C; Rodrigues-Morais, Taislene B; Sluys, Marie-Anne Van; Domingues, Douglas S; Maccheroni Júnior, Walter; Jordão Júnior, Hamilton; Souza, Anete P; Marconi, Thiago G; Mollinari, Marcelo; Gazaffi, Rodrigo; Garcia, Antonio Augusto F; V
Fonte: BIOMED CENTRAL LTD; LONDON Publicador: BIOMED CENTRAL LTD; LONDON
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
57.858975%
Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs...

‣ A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

Palhares, Alessandra C.; Rodrigues-Morais, Taislene B.; Van Sluys, Marie-Anne; Domingues, Douglas S.; Maccheroni, Walter, Jr.; Jordao, Hamilton, Jr.; Souza, Anete P.; Marconi, Thiago G.; Mollinari, Marcelo; Gazaffi, Rodrigo; Garcia, Antonio Augusto F.; Ca
Fonte: Biomed Central Ltd; London Publicador: Biomed Central Ltd; London
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
57.792583%
Background: The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results: The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs...