This study comprised three major parts: a comparative physiological study of drought responses under controlled conditions; a genetic study to construct the skeleton map of a doubled haploid (DH) population; and a quantitative trait loci (QTL) analysis to identify QTLs associated with drought tolerance traits in the field. In the first part (Chapter 3), three cultivars of wheat (Triticum aestivum L.) adapted to South Australian conditions were tested for drought tolerance under cyclic drought in growth rooms and glasshouse. Extensive physiological traits, including stomatal conductance, chlorophyll content and fluorescence, ABA content, water status traits (e.g. osmotic adjustment, RWC and leaf water potential), water soluble carbohydrates (WSC) and carbon isotope discrimination (Δ¹ ³C) were measured during experiments. Through these experiments, the drought responses of the three cultivars were physiologically dissected and the likely processes contributing most to drought tolerance were identified. In the South Australian wheatbelt, cyclic drought is a frequent event, represented by intermittent periods of rainfall which can occur around anthesis and post-anthesis in wheat. Three South Australian bread wheat cultivars, Excalibur, Kukri and RAC875, were evaluated in two growth room experiments under cyclic water-limiting conditions. In the first experiment, where plants were subjected to severe water stress, RAC875 and Excalibur (drought tolerant) showed significantly (P < 0.05) higher grain yield under cyclic water availability compared to Kukri (drought susceptible), producing 44% and 18% more grain yield compared to Kukri, respectively. In the second growth room experiment, where plants were subjected to a milder drought stress, the differences between cultivars were less pronounced, with only RAC875 showing significantly higher grain yield under the cyclic water treatment. Grain number per spike and the percentage of aborted tillers were the major yield components that affected yield under cyclic water stress. Excalibur and RAC875 adopted different morpho-physiological traits and mechanisms to reduce water stress. Excalibur was most responsive to cyclic water availability and showed the highest level of osmotic adjustment (OA), highest stomatal conductance, lowest ABA content and most rapid recovery from stress under cyclic water stress. RAC875 was more ‘conservative’ in its responses, with moderate OA, high leaf waxiness, high chlorophyll content and slower recovery from stress. Within this germplasm, the capacity for osmotic adjustment was the main physiological attribute associated with tolerance under cyclic water stress, which enabled plants to recover from water deficit. In the second part (Chapter 4), the genetic linkage map of a DH population including 368 lines, which was developed from a cross between ‘RAC875’ and ‘Kukri’, was constructed. The genetic linkage map consisted of about 500 molecular markers including ~300 DArT (Diversity array technology) and ~200 SSR (Microsattelite markers). In the third part (Chapter 5), Quantitative Trait Loci (QTLs) linked to plant phenology and production traits under irrigated and drought stress conditions were mapped by means of a DH population. To phenotype the population, 368 DH lines were cultivated in two replicates in five environments (three sites across South Australian wheatbelt in collaboration with Australian Grain Technology (AGT) in 2006, and two trials in Mexico in collaboration with CYMMIT, 2007). Data of grain yield, yield components, maturity related traits and some morpho-physiological traits such as leaf chlorophyll content, leaf waxiness, plant height, peduncle length, flag leaf and spike length were measured. Raw data were then analysed for spatial variation for each single trial using the REML procedure in GenStat (version 6). The DH lines showed significant variation for plant phenology, grain yield and yield components under irrigated and drought stress conditions. QTL analyses were performed using QTLCartographer and QTLNetwork for each trait in each site. Two major QTL for maturity traits were identified on chromosomes 2BS and 2DS corresponding to Ppd-B1 and Ppd-D1, respectively. A region was identified on chromosome 7A that harbored major QTL for grain yield, number of grains per square meter, number of grain per spike and spike fertility under drought stress. For yield data in the irrigated trial, two major QTL were identified on chromosome 3B which were not detected in drought stress environments. By using different datasets in the QTL analysis (splitting the population into two subpopulation based on heading time and also adjusting the phenotypic data for heading time to eliminate heading time effect), a QTL for grain yield was consistently detected on chromosome 7A in drought-affected environments. The coincidence of a drought response index QTL on this chromosome indicated that it might be a QTL for yield response under drought. This study demonstrated that the region on the long arm of chromosome 7A identified for grain yield and yield components is a drought response QTL which is closely linked to, but separate from, a heading time QTL. This QTL cluster on chromosome 7A could be used as a good target for positional cloning and gene isolation. However further work would be required to confirm and validate the identified QTLs in this preliminary QTL analysis. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1340056 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

