Submitted by DIEGO GABRIEL TORRES DINI null (diego.torres.dini@gmail.com) on 2017-02-25T21:08:29Z No. of bitstreams: 1 Diego Torres Dini Tese Doutoral.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2017-03-07T13:42:52Z (GMT) No. of bitstreams: 1 torresdini_dg_dr_ilha.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) / Made available in DSpace on 2017-03-07T13:42:52Z (GMT). No. of bitstreams: 1 torresdini_dg_dr_ilha.pdf: 1232376 bytes, checksum: dc45dfe7c23a8fd647db24acb963c71c (MD5) Previous issue date: 2017-02-03 / Outra / In Uruguay, reforestation with Eucalyptus sp. is of fundamental importance to produce paper, pulp and wood. The productivity of these continually grows due to application of breeding techniques, such as hybridization. This study aimed to investigate genetic parameters, productivity, stability, adaptability and to identify SNP markers associated with the diameter breast height (DBH) for to select Eucalypts grandis x Eucalyptus globulus full-sibs hybrid clones. The study was conducted in a clonal test, repeated at two different soils, in the state of Rio Negro, Uruguay. The population was phenotypically characterized to the DBH at 48 months of age and cambium tissues of each individual were sampled for genotyping with EuCHIP60K chip. The mean growth in DBH was similar between both places. The genotype-environment interaction was the simple type, with high genotype correlation in clones’ performance between environments (0.708), indicating the possibility of the same clones being selected for both places. Mean heritability between clones (0.724), coefficient of individual genetic variation (10.9%) and relative variation (0.916), showed the possibility of obtaining gains by selecting clones with higher growth, which was estimated in 3.1% for both sites together. A total of 15,196 markers SNPs were used in the genomic selection for the DBH, but after cleaning of SNPs data, the number was reduced for 15,196 (23.5%). The predictive capacity was expected to be low or negative (-0.15) for this population given the population size (78 individuals). We used the model rrBLUP with a validation of Jackknife. The model do not showed precision to predict the DBH. These results were consistent with theoretical expectations, which indicate that it is necessary to have an improvement population of at least 1,000 phenotyped and genotyped individuals. The DBH is the most important trait in the breeding of the genus Eucalyptus. However its quantitative nature added to the time necessary for this phenotype to develop makes the early detection of this trait are difficult. The identification of molecular markers associated with quantitative phenotypes is a good choice for the identification of QTLs that will help the early detection of individuals with high DBH. Significant markers associated to DBH , were indentificated into the chromosome 6, suggesting the presence of a QTL in this chromosome. Since they are clones originated from vegetative propagation and a full-sibs single-progeny, they should preferably be used for reforestation based on their cloning, since mating between clones can generate endogamy by biparental inbreeding. The utilization of SNPs helped to confirm the degree of parentage between the clones as well as clonal identity control.

