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QTL detected for the trait number of adventitious roots. Phenotypic variance explained by each QTL interval identified for number of root traits. Respective linkage group (LG), flanking markers location, LOD peak and origin of positive allele. (DOCX 16Â kb)

Differentially regulated genes between time points. Number of genes differentially expressed when contrasting consecutive time points. (DOCX 44Â kb)

Cumulative number of roots formed in the parents of pedigree 52–124. Least-square means of number of adventitious roots developed on the female hybrid parent Populus trichocarpa × P. deltoides 52–225 (red line), and the unrelated male parent P. deltoides D124 (blue line), maintained in hydroponic solution for 25 days. (DOCX 67 kb)

Frequency distribution of root architectural and biomass traits. Frequency distribution of least-square means of root architectural and biomass traits measured on 225 individuals of pedigree 52–124. Parents ‘P. deltoides’ (D) and (P. trichocarpa × P.deltoides) × P.deltoides (TD) are indicated. Measurements were made after 18 days of growth in hydroponic solution. Traits are total root length (cm, panel A), total root surface area (cm2, panel B), total root volume (cm3, panel C), average diameter (mm, panel D), length of root branches (cm, panel E), surface area of root branches (cm2, panel F), volume of root branches (cm3, panel G), total length of primary roots (cm, panel H), surface area of primary roots (cm2, panel I), volume of primary roots (cm3, panel J), number of adventitious roots at 18 days (panel K) and root biomass (mg, panel L). (DOCX 326 kb)

Clustering the difference in transcriptome response of PtQTL and PdQTL genotypes. Modulated Modularity Clustering of genes displaying a similar pattern of expression differences between genotypes from the PtQTL and PdQTL categories, at all time points. (DOCX 25Â kb)

QTL detected for root architecture traits and root biomass. Phenotypic variance explained by each QTL interval detected for root architecture traits and root biomass. Respective linkage group (LG), flanking marker location, LOD score and origin of positive allele. (DOCX 17Â kb)

Plants from temperate regions adapt to changing environmental conditions along the year. Trees have evolved mechanisms that allow them to monitor and anticipate the seasons, and cycle between growth and winter dormancy states. Dormancy is initiated by shortening of photoperiod, and afterwards, as a result of a drop in temperature, trees reach a state of endodormancy, the inability of resume growth in response to inductive conditions. Chilling requirement needs to be fulfilled in order to release from endodormancy and gain the ability to resume growth in response to good conditions. The signalling networks that regulate dormancy in perennials are poorly understood. We had previously shown that CsRAV1, a chestnut homolog of Arabidopsis TEM1 and TEM2, induced sylleptic branching in poplar [1]. In this work we characterize the role of chestnut and poplar RAV genes in dormancy. The expression profile of CsRAV1, PtaRAV1 and PtaRAV2 along the year showed that all three genes were induced during winter and maintained high expression levels until early spring. These data suggested that CsRAV1, PatRAV1 and PtaRAV2 were involved in the regulation of winter dormancy in trees. To test this hypothesis we have used over-expressing CsRAV1, and knock-down PtaRAV1 and PtaRAV2 transgenic poplars. The phenology of the transgenic lines will be discussed. It has been reported that Arabidopsis TEM1 binds to the FT promoter. An in silico screening of TEM1 DNA recognition sites in the promoter region of the Populus trichocarpa homologous FT genes revealed that the RAV1 motif was not conserved. Moreover, the over-expression of CsRAV1 in Arabidopsis did not phenocopy the over-expression of AtTEM1 and AtTEM2, suggesting a functional divergence of RAV family members. To gain insight on the molecular function of tree RAV genes, we performed a transcriptomic analysis with RNA from the poplar transgenic lines, and protein-binding microarrays to identify the cis-acting elements for CsRAV1, PtaRAV1 and PtaRAV2. The identification of the binding elements and their occurrence in the genes differentially expressed will be presented. In conclusion, our study reveals a possible function of RAV transcriptional regulators in the control of winter dormancy in trees.

Made available in DSpace on 2016-10-10T03:52:19Z (GMT). No. of bitstreams: 5 High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome.pdf: 378008 bytes, checksum: b646acffa2bda86a31599cd4bac0aace (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24259 bytes, checksum: f1f24f769b03eb8f9cd3f53c1090841c (MD5) license_rdf: 24658 bytes, checksum: 9d3847733d3c0b59c7c89a1d40d3d240 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2008 With the purpose of generating the first broad survey of gene sequences in Eucalyptus grandis, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of Arabidopsis genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta () parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multigenotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches. Sim Publicado

Made available in DSpace on 2016-10-10T03:52:28Z (GMT). No. of bitstreams: 5 Power of Microsatellite Markers for.PDF: 169600 bytes, checksum: 0cebf6d524273623470610eb1df3661c (MD5) license_url: 52 bytes, checksum: 3d480ae6c91e310daba2020f8787d6f9 (MD5) license_text: 23851 bytes, checksum: 294cb7010cc40c47642971e073de3dba (MD5) license_rdf: 23892 bytes, checksum: afd5dad10b1d1e6dc10c8c5d25222c7a (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2005 We report the genetic analysis of 192 unrelated individuals of an elite breeding population of Eucalyptus grandis (Hill ex Maiden) with a selected set of six highly polymorphic microsatellite markers developed for species of the genus Eucalyptus. A full characterization of this set of six loci was carried out generating allele frequency distributions that were used to estimate parameters of genetic information content of these loci, including expected heterozygosity, polymorphism information content (PIC), power of exclusion, and probability of identity. The number of detected alleles per locus ranged from 6 to 33, with an average of 19.86 9.2. The average expected heterozygosity was 0.86 6 0.11 and the average PIC was 0.83 6 0.16. Using only three loci, it was possible to discriminate all 192 individuals. The overall probability of identity considering all six EMBRA microsatellite markers combined was lower than 1 in 2 billion. An analysis of the sample size necessary to estimate expected heterozygosity with minimum variance indicated that at least 64 individuals have to be genotyped to characterize this parameter with adequate accuracy for most microsatellites in Eucalyptus. The high degree of multiallelism and the clear and simple codominant Mendelian inheritance of the set of microsatellites used provide an extremely powerful system for the unique identification of Eucalyptus individuals for fingerprinting purposes and parentage testing. Sim Publicado

Made available in DSpace on 2016-10-10T03:52:48Z (GMT). No. of bitstreams: 5 Microsatellite markers for Ceiba pentandra_ Bombacaceae an endangered tree species of the Amazon forest.pdf: 72426 bytes, checksum: 1b04b4cf80b601f9a80d3227cc9a8773 (MD5) license_url: 52 bytes, checksum: 2f32edb9c19a57e928372a33fd08dba5 (MD5) license_text: 24372 bytes, checksum: 94b0a37ff5ec51de8c55507bff4a7ff9 (MD5) license_rdf: 24623 bytes, checksum: 378d22d8fe50e084ee2f354be78cbe62 (MD5) license.txt: 1887 bytes, checksum: 445d1980f282ec865917de35a4c622f6 (MD5) Previous issue date: 2003 From a genomic library enriched for AG/TC repeats, eight polymorphic microsatellite markers were developed for Ceiba pentandra, a pan-tropical forest tree. Polymorphism was evaluated using a panel of 74 adult trees. Using automated fluorescence detection, a total of 112 alleles was detected with an average of 14 alleles per locus. All microsatellite loci showed very high levels of genetic information content, with expected heterozygosity ranging from 0.814 to 0.895. These microsatellite markers represent a powerful tool to investigate refined questions of mating systems, gene flow, family structure and population dynamics in natural populations of C. pentandra. Sim Publicado