This study comprised three major parts: a comparative physiological study of drought responses under controlled conditions; a genetic study to construct the skeleton map of a doubled haploid (DH) population; and a quantitative trait loci (QTL) analysis to identify QTLs associated with drought tolerance traits in the field. In the first part (Chapter 3), three cultivars of wheat (Triticum aestivum L.) adapted to South Australian conditions were tested for drought tolerance under cyclic drought in growth rooms and glasshouse. Extensive physiological traits, including stomatal conductance, chlorophyll content and fluorescence, ABA content, water status traits (e.g. osmotic adjustment, RWC and leaf water potential), water soluble carbohydrates (WSC) and carbon isotope discrimination (Δ¹ ³C) were measured during experiments. Through these experiments, the drought responses of the three cultivars were physiologically dissected and the likely processes contributing most to drought tolerance were identified. In the South Australian wheatbelt, cyclic drought is a frequent event, represented by intermittent periods of rainfall which can occur around anthesis and post-anthesis in wheat. Three South Australian bread wheat cultivars, Excalibur, Kukri and RAC875, were evaluated in two growth room experiments under cyclic water-limiting conditions. In the first experiment, where plants were subjected to severe water stress, RAC875 and Excalibur (drought tolerant) showed significantly (P < 0.05) higher grain yield under cyclic water availability compared to Kukri (drought susceptible), producing 44% and 18% more grain yield compared to Kukri, respectively. In the second growth room experiment, where plants were subjected to a milder drought stress, the differences between cultivars were less pronounced, with only RAC875 showing significantly higher grain yield under the cyclic water treatment. Grain number per spike and the percentage of aborted tillers were the major yield components that affected yield under cyclic water stress. Excalibur and RAC875 adopted different morpho-physiological traits and mechanisms to reduce water stress. Excalibur was most responsive to cyclic water availability and showed the highest level of osmotic adjustment (OA), highest stomatal conductance, lowest ABA content and most rapid recovery from stress under cyclic water stress. RAC875 was more ‘conservative’ in its responses, with moderate OA, high leaf waxiness, high chlorophyll content and slower recovery from stress. Within this germplasm, the capacity for osmotic adjustment was the main physiological attribute associated with tolerance under cyclic water stress, which enabled plants to recover from water deficit. In the second part (Chapter 4), the genetic linkage map of a DH population including 368 lines, which was developed from a cross between ‘RAC875’ and ‘Kukri’, was constructed. The genetic linkage map consisted of about 500 molecular markers including ~300 DArT (Diversity array technology) and ~200 SSR (Microsattelite markers). In the third part (Chapter 5), Quantitative Trait Loci (QTLs) linked to plant phenology and production traits under irrigated and drought stress conditions were mapped by means of a DH population. To phenotype the population, 368 DH lines were cultivated in two replicates in five environments (three sites across South Australian wheatbelt in collaboration with Australian Grain Technology (AGT) in 2006, and two trials in Mexico in collaboration with CYMMIT, 2007). Data of grain yield, yield components, maturity related traits and some morpho-physiological traits such as leaf chlorophyll content, leaf waxiness, plant height, peduncle length, flag leaf and spike length were measured. Raw data were then analysed for spatial variation for each single trial using the REML procedure in GenStat (version 6). The DH lines showed significant variation for plant phenology, grain yield and yield components under irrigated and drought stress conditions. QTL analyses were performed using QTLCartographer and QTLNetwork for each trait in each site. Two major QTL for maturity traits were identified on chromosomes 2BS and 2DS corresponding to Ppd-B1 and Ppd-D1, respectively. A