Os conceitos e métodos provindos das teorias de integração morfológica e de genética quantitativa formam o arcabouço teórico para o estudo da evolução de estruturas complexas, compostas de múltiplos caracteres que interagem entre si. Nesse trabalho, utilizamos o crânio como modelo de estrutura complexa e estudamos sua diversificação nas espécies de sapo do grupo Rhinella granulosa. As perguntas do trabalho foram: (1) A organização da (co)variação é similar entre as espécies?; (2) A organização da (co)variação é modular nas espécies, conforme expectativas baseadas em desenvolvimento ou função?; (3) Fatores externos, como filogenia e clima, estruturam a similaridade no padrão de covariação entre as espécies?; (4) A diversificação da morfologia média do crânio se deu por deriva ou seleção natural?; (5) A divergência na morfologia média do crânio está associada à variação climática entre as espécies?; e finalmente (6) Restrições evolutivas atuaram na divergência entre as espécies? Os espécimes foram escaneados e validamos o uso de imagens 3D para a mensuração de 21 distâncias lineares. Os crânios das espécies foram representados como matrizes fenotípicas (P) de covariância e de correlação entre as distâncias. A similaridade entre as P das espécies é alta. As P de todas as espécies se conformam a um padrão modular compatível com interações funcionais entre ossos. As diferenças entre as P concentram-se no rostro e são associadas a diferenças no clima entre as espécies. Detectamos sinal de seleção natural nos nós mais basais da filogenia e variação local no crânio está associada à variação na sazonalidade da chuva entre as espécies. Restrições evolutivas atuaram na diversificação do crânio das espécies, defletindo as respostas evolutivas para tamanho. Concluímos que tanto seleção estabilizadora e direcional, conectadas à variação climática, quanto restrições evolutivas atuaram na diversificação do crânio das espécies / Concepts and methods within the theories of morphological integration and quantitative genetics characterize the foundation to study the evolution of complex structures, composed of several traits that interact with each other. In this work, we used the skull as a model of complex structure and we studied its diversification in toad species belonging to the Rhinella granulosa group. The questions addressed were: (1) Is the (co)variance structure similar across species?; (2) Is the (co)variance structure modular in the species, and compatible with developmental or functional interactions among traits?; (3) Do external factors, such as phylogeny and climate, structure the similarity in covariance pattern across species?; (4) Was the diversification of skull mean morphology driven by drift or natural selection?; (5) Is skull divergence associated to climatic variation across species?; and finally, (6) Is there a role for evolutionary constraints in species skull divergence? We scanned all specimens and we validated the use of 3D images to measure 21 linear distances. The skull was represented as covariance and correlation phenotypic matrices (P) among distances. P similarity is very high among species. All species\' P had a modular pattern compatible with functional interactions among bones. Differences in P were concentrated in the snout and associated to differences in climate across species. We detected a selection signal in the three most basal nodes of the phylogeny and local variation in the skull is explained by between-species variation in precipitation seasonality. Evolutionary constraints played a major role in species skull diversification, biasing evolutionary responses towards the direction of size. We conclude that stabilizing and directional selection, connected to climatic variation, as well as evolutionary constraints, acted in species skull diversification

O objetivo deste estudo foi compreender como seleção natural age sobre a variação fenotípica a fim de determinar como espécies respondem às mudanças ambientais. Para isso, usei esquilos do gênero Tamias (subgênero Neotamias, família Sciuridae) como um modelo em uma escala tanto macro quanto micro-evolutiva. Esse conjunto de 23 espécies de Neotamias é parte de uma radiação recente, ocupando uma ampla gama de hábitats com marcada partição de nicho entre as espécies. Um aspecto essencial que molda evolução fenotípica são características ambientais, tais como variações climáticas. Dessa forma, no primeiro capítulo eu examinei se as diferenças fenotípicas entre as espécies estão relacionadas às diferenças climáticas entre os hábitats que ocupam. Diversas características ambientais foram significativamente correlacionadas com atributos morfológicos, indicando que estas tiveram um papel importante como possíveis pressões seletivas conduzindo à divergência entre as espécies. Como consequência, é razoável supor que mudanças climáticas em tempo histórico (isto é, durante o Antropoceno) também afetam variação morfológica dentro de uma escala microevolutiva. No segundo capítulo, portanto, eu examinei esta expectativa usando espécimes de seis diferentes espécies, coletados com cerca de 100 gerações entre coletas (um século). Neste capítulo, não foi encontrada uma associação ente o grau de mudanças climáticas ao longo deste período e a magnitude de mudança morfológica ou de pressão seletiva. Contudo, as estimativas de força de seleção variaram substancialmente entre espécies: para a espécie Tamias alpinus observou-se uma alta estimativa de força de seleção, quase duas vezes maior do que para a espécie Tamias speciosus, a qual as menores forças de seleção foram observadas. Desta forma, a fim de avaliar o impacto de seleção direcional nos padrões de (co)variação fenotípica, no terceiro capítulo eu utilizei estas duas espécies, dado que representam extremos em termos de força de seleção dentre as populações analisadas. Estudos teóricos preveem que sob seleção direcional os padrões de (co)variação podem evoluir, realinhando-se com a paisagem adaptativa subjacente, aumentando a quantidade de variância genética na direção da seleção. Este padrão foi observado para T. alpinus, como esperado, dado que esta espécie sofreu a maior força de seleção. Além disso, para esta espécie foram observadas mudanças nos padrões de correlações entre os caracteres. Estes resultados apoiam expectativas obtidas a partir de modelos teóricos que consideram a evolução do mapa genótipo- fenótipo em resposta à seleção natural / The aim of this study was to understand how natural selection acts on phenotypic variation to determine species\' response to environmental change. I used chipmunks of the genus Tamias (subgenus Neotamias; family Sciuridae) as a model at both a macro and micro-evolutionary scales. This set of 23 species is part of a recent radiation that occupy a wide range of habitats with marked niche partitioning among co-distributed members. As climate variation is an essential aspect believed to shape phenotypic evolution, in the first chapter I examined how phenotypic differences among these species were related to climatic differences among the habitats occupied. Several climatic variables were significantly correlated with morphological attributes differentiating taxa, suggesting a possible causal link between climate, through selection, and species divergence. As a consequence, it is reasonable to suggest that climate change within historic times (the Anthropocene) has also affected cranial morphological variation within species at a microevolutionary scale. In the second chapter, therefore, I examined this expectation using specimens from six different species, each collected about 100 generations apart (one century). Here, no relationship was found between the degree of climate change over this period and the magnitude of observed morphological change, or in a measure of selection strength. Nevertheless, the estimates of selection strength varied substantially among these species: those for the alpine chipmunk (Tamias alpinus) were the strongest and nearly twice that of the co-distributed lodgepole chipmunk (Tamias speciosus). As a result, to assess the impact of directional selection on the observed patterns of phenotypic (co)variation, in the third chapter I contrasted these two species, since they represent the extremes in the estimated strength of selection among all the species\' populations I examined. Theory predicts that, under directional selection, patterns of phenotypic (co)variation might evolve in order to match the subjacent adaptive landscape. This prediction was upheld in the populations of alpine chipmunks, as perhaps expected since they exhibited the strong selective response. Equally importantly, I also observed changes in the overall correlation between traits for the alpine chipmunk in a pattern consistent with that expected under theoretical models that consider the evolution of the genotype-phenotype map in response to directional selection

