Papers by Luiz Filipe Pereira
X Simpósio de Pesquisa dos Cafés do Brasil, Sep 20, 2019
Crop Breeding and Applied Biotechnology, Mar 31, 2001
A system for in vitro plant regeneration from thin transversal epicotyl sections of sweet orange ... more A system for in vitro plant regeneration from thin transversal epicotyl sections of sweet orange (Citrus sinenis L Osbeck cvs Pera, Valencia and Folha Murcha) was developed. Thin section explants (1-2 mm) from seedlings produced adventitious shoot buds on MS medium supplemented with BA (0.5-5 µM). Optimal shoot induction was achieved on 2-5 µM BA. Explants with buds were transferred to elongation media in order to improve the recovery of normal shoots. Higher number of elongated shoots was obtained on medium with 0.5 µM BA. Elongated shoots were rooted on half strength MS medium without growth regulators and transferred to soil for acclimatization. The advantages of this system for transformation are discussed.
Scientia Horticulturae, Feb 1, 2004
Increasing salinity in Mediterranean soils and the wide spread of citrus tristeza virus have chal... more Increasing salinity in Mediterranean soils and the wide spread of citrus tristeza virus have challenged the use of sour orange (Citrus aurantium) and have accelerated the process of seeking alternative rootstocks. In the present study, nine cultivars of citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) were evaluated for salt tolerance. Two month-old seedlings were raised under greenhouse conditions and irrigated with a half strength Hoagland solution supplemented with different concentrations of NaCl, i.e., 0 mM, 35 mM and 85 mM. Tolerance was assessed after two months of stress by measuring stem growth, number of leaves, fresh and dry weight organs and leaf water, chlorophyll and chloride contents. A differential behavior was noticed among the seedlings we studied. When using increased concentration of salt in irrigation water, all the parameters were significantly reduced except for leaf chloride content which highly increased in response to stress. At 85 mM, the cultivar SC2 showed a high tolerance resulting in less apparent leaf symptoms, higher growth and higher leaf chlorophyll content when compared to other seedlings. Similarly, the cultivar C4475-C was shown to be a strong root chloride excluder with less than 2.6% DW (dry weight) chloride accumulation at leaf level. By contrast, our results suggest that C4475-A and C4475-B are salt sensitive cultivars regarding to all the parameters studied while the other citrumelos were considered as moderately tolerant.
Plant Gene, Jun 1, 2021
Abstract Coffee synthesizes two unique isoprenoid diterpenes, cafestol (C20H28O3) and kahweol (C2... more Abstract Coffee synthesizes two unique isoprenoid diterpenes, cafestol (C20H28O3) and kahweol (C20H26O3), ent-kaurene compounds produced through the mevalonate or mevalonate-independent pathway. These compounds are relevant to beverage quality, plant defense, human health and nutraceutical properties. We investigate the expression profile of genes in the early (CaHMGR, CaMVD, CaDXR and CaIDS) and final steps of isoprenoid diterpenes biosynthesis (Coffea arabica L. cytochrome P450s: CaCYP82C2, CaCYP71A25, CaCYP74A1 and CaCYP701A3) in two fruits development stages (90 and 210 days after flowering). We also observed total lipid, cafestol and kahweol accumulation in C. arabica grown using two crop systems (full sun and agroforestry) at Parana State Agriculture Institute, Londrina, PR, Brazil. Plants in full sun presented higher gene expression than plants grown in agroforestry systems, except for CaHMGR. Fruits showed higher levels of transcript activity 210 days after flowering, about 2.8 times more in the genes expressed during the first steps and 3.6 times in those in the later steps. Although lipid, cafestol and kahweol were higher in the full sun than the agroforestry system, only increased lipid content was statistically significant. Cultivation system plays an important role in the expression of the genes, particularly as regards light incidence.
Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a so... more Jerusalem artichoke (Helianthus tuberosus L.) has long been cultivated as a vegetable and as a source of fructans (inulin) for pharmaceutical applications in diabetes and obesity prevention. However, transcriptomic and genomic data for Jerusalem artichoke remain scarce. In this study, Illumina RNA sequencing (RNA-Seq) was performed on samples from Jerusalem artichoke leaves, roots, stems and two different tuber tissues (early and late tuber development). Data were used for de novo assembly and characterization of the transcriptome. In total 206,215,632 paired-end reads were generated. These were assembled into 66,322 loci with 272,548 transcripts. Loci were annotated by querying against the NCBI non-redundant, Phytozome and UniProt databases, and 40,215 loci were homologous to existing database sequences. Gene Ontology terms were assigned to 19,848 loci, 15,434 loci were matched to 25 Clusters of Eukaryotic Orthologous Groups classifications, and 11,844 loci were classified into 142 Kyoto Encyclopedia of Genes and Genomes pathways. The assembled loci also contained 10,778 potential simple sequence repeats. The newly assembled transcriptome was used to identify loci with tissue-specific differential expression patterns. In total, 670 loci exhibited tissue-specific expression, and a subset of these were confirmed using RT-PCR and qRT-PCR. Gene expression related to inulin biosynthesis in tuber tissue was also investigated. Exsiting genetic and genomic data for H. tuberosus are scarce. The sequence resources developed in this study will enable the analysis of thousands of transcripts and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke.
A demanda crescente por cafes especiais e os melhores precos alcancados por eles tem estimulado c... more A demanda crescente por cafes especiais e os melhores precos alcancados por eles tem estimulado cada vez mais a participacao de produtores neste segmento. Alem da origem, da sustentabilidade na producao e da avaliacao dos cafes diferenciados quanto aos aspectos fisicos e sensoriais, a rastreabilidade da producao e uma das principais exigencias para a certificacao do produto. Dentro deste processo, a crescente demanda pelo atestado da pureza varietal vem exigindo o desenvolvimento de ferramentas que possam garantir a diferenciacao inequivoca do produto comercial, e que viabilizem sua protecao intelectual. Assim, nosso objetivo foi desenvolver marcadores SNP, identificados em analises de genotipagem pelo sequenciamento (GBS), voltados a discriminacao de cultivares de cafe arabica. Quarenta e oito cultivares foram genotipadas pelo sequenciamento em plataforma Illumina e 192.730 TAGs foram alinhadas ao genoma de Coffea arabica, gentilmente cedido pelo Consorcio Internacional de Sequenci...
Genome, 2021
Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around... more Coffea spp. chromosomes are very small and accumulate a variety of repetitive DNA families around the centromeres. However, the proximal regions of Coffea chromosomes remain poorly understood, especially regarding the nature and organisation of the sequences. Taking advantage of the genome sequences of C. arabica (2n = 44), C. canephora, and C. eugenioides (C. arabica progenitors with 2n = 22) and good coverage genome sequencing of dozens of other wild Coffea spp., repetitive DNA sequences were identified, and the genomes were compared to decipher particularities of pericentromeric structures. The searches revealed a short tandem repeat (82 bp length) typical of Gypsy/TAT LTR retrotransposons, named Coffea_sat11. This repeat organises clusters with fragments of other transposable elements, comprising regions of non-coding RNA production. Cytogenomic analyses showed that Coffea_sat11 extends from the pericentromeres towards the middle of the chromosomal arms. This arrangement was obs...
Physiologia Plantarum, 2007
Proline accumulates in a variety of plant species in response to stresses such as drought, salini... more Proline accumulates in a variety of plant species in response to stresses such as drought, salinity and extreme temperatures. Although its role in plant osmotolerance remains controversial, proline is thought to contribute to osmotic adjustment, detoxification of reactive oxygen species and protection of membrane integrity. In the present study, we evaluated the effects of stress‐inducible proline production on osmotic adjustment, chlorophyll fluorescence and oxidative stress protection in transgenic sugarcane transformed with a heterologous P5CS gene. In well‐watered conditions, free proline, malondialdehyde (MDA) levels, Fv/Fm ratios and chlorophyll contents (Chls) in transgenic sugarcane were not statistically different from non‐transformed control plants. After 9 days without irrigation, proline content in transgenic events was on the average 2.5‐fold higher than in controls. However, no osmotic adjustment was observed in plants overproducing proline during the water‐deficit per...
Genome, 2012
The genus Coffea possesses about 100 species, and the most economically important are Coffea cane... more The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP–PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa0...
