SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E..

ABSTRACT: Ruzigrass (Urochloa ruziziensis) is a diploid, tropical forage grass native to Africa, widely planted in Brazil, and known for its high nutritional quality. It is closely related to other important forage species of Urochloa, playing a crucial role in the breeding program of brachiaria grasses, which is mostly focused on inter-specific hybrids. Previous studies from our group based on shallow Illumina sequencing resulted in the development of the first molecular markers for the species, as well as in assessments of germplasm diversity and structure. Assembly and analysis of complete plastid genomes for four Urochloa species allowed the characterization of their phylogenetic divergence. Here, we strengthen the set of genomic tools for tropical...

A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species.

Palavras-chave: Montagem de sequência de DNA; Bioinformática; De novo Assembly; Brachiaria Ruziziensis; Pastagem; Genoma.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1099953

SILVA JUNIOR, O. B. da; FARIA, D. A.; GRATTAPAGLIA, D..

2015

A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree.

Palavras-chave: Myrtaceae; Pooled resequencing; Population structure; Single-nucleotide polymorphism (SNP) ascertainment bias; Trans-spe.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1031208

COLLEVATTI, R. G.; NOVAES, E.; SILVA JUNIOR, O. B. da; VIEIRA, L. D.; LIMA-RIBEIRO, M. S.; GRATTAPAGLIA, D..

bitstream/item/199571/1/s41437-019-0188-0.pdf

A phased diploid genome assembly for the forage grass urochloa ruziziensis based on single-molecule real-time sequencing.

Palavras-chave: Conservation genomics; Genetic variation.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1110632

PESSOA FILHO, M. A. C. de P.; SOUZA SOBRINHO, F. de; FRAGOSO, R. da R.; SILVA JUNIOR, O. B. da; FERREIRA, M. E..

Ruzigrass (Urochloa ruziziensis) is a diploid, tropical forage grass native to Africa, widely planted in Brazil, known for its high nutritional quality. It is closely related to important forage species of Urochloa, and plays a crucial role in the breeding program of brachiaria grasses, mostly focused on inter-specific hybirds. Previous studies from our group based on shallow Illumina sequencing resulted in the development of the first molecular markers for the species (Silva et al., 2013), as well as in assessments of germplasm diversity and structure (Pessoa-Filho et al., 2015). Assembly and analysis of complete plastid genomes for four Urochloa species allowed the characterization of their phylogenetic divergence (Pessoa-Filho et al., 2017). Here, we...

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development.

Palavras-chave: Brasil; Genoma; Capim Urochloa.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1107378

PASSOS, M. A. N.; CRUZ, V. O. de; EMEDIATO, F. L.; TEIXEIRA, C. C. de; AZEVEDO, V. C. R.; BRASILEIRO, A. C. M.; AMORIM, E. P.; FERREIRA, C. F.; MARTINS, N. F.; TOGAWA, R. C.; PAPPAS JÚNIOR, G. J.; SILVA JUNIOR, O. B. da; MILLER, R. T N. G..

Background: Although banana (Musa sp.) is an important edible crop, contributing towards poverty alleviation and food security, limited transcriptome datasets are available for use in accelerated molecular-based breeding in this genus. 454 GS-FLX Titanium technology was employed to determine the sequence of gene transcripts in genotypes of Musa acuminata ssp. burmannicoides Calcutta 4 and M. acuminata subgroup Cavendish cv. Grande Naine, contrasting in resistance to the fungal pathogen Mycosphaerella musicola, causal organism of Sigatoka leaf spot disease. To enrich for transcripts under biotic stress responses, full length-enriched cDNA libraries were prepared from whole plant leaf materials, both uninfected and artificially challenged with pathogen...

Analysis of the transcriptome in Aspergillus tamarii during enzymatic degradation of sugarcane bagasse.

Palavras-chave: Banana; Fungo; Musa Acuminata; Mycosphaerella Musicola; Transcriptome; Microsatellite repeats.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/964212

MIDORIKAWA, G. E. O.; CORREA, C. L.; NORONHA, E. F.; FERREIRA FILHO, E. X.; TOGAWA, R. C.; COSTA, M. M. do C.; SILVA JUNIOR, O. B. da; GRYNBERG, P.; MILLER, R. N. G..

bitstream/item/183671/1/Midorikawa-et-al-2018-Frontiers-in-Bioengineering-and-Biotechnology.pdf

Application of the Axiom 3K SNP genotyping array in cassava breeding and genetics.