[Truncated abstract] Under prolonged wet and damp conditions, barley grain with low dormancy can germinate precociously, a condition known as preharvest sprouting that causes a number of detrimental effects in grain quality. In particular, preharvest sprouting renders the grain unsuitable for malting. The aim of this study was to take a genomics approach to identify and characterise candidate genes that could be linked to the control of seed dormancy in barley. This thesis developed a bioinformatic strategy that exploited the availability of gene sequences with functional evidence in the model species of Arabidopsis and rice. The bioinformatic strategy integrated phenotypic data (QTL data) and comparative genomics for a targeted approach in identifying candidate genes with a high probability of having a conserved function in cereals. This bioinformatic study identified two candidate genes ERA1 and ABI2 with strong evidence for a role in seed dormancy based on their function in Arabidopsis in abscisic acid (ABA) signal transduction and their co-location to seed dormancy QTLs in Arabidopsis, rice and wheat. In order to establish whether the candidate genes mapped to seed dormancy QTLs in barley, QTL analyses were performed on a double haploid population, not previously studied, developed from a cross between Stirling, a major Australian malting cultivar, and Harrington, a major Canadian malting cultivar. This cross was specifically chosen for this study, as elucidation of chromosomal regions associated with seed dormancy in the background of a malting cultivar would make a significant contribution for the malting industry. '...' Identification of a seed dormancy QTL on the long arm of 3H, in a region syntenic to the wheat chromosome locations of ESTS aligning to the ERA1 and ABI2 genes, laid the foundation for physical and genetic mapping of the candidate genes to investigate whether the genes co-located to the QTL on 3H. Physical mapping of the genes in wheat barley addition lines confirmed their positions on the long arm of 3H. Genetic mapping of the ERA1 gene was performed using a CAPS marker developed in this thesis. The genetic mapping of the ERA1 gene did not place the gene within either of the minor QTLs on 3HL, although segregation distortion may have influenced the map position of this gene. Further investigation is required to resolve the positioning of the ERA1 and ABI2 genes in relation to the 3H seed dormancy QTL. The main outcomes of this study have been 1) identification of candidate genes for further study; 2) identification of QTLs on the long arm of 3H that were previously unknown; 3) demonstration of the potential differences in dormancy that can be achieved through the use of specific gene combinations, highlighting the importance of minor genes and the epistatic interactions that occur between them and; 4) the development of a CAPS marker for the ERA1 gene, which can be used to track the gene in barley breeding programs to observe its association with important agronomic traits. This thesis also pioneered the implementation of several new technologies including multiplex-ready PCR (Hayden et al. 2008) for fluorescence–based SSR genotyping and QTLNetwork (Yang et al. 2008) for statistical analysis of QTLs. Seed dormancy is a complex trait and is likely to involve the interplay of a number of genes that have a role in other developmental and regulatory processes.