Frontiers in Plant Science, Mar 30, 2022
Although Brazil is currently the largest soybean producer in the world, only a small number of st... more Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop's region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean's regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.
Genetic Resources and Crop Evolution
RATIONALE. The use of the genetic diversity of Coffea arabica is a source of high genetic gains f... more RATIONALE. The use of the genetic diversity of Coffea arabica is a source of high genetic gains for adaptation and coffee quality. First, we evaluated Ethiopian wild accessions and coffee varieties for their diversity and adaptation to various conditions, namely Cerrados and Northern Parana in Brazil, French Guiana, and Cameroon, with special attention to drought and high temperatures. We analyzed biochemical contents related to cup quality. We crossed a selection of progenitors with local cultivars. The oldest hybrid progenies are now two years old. METHODS. To evaluate wild Ethiopian accessions and varieties we first used data obtained from collections established in various sites. From 2013 onwards, we crossed chosen plants with various dwarf cultivars. We established factorial hybrid trials at CPAC (Brazil, Cerrados), IAPAR (Parana), IRAD (Cameroon), and Cirad (French Guyana). Depending on the site, we use randomized design by tree, or by rows of 5 to 10 trees, with or without b...
As mudancas climaticas globais tem causados danos a produtividade agricola cafeeira com impactos ... more As mudancas climaticas globais tem causados danos a produtividade agricola cafeeira com impactos economicos e sociais, e apresentam o potencial de reduzir areas disponiveis para o plantio de cafeeiros. Diante deste cenario foi investigado o potencial do promotor da galactinol sintase ( GolS ) do genero Coffea , que catalisa a primeira etapa da via de sintese de oligossacarideos da familia da Rafinose, cujo acumulo ocorre principalmente em resposta a estresses abioticos. Entender a estrutura e composicao de sequencias genicas promotoras de cafeeiros e de fundamental importância para compreender melhor os mecanismos geneticos e os processos de regulacao da expressao genica induzidos em periodos de estresse hidrico e salino. Neste estudo identificamos 14 promotores GolS presentes nos genomas de Coffea arabica , C. canephora e C. eugenioides . Dentro das regioes promotoras desses genes, foram observados 12 cis -elementos relacionados a regulacao de genes em resposta a condicoes adversas...
Marcadores microssatelites foram utilizados na discriminacao de novos acessos de Coffea arabica q... more Marcadores microssatelites foram utilizados na discriminacao de novos acessos de Coffea arabica que foram introduzidos na colecao da Etiopia do IAPAR, provenientes de uma colecao similar na Republica de Camaroes. Inicialmente 46 acessos de Camaroes foram repassados para a Embrapa CPAC (Embrapa Cerrados – Planaltina-DF), onde ficaram em quarentena. Em seguida, estes acessos foram transferidos para o IAPAR, porem durante os processos de quarentena e transferencia, alguns dos acessos foram misturados. Visando identificar corretamente os acessos e tambem validar os SSRs previamente identificados, todos os 46 acessos foram analisados em geis de poliacrilamida. Os 8 locos microssatelites utilizados geraram um total de 19 alelos, com uma media de 2,3 alelos por loco. A variacao alelica foi de 2 a 3 alelos por loco. Para realizar as analises de divergencia genetica uma matriz de distância foi computada e utilizada para obter uma arvore (dendograma) de diversidade global. Observou-se 3 difer...
The genetic diversity of C. arabica in Ethiopia, its region of origin, was explored. Its use for ... more The genetic diversity of C. arabica in Ethiopia, its region of origin, was explored. Its use for C. arabica breeding, though limited to a few F1 crosses with cultivars, proved to be efficient in terms of genetic gain regarding important coffee agronomic characteristics such as vigor, adaptability and quality. A collection derived from the 1964-65 FAO survey in Ethiopia was established at IAPAR in Londrina, PR, Brazil in 1976. Genotyping was undertaken using SSR markers that were polymorphic within these accessions. Preliminary results regarding the relation between genetic and phenotypic diversity are presented. Self pollinated progenies of 179 plants representing 115 Ethiopian accessions were established at IAPAR, from 2009 to 2012. 47 of them were also established at CPAC, DF. Various growth parameters were measured. (Resume d'auteur)
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Papers by Luiz Filipe Pereira