Palavras-chave: Carbohydrate-active enzymes; XlnR; Sugar transporters; ClrA; Aspergillus tamarii; Transcriptome; Lignocellulose; Bioethanol.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1096563

PESSOA FILHO, M. A. C. de P.; SILVA, P. I. T.; RESENDE, L. V.; VIEIRA, E. A.; FALEIRO, F. G.; GRATTAPAGLIA, D.; SILVA JUNIOR, O. B. da.

bitstream/item/171614/1/apagar1.pdf

Coupling in-depth genome annotations with genome editing technology for harnessing genomic variation to promote precision breeding in tropical soybean.

Palavras-chave: Polimorfismo de nucleotídeo único; Single nucleotide polymorphism; Mandioca; Melhoramento genético vegetal; Germoplasma.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1086247

SILVA JUNIOR, O. B. da; PESSOA FILHO, M. A. C. de P.; SA, M. E. L.; DEAL, R.; RAGOUSSIS, I.; GRATTAPAGLIA, D.; RECH FILHO, E. L..

ABSTRACT: Directional selection during crop domestication and advanced breeding has resulted in significant changes in plant genomes. The extent of intraspecific variation in a crop documents domestication and highlights variants underlying complex traits. Studies demonstrate that most naturally occurring variants in crops are low frequency, and only a small fraction of those might have important functions to trait variation. To understand the inheritance of quantitative traits, diversity panels have become available by crossing inbred lines to produce genomic maps that relate phenotypic variation to recombination and ultimately to genome structure. Using these resources, genomics studies have suggested that selection performs poorly in pericentromeric...

Desenvolvimento de novos microssatélites em Araucaria angustifolia via redução de complexidade genômica e sequenciamento.

Palavras-chave: Análise genômica; Seqüenciamento de longa duração; Soja; Genoma; Melhoramento Genético Vegetal.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1100401

RESENDE, L. V.; SOUSA, V. A. de; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D..

2014

Desenvolvimento de novos microssatélites em Araucaria angustifolia via redução de complexidade genômica e sequenciamento.

Palavras-chave: Araucaria angustifolia; Espécie nativa; Teste de procedências e progênies; Locos SSR; RAD sequencing.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1002110

RESENDE, L. V.; SOUSA, V. A. de; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D..

2014

Desenvolvimento e validação do chip de genotipagem 26K Axiom® SNP array em Coffea canephora.

Palavras-chave: Araucaria angustifolia; Espécie nativa; Teste de procedências e progênies; Locos SSR; RAD sequencing.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1001258

CARNEIRO, F. de A.; MARRACCINI, P.; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D.; ANDRADE, A. C..

A produção mundial de café é altamente afetada pelas mudanças climáticas, consequentemente, obter plantas adaptadas a este cenário de clima alterado torna-se muito importante. Com os recentes avanços na genômica do cafeeiro, como o sequenciamento do genoma de C. canephora, o objetivo deste trabalho foi desenvolver e validar o chip de genotipagem de DNA para C. canephora (26K Axiom SNP array), visando uma plataforma de genotipagem confiável e de alto rendimento, a ser utilizada nos programas de melhoramento da espécie. A construção do chip foi feita utilizando-se dados gerados a partir do resequenciamento genômico de pools formados por indivíduos dos diferentes grupos de diversidade encontrados na espécie e por indivíduos de C. canephora Conilon,...

Design and evaluation of a sequence capture systemfor genome-wide SNP genotyping in highly heterozygous plant genomes: a case studywith a keystone Neotropical hardwood tree genome.

Palavras-chave: Genotipagem; SNP array; Coffea canephora; DNA; Gene; Melhoramento genético; Genoma.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084718

SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D.; NOVAES, E.; COLLEVATTI, R. G..

bitstream/item/185941/1/dsy023.pdf

Development and validation of a 26K Axiom® SNP array for Coffea canephora.

Palavras-chave: Target enrichment; Sequence capture; SNPs; Handroanthus.

Ano: 2018

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1099287

CARNEIRO, F. de A.; MARRACCINI, P.; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D.; ANDRADE, A. C..

World coffee production is higly affected by climate changes due to the occurrence of severe droughts and high temperatures resulting in low flow er viability, fruit development and yield. Faster breeding methods are required to obtain adapted coffee plants to a changed climate cenario, as conventional breeding in perennial crops such as coffee, requires a long time. With the recent advances in coffee genomics, such as the availability of a C. canephora reference genome , the objective of this work was to develop and validate a 26K Axiom SNP array for C. canephora aiming at a reliable high throughput genotyping platform to be used in the breeding programmes of the species. The chip design was based on a whole - genome resequencing panel comprised by DNA...

Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata.

Palavras-chave: Coffe canephora Conilon; Coffee genomics; Climate change; Genomic selection; Genetic diversity; Coffea canephora; Coffee plant.