region was identified on chromosome 7A that harbored major QTL for grain yield, number of grains per square meter, number of grain per spike and spike fertility under drought stress. For yield data in the irrigated trial, two major QTL were identified on chromosome 3B which were not detected in drought stress environments. By using different datasets in the QTL analysis (splitting the population into two subpopulation based on heading time and also adjusting the phenotypic data for heading time to eliminate heading time effect), a QTL for grain yield was consistently detected on chromosome 7A in drought-affected environments. The coincidence of a drought response index QTL on this chromosome indicated that it might be a QTL for yield response under drought. This study demonstrated that the region on the long arm of chromosome 7A identified for grain yield and yield components is a drought response QTL which is closely linked to, but separate from, a heading time QTL. This QTL cluster on chromosome 7A could be used as a good target for positional cloning and gene isolation. However further work would be required to confirm and validate the identified QTLs in this preliminary QTL analysis. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1340056 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Made available in DSpace on 2016-06-02T20:21:21Z (GMT). No. of bitstreams: 1 2646.pdf: 870244 bytes, checksum: b88bf96aa8cafe0798c953895db021a7 (MD5) Previous issue date: 2009-08-28 / Financiadora de Estudos e Projetos / A preliminary genetic linkage map was constructed for the species Prochilodus argenteus, an endemic fish from the São Francisco river basin, using 23 microsatellite markers in a progeny with 95 individuals from a single cross by the pseudo-testcross strategy. The male and female parents were collected in different regions, downstream of the dam of the Três Marias (MG). Only 11 (52.4%) markers grouped in some linkage group and the the remaining was unlinked. Twenty-one (91.5%) markers appeared to segregate according to Mendelian inheritance, and only two (8.7%) showed segregation distortion. The map covered 297.58 cM of the genome, according to the Kosambi s function. The number of linkage groups (3) found in this study was much lower than expected for the species (equivalent to the haploid number of chromosomes, n = 27), demonstrating the importance of using a larger number of molecular markers in future studies. The data obtained in this work will be compiled with the marks obtained by AFLP by Rojas (2008) in order to obtain a denser genetic map. Although the number of linkage groups found have been lower than expected for the species, the results can be considered promising for the Brazillian Fish Genetics, since genetic mapping studies are virtually absent in Neotropical fish. / Um mapa genético preliminar foi construído para a espécie Prochilodus argenteus, um peixe endêmico da bacia hidrográfica do rio São Francisco, através de 23 marcadores moleculares microssatélites em uma progênie com 95 indivíduos provenientes de um único cruzamento através da estratégia pseudo-testcross . Os genitores masculino e feminino foram coletados em diferentes regiões, à jusante da barragem de Três Marias (MG). Apenas 11 (52.4%) marcadores foram alocados em algum grupo de ligação e os restantes não estavam ligados. Vinte e um (91.5%) marcadores segregaram de acordo com a herança mendeliana e apenas dois (8.7%) apresentaram distorção da segregação. O mapa cobriu 297.58 cM do genoma, de acordo com a função de Kosambi. O número de grupos de ligação (3) encontrado no presente trabalho foi muito inferior ao esperado para a espécie (equivalente ao número de cromossomos haplóides, n = 27), demonstrando a importância da utilização de um número maior de marcadores moleculares em estudos futuros. Os dados obtidos no presente trabalho serão compilados com as marcas AFLP obtidas por Rojas (2008), visando um mapa genético mais denso. Embora o número de grupos de ligação encontrado tenha sido inferior ao esperado para a espécie, os resultados podem ser considerados como promissores na área de Genética de Peixes do Brasil, já que estudos de mapeamento genético são praticamente inexistentes em peixes neotropicais.