Conselho Nacional de Desenvolvimento Cientifico e Tecnologico Foram desenvolvidos três sistemas de genotipagem multilocos (sistemas Multiplex) semi-automatizados, baseados na amplificação e análise simultânea de locos microssatélites via florescência, para análise genética de espécies do gênero Eucalyptus. Tabelas de frequências alélicas e estimativas do conteúdo de informação genética foram geradas para seis espécies comercialmente importantes do gênero Eucalyptus (subgênero Symphyomyrtus). Inicialmente, microssatélites desenvolvidos a partir de genótipos de E. grandis e E. urophylla foram avaliados quanto à especificidade de amplificação. Dentre os locos que apresentaram boa qualidade de amplificação, 11 foram selecionados para o desenvolvimento de sistemas Multiplex. Três sistemas Multiplex, comportando cada um a análise simultânea de três locos, foram selecionados. Foi estudado o tamanho mínimo de amostra necessário para se obterem estimativas acuradas da heterozigosidade de cada loco. Para isso, foram genotipados 192 indivíduos de E. grandis provenientes de uma população de melhoramento. Com essa informação, avaliou-se o comportamento de estimadores para heterozigosidade esperada com vários tamanhos de amostra, analisando-se a sua variância por meio da sua fórmula exata e por reamostragem numérica. Concluiu-se que uma amostra de 64 indivíduos dessa população seria satisfatória para estimar a heterozigosidade esperada com boa precisão. Os três sistemas Multiplex foram utilizados para genotipar indivíduos provenientes de cinco procedências de E. grandis. Com os dados genotípicos, foram construídas tabelas de frequências alélicas para cada loco e procedência, além de serem registrados 0 número de alelos/loco e a amplitude alélica e estimados os parâmetros heterozigosidade esperada, conteúdo de informação de polimorfismo, probabilidade de identidade e poder de exclusão, os quais indicaram que os locos utilizados possuía alto conteúdo de informação genética. Foram ainda estimadas as distâncias genéticas de Nei entre as procedências; uma AMOVA realizada entre as procedências indicou variação significativa entre elas, embora a maior porção da variabilidade fosse encontrada dentro de procedências. Em seguida, os sistemas Multiplex foram otimizados e caracterizados para outras cinco espécies do gênero Eucalyptus: E. camaldulensis, E. dunnii, E. globulus, E. saligna e E. urophylla. As estimativas dos parâmetros de informação genética da maioria dos locos indicaram que eles são apropriados para genotipagem de indivíduos dessas espécies. Finalmente, os sistemas Multiplex foram utilizados na avaliação de uma população de melhoramento de E. urophylla e de uma coleção de clones-elite, em que foi possível a detecção de erros de identificação do material genético, além de uma avaliação da diversidade genética e da similaridade entre clones. Three semi-automated multilocus genotyping systems, based on microsatellites, were developed for the analysis of Eucalyptus species. Allele frequency tables and estimates of the genetic information content of these loci were generated for six economically important species of Eucalyptus (subgenus Symphyomyrtus). A set of microsatellites, developed from E. grandis and E. urophylla genotypes. was evaluated based on their PCR amplilication quality and transferability across species. Eleven microsatellites and tifteen combinations of three Ioci were tested. Among these, three triplex systems were chosen. The minimum number of individuals necessary to obtain accurate estimates of He was evaluated. A population of 192 individuals of E. Grandis was typed with six microsatellites and the behavior of the estimate of He with increased sample sizes was analyzed using the gene diversity variance formula and numeric resampling. Congruent results using both approaches showed that a sample size of 64 individuals would be appropriate to estimate He with good accuracy. The multiplex systems were used to type individuals from live Eucalyptus provenances. Allele frequency tables were generated for every locus, and estimates of parameters of genetic information content were obtained (He, PIC, I and Q). AII loci showed to be highly informative with average values of He (0,85), PIC (0,84), combined Q (99,99%) and combined I (10-14). Nei's genetic distances estimated among provenances. An AMOVA showed that there is significant genetic variation among provenances. Although the majority of the variation was found within provenances. The multiplex systems were then optimized and evaluated for other tive species of Eucalyptus: E. camaldulensis, E. dunnii, E. globulus, E. saligna and E. urophylla. The estimates of genetic information content parameters showed once more that these Ioci are highly appropriate for genotyping Eucalyptus species. As a final step to evaluate the usefulness of these genotyping systems, a breeding population of E. urophylla and a collection of elite clones were analyzed. Several clonal identification errors were detected within this population. Based on the multilocus genotypes, an evaluation of the genetic variability and similarity among clones was also performed.