Ano: 2017

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1084572

PASSOS, M. A. N.; CRUZ, V. de O.; EMEDIATO, F. L.; TEIXEIRA, C. de C.; SOUZA JUNIOR, M. T.; MATSUMOTO, T.; AZEVEDO, V. C. R.; FERREIRA, C. F.; AMORIM, E. P.; FIGUEIREDO, L. F. de A.; MARTINS, N. F.; CAVALCANTE, M. de J. B.; BAURENS, F. C.; SILVA JUNIOR, O. B. da; PAPPAS JUNIOR, G. J.; PIGNOLET, L.; ABADIE, C.; CIAMPI, A. Y.; PIFFANELLI, P.; MILLER, R. N. G..

Banana (Musa acuminata) is a crop contributing to global food security. Many varieties lack resistance to biotic stresses, due to sterility and narrow genetic background. The objective of this study was to develop an expressed sequence tag (EST) database of transcripts expressed during compatible and incompatible banana-Mycosphaerella fijiensis (Mf) interactions. Black leaf streak disease (BLSD), caused by Mf, is a destructive disease of banana. Microsatellite markers were developed as a resource for crop improvement.

Estrutura e diversidade genética de uma população de Coffea canephora conilon utilizando marcadores SNPs identificados por nextRAD.

Palavras-chave: Plátano; Marcador microssatélite; Melhoramento genético vegetal; Banana; Musa acuminata; Marcador genético; Variedade resistente; Doença de planta; Melhoramento vegetal; Fungo; Sigatoka negra; Mycosphaerella fijiensis; Plant breedind; Bananas; Genetic markers; Microsatellite repeats; Plant diseases and disorders; Firomejoramiento; Fungi; Black sigatoka; Bananos; Marcadores genéticos; Repeticiones de microsatélite; Enfermedades y desórdenes de las plantas.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/953929

Gene expression revealed during the interaction of resistant Arachis stenosperma and Meloidogyne arenaria.

CARNEIRO, F. de A.; RÊGO, É. C. S.; AQUINO, S. O. de; COSTA, T. S.; LIMA, E. A. de; ROCHA, O. C.; RODRIGUES, G. C.; CARVALHO, M. A. de F.; MARRACCINI, P.; BARTHOLO, G. F.; GUERRA, A. F.; SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D.; ANDRADE, A. C..

Este trabalho objetivou (i) avaliar e caracterizar, por meio da técnica de genotipagem nextRAD (Nextera-tagmented reductively-amplified DNA), a diversidade e a estrutura genética de indivíduos de C. canephora Conilon, pertencentes a uma população localizada em campo experimental da Embrapa Cerrados.

Tipo: Artigo em anais de congresso (ALICE)

Palavras-chave: Diversidade genética; Genotipagem nextRAD; Genetic diversity; Coffea canephora; Single nucleotide polymorphism; Genotyping; Genetic variation.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1029881

GUIMARAES, P. M.; MORGANTE, C. V.; ROBERTS, P. A.; SILVA JUNIOR, O. B. da; ARRAIS, L; BERTIOLI, S. C. de M. L.; ARAUJO, A. C. G. de; MORETZSOHN, M. de C.; BERTIOLI, D.; BRASILEIRO, A. C. M..

The plant-parasitic root-knot nematodes have evolved sophisticated strategies for exploiting plants with high impacts in agriculture worldwide. The wild species Arachis stenosperma shows high levels of resistance to M. arenaria and other parasites. A genome-wide overview of differential gene expression during this plant?nematode interaction at different time points (3, 6 and 9 DAI)and healthy roots was conducted using Illumina Hi-Seq 2000. Eight cDNA libraries produced a total of 38´241´633 reads with an average sequence size of 200 bp and were assembled into 44,133 contigs. These unique sequences were grouped into eight clusters corresponding to their expression profile estimated by RPKM values. We found that a comparable number of genes were up- and...

Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis.

Palavras-chave: Nematoide; Melhoramento genético vegetal; Arachis stenosperma; Meloidogyne arenaria.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/handle/doc/952169

SILVA JUNIOR, O. B. da; GRATTAPAGLIA, D..

2015

Genomic prediction of growth traits in Pinus taeda using genome-wide sequence-based DArT-seq markers.

Palavras-chave: Ancestral recombination graphs; Effective population size; Linkage disequilibrium (LD); Mutation rate; Nucleotide diversity; Population recombination rate; Whole-genome pooled resequencing; Eucalyptus.

Ano: 2015

URL: http://www.alice.cnptia.embrapa.br/handle/doc/1031226