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2015-10-20T16:00:07Z No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-21T10:02:07Z (GMT) No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-10-21T10:02:07Z (GMT). No. of bitstreams: 2 Dissertação - Daniel Garcia Silva - 2012.pdf: 2191471 bytes, checksum: 68bc7d63efc7307ce6b62a63489d372d (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2012-06-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Sugarcane is an important crop, cultivated in more than 90 countries, occupying an area of approximately 20 million of hectares. Modern varieties (Saccharum spp.) are highly heterozygous interspecific hybrids, polyploids and often aneuploids, with chromosome numbers between 100 and 130. Such characteristics explain the common opinion that the genome of sugarcane is the most complex among cultivated species, posing a challenge to breeding programs. As a contribution to the understanding of this complex genomic architecture, this study aimed to build the first linkage maps using exclusively DArT markers in sugarcane. The maps were built using a progeny derived from the cross between varieties largely used in the Brazilian breeding program of RIDESA (RB97327 x RB72454). The initial mapping population comprised 186 individuals. Total genomic DNA was extracted from axial buds, following the protocol of Al-Janabi et al. (1999). Using the DArT P/L core facility to generate DArT data, a total of 7680 markers were analyzed, of which 850 were polymorphic. The analysis of segregation patterns in the progeny revealed that 47% of the individuals in the progeny were in fact derived from selfing of the female parent RB97327. These individuals were analyzed as a distinct generation. Linkage analyses were then performed on two populations (from selfing and crossing) separately. The software OneMap was used to construct the maps. The established linkage criteria for linkage analysis were LOD-score ≥ 3.5 and recombination fraction ≤ 0.4. In the first map, built using data from individuals originated from selfing, from 850 polymorphic markers, 392 markers (segregating in a 3:1 manner) were used to create 80 linkage groups related to the variety RB97327. For the population derived from the biparental crossing, four linkage maps were built: an integrated map composed of 98 linkage groups including 632 markers (1:1 and 3:1); an integrated framework map, using a more conservative ordering criteria for the linkage groups, which was composed of 94 linkage groups; and two other linkage maps, one for each parent (RB97327 and RB72454), built to estimate the genome size of the varieties involved in this study. The total length of the linkage map built using data from individuals derived from selfing of the variety RB97327 was 828 cM. The total length of the integrated linkage map was 2848 cM. The lengths of the maps built for each parent, using data from individuals derived from crossing, were 1465 cM (RB97327) and 1976 cM (RB72454). Using the methodology of Hulbert et al. (1988), the estimated genome sizes for these varieties were 2811 cM e 3471 cM, respectively. The maps obtained in these cases covered a low percentage of the estimated genome sizes (52% and 57%). In spite of the low polymorphism, DArT markers showed to be an efficient technique to perform genotyping of sugarcane. Hundreds of polymorphic markers were generated in only one assay, using two methods of genome complexity reduction. These markers represent a new tool for genetic studies in sugarcane, especially if the low cost (USD/marker) involved in data production is considered. / A cana-de-açúcar é uma importante cultura, cultivada em mais de 90 países, ocupando uma área total de aproximadamente 20 milhões de hectares. As variedades modernas (Saccharum spp.) são híbridos interespecíficos altamente heterozigóticos, poliploides e frequentemente aneuploides, com número cromossômico variando de 100 a 130. Tais características proporcionaram ao genoma da cana-de-açúcar o título de mais complexo entre as espécies cultivadas, o que representa um desafio para os programas de melhoramento genético da cultura. No intuito de contribuir com dados que auxiliem na compreensão dessa complexa arquitetura genômica, o presente estudo objetivou a construção dos primeiros mapas de ligação para cana-de-açúcar utilizando exclusivamente marcadores DArT, avaliados na progênie derivada do cruzamento de variedades amplamente utilizadas nos programas de melhoramento da RIDESA (RB97327 x RB72454). A população inicial de mapeamento foi composta por 186 indivíduos. O DNA genômico foi extraído de gemas axiais, seguindo o protocolo proposto por Al-Janabi et al. (1999). Após a extração, quantificação e homogeneização da concentração de DNA das amostras, o material foi enviado para a empresa DArT P/L para a geração dos marcadores DArT. Um total de 7680 locos foi analisado, dos quais 850 se apresentaram polimórficos. A análise dos padrões de segregação obtidos na progênie revelou que 47% dos indivíduos da progênie avaliada foram provenientes de autofecundação do genitor feminino RB97327. Os indivíduos identificados como provenientes de autofecundação foram analisados como uma geração distinta. As análises de ligação foram realizadas nas duas populações separadamente. O software OneMap foi utilizado para a construção dos mapas. Os critérios estabelecidos para proceder com as análises de ligação foram LOD-score ≥ 3,5 e fração de recombinação ≤ 0,4. No primeiro