Includes bibliographical references (leaves 192-211). Maps major genes or quantitative trait loci associated with zinc nutrition in the vegetative and reproductive tissues of barley (Hordeum vulgare)

Title from container / Includes bibliographies and indexes / 4 v. : / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (D. Sc.)--University of Adelaide, Waite Agricultural Research Institute, 1987

Includes bibliographical references (leaves 192-211). / x, 211 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Maps major genes or quantitative trait loci associated with zinc nutrition in the vegetative and reproductive tissues of barley (Hordeum vulgare) / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 2001

"August, 2003" / Includes bibliographical references (leaves 260-292) / v, 294 leaves : ill. (some col.), plates (col.), maps (col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, School of Agriculture and Wine, 2003

Biological invasions provide opportunities to study evolutionary processes occurring during contemporary time scales. Here, I combine a literature review of common garden studies of invasive plant species, with field and glasshouse experiments on populations of the outcrossing, perennial, wetland invader Lythrum salicaria (purple loosestrife - Lythraceae), to investigate the evolutionary genetics of local adaptation in reproductive and life-history traits. A review of 32 common garden studies of 28 introduced species identified previously unrecognized latitudinal clines in phenotypic traits in both native and introduced populations. To obtain direct evidence for clinal variation and local adaptation, I investigated populations of L. salicaria sampled along a latitudinal gradient of growing season length in eastern North America. Controlled pollinations of plants from 12 populations provided no evidence for the breakdown of self-incompatibility to self-compatibility towards the northern range limit. However, a quantitative genetic experiment involving 20 populations revealed latitudinal clines in population mean, variance and skew for days to flower and vegetative size. Broad-sense estimates of genetic variance were significant for most traits; however, strong inter-correlations among traits suggested that fitness trade-offs have constrained population divergence. The observed clines supported a model of selection for early flowering in northern populations constrained by a trade-off between age and size at flowering. A comparison of variance-covariance matrices of family and population means (G and D, respectively) of life-history traits demonstrated that populations have evolved in response to selection under genetic constraints, rather than through neutral processes. A reciprocal transplant experiment involving six populations and three common gardens spanning the latitudinal range provided direct evidence for local adaptation in flowering phenology. Populations maintained the same rank-order for time to flowering and vegetative size at each site, and southern populations had the highest fecundity at the southern site but the lowest at the northern site. Finally, a phenotypic selection analysis in each common garden involving 61 F2 families of crosses between a northern × southern populations confirmed that selection favours earlier flowering in northern populations. These results demonstrate that natural selection on reproductive phenology has accompanied the invasive spread of L. salicaria in eastern N. America.

Biological invasions provide opportunities to study evolutionary processes occurring during contemporary time scales. Here, I combine a literature review of common garden studies of invasive plant species, with field and glasshouse experiments on populations of the outcrossing, perennial, wetland invader Lythrum salicaria (purple loosestrife - Lythraceae), to investigate the evolutionary genetics of local adaptation in reproductive and life-history traits. A review of 32 common garden studies of 28 introduced species identified previously unrecognized latitudinal clines in phenotypic traits in both native and introduced populations. To obtain direct evidence for clinal variation and local adaptation, I investigated populations of L. salicaria sampled along a latitudinal gradient of growing season length in eastern North America. Controlled pollinations of plants from 12 populations provided no evidence for the breakdown of self-incompatibility to self-compatibility towards the northern range limit. However, a quantitative genetic experiment involving 20 populations revealed latitudinal clines in population mean, variance and skew for days to flower and vegetative size. Broad-sense estimates of genetic variance were significant for most traits; however, strong inter-correlations among traits suggested that fitness trade-offs have constrained population divergence. The observed clines supported a model of selection for early flowering in northern populations constrained by a trade-off between age and size at flowering. A comparison of variance-covariance matrices of family and population means (G and D, respectively) of life-history traits demonstrated that populations have evolved in response to selection under genetic constraints, rather than through neutral processes. A reciprocal transplant experiment involving six populations and three common gardens spanning the latitudinal range provided direct evidence for local adaptation in flowering phenology. Populations maintained the same rank-order for time to flowering and vegetative size at each site, and southern populations had the highest fecundity at the southern site but the lowest at the northern site. Finally, a phenotypic selection analysis in each common garden involving 61 F2 families of crosses between a northern × southern populations confirmed that selection favours earlier flowering in northern populations. These results demonstrate that natural selection on reproductive phenology has accompanied the invasive spread of L. salicaria in eastern N. America.