mapa, originário da população de autofecundação, dos 850 marcadores polimórficos, 392 marcadores com segregação 3:1 foram utilizados para originar 80 grupos de ligação referentes à variedade RB97327. Para a população derivada do cruzamento biparental foram construídos quatro mapas de ligação: um mapa integrado composto por 98 grupos de ligação a partir da análise de 632 marcadores (com segregações 1:1 e 3:1); um mapa framework integrado, construído a partir de uma ordenação mais refinada dos marcadores dentro de cada um dos grupos de ligação, o qual foi composto por 94 grupos de ligação; e, com o objetivo de se estimar o tamanho do genoma das variedades envolvidas neste estudo, dois mapas de ligação, um para cada genitor (RB97327 e RB72454). O comprimento total do primeiro mapa, referente à variedade RB97327, foi de 828cM. O comprimento total do mapa integrado foi de 2848 cM. Os comprimentos totais dos mapas obtidos para cada um dos genitores, gerados a partir de dados da população de cruzamento biparental, foram de 1465Cm (RB97327) e de 1976 cM (RB72454). Utilizando a metodologia de Hulbert et al. (1988), os tamanhos estimados dos genomas das variedades RB97327 e RB72454 foram 2811 cM e 3471 cM, respectivamente. Assim, pode-se afirmar que os mapas obtidos neste caso apresentaram baixa cobertura (52% e 57%), perante o tamanho estimado dos genomas. Apesar do baixo polimorfismo, os marcadores DArT se mostraram eficientes na genotipagem de progênies de cana-de-açúcar, pois, centenas de marcas polimórficas foram geradas em apenas um ensaio, com dois métodos de redução de complexidade. Estes marcadores representam uma nova ferramenta para o desenvolvimento de estudos genéticos em cana-de-açúcar, principalmente se considerado o baixo custo (R$/marcador) envolvido na obtenção dos genótipos.

Soybeans are an economically important plant, with an annual crop value that consistently exceeds 20 billion dollars in the United States alone. A recent increase in demand for soybeans, stemming from its diverse applications in products such as animal feed, oil, and biofuel, has created an emphasis for soybean breeders in value added cultivars. These cultivars, have improved, or altered, agronomic or seed composition traits, allowing them to be efficiently utilized in a specific niche of the processing industry. Facilitating the development of such cultivars requires a thorough understanding of the genetic factors that affect the manifestation of value added traits. Value added traits investigated in this study include seed sucrose, raffinose, stachyose, and phytate content, seed weight, and maturity. The objective of the first part of this project was to characterize the source of low seed stachyose in soybean line PI200508. Two F2 populations, developed from PI200508 and soybean introductions which exhibited higher seed stachyose content were utilized in a QTL analysis approach that incorporated the use of the Williams82 whole genome shotgun (WGS) sequence (http://www.phytozome.org) in a candidate gene mapping approach. A predicted soybean galactosyltransferase gene was established as a candidate gene due to its observed segregation with the single low stachyose QTL observed on molecular linkage group (MLG) C2 in both populations. Sequencing of this putative gene revealed a unique 3 bp deletion in PI200508. A marker developed to exploit this deletion accounted for 88% and 94% of the phenotypic variance for seed stachyose content in the two experimental populations, highlighting its potential for use in marker assisted selection of the PI200508 source of low raffinose and stachyose. The second part of this project involved QTL analysis of seed sucrose, raffinose, stachyose, and phytate content, as well as seed weight in a linkage map for a F8 RIL population developed from the Glycine max line V71-370 and the Glycine soja introduction PI40712. Analysis across all 20 soybean MLG identified 25 QTL for these traits on MLG A1, A2, C2, D1b, D2, F, G, H, I, L, M, O. Nine of these QTL were supported across multiple environments, indicating that they, and their associated markers, could be useful to breeders working with these traits. The third part of this project used the same F8 RIL linkage map to investigate time to maturity (Reproductive stage R8). V71-370 and PI407162 differ in time to maturity when grown in Virginia, and the RILs developed from this cross displayed a wide range in maturity. Two major QTL were identified on MLG H and L. Examination of the Williams82 WGS sequence in these QTL regions revealed two predicted genes with homology to Arabidopsis thaliana light response and photoperiodism genes which were investigated as candidate soybean maturity genes. Markers developed from these predicted genes showed close association with the observed QTL, and could facilitate the further investigation of this complex trait. / Ph. D.

Soybean has become one of the most important crops to the United States, resulting in a need to improve its disease resistance. The objectives of this study were to 1) design primers and develop PCR-based markers from disease-related expressed sequence tags (ESTs) and resistance gene analogues (RGAs), 2) assess the utility of such markers by diversity analysis of 12 soybean parental lines, and 3) search for possible association of the markers with known disease resistance genes by constructing a linkage map. The diversity analysis will allow this study to determine how well each marker can distinguish genotypes in soybean. Identifying the location of our markers in the soybean genome with the linkage map, will allow those related to disease resistance to be selected. A total of 202 simple sequence length polymorphism (SSLP) markers were constructed using a set of 1218 disease-related ESTs. Furthermore, 22 markers were constructed using previously identified RGA sequences. Both sets of markers were able to detect polymorphism in the diversity analysis. Also, 48 of the SSLPs, five of the RGAs, and 150 molecular markers were used to construct a soybean linkage map using 114 recombinant inbred lines (RILs). Several markers mapped to chromosomal regions known to contain disease resistance genes. This study has created a framework map, which will be useful for identifying the location of resistance genes, marker-assisted selection for resistance, discovering novel resistance genes, and understanding genome organization of resistance pathways in soybean. An effective approach to develop "candidate gene" markers has been demonstrated. / Master of Science

La famille des Fagacées regroupe des espèces présentant un intérêt économique, écologique et social non négligeable. Par ailleurs, ces espèces, et plus particulièrement celles du genre Quercus que l’on retrouve dans des milieux extrêmement diversifiés, constituent de bons modèles d’étude de l’adaptation des arbres à leur environnement. Pour comprendre l’architecture génétique des caractères liés à l’adaptation chez le chêne, des cartes génétiques ont été établies essentiellement sur la base de marqueurs moléculaires dominants. Le travail qui a fait l’objet de cette thèse, a consisté à développer une carte génétique de seconde génération à partir des ressources génomiques disponibles chez cette espèce. Dans un premier temps, nous avons recherché des motifs microsatellites (SSR, simple sequence repeats) au sein des séquences exprimées (EST) assemblées sous la forme d’un unigène de 28 000 éléments non redondant. Un jeu de 748 marqueurs a été développé et 255 d’entre eux ont été localisés sur la carte génétique du chêne pédonculé (Q. robur L.) en utilisant une approche dite de « bin mapping ». Leur transférabilité a été testée chez le châtaignier européen (Castanea sativa Mill.) et le hêtre commun (Fagus sylvatica L.), deux espèces phylogénétiquement proche du chêne. Un taux de transférabilité de 28% a été observé pour le hêtre et de 56,6% pour le châtaigner. Une carte génétique a alors été établie pour le châtaigner en utilisant les marqueurs SSR localisés sur la carte du chêne. La comparaison des cartes de liaison du chêne et du châtaignier a mis en évidence une bonne conservation de la macro synténie et de la macro colinéarité entre les deux espèces, ce qui ouvre des perspectives intéressantes pour le transfert d’informations génétiques (QTL par exemple) d’une espèce à l’autre. Cette étude sera prochainement enrichie par la cartographie de marqueurs orthologues dérivés de polymorphismes ponctuels (SNP), ce qui permettra de comprendre l’évolution conjointe des trois espèces majeures de la famille des Fagacées. / The Fagaceae family comprises species of economic, ecological and social importance. In addition, these species and particularly those belonging to the Quercus genus that are present in very diverse ecological niches, constitute good models to study the adaptation of forest trees to their natural environment. To understand the genetic architecture of adaptive traits in oak, genetic linkage maps have been previously established based on dominant markers. In this thesis, we developed a second generation genetic map using the genomic resources that were available in this species. First, we bioinformatically screened an expressed sequence tags catalog assembled into a 28 000 unigene elements, for simple sequence repeats (SSRs). A set of 748 markers was developed and 255 were localized on the pedunculate oak (Q. robur L.) linkage map using a bin mapping approach. Their transferability was tested in the European chestnut (Castanea sativa Mill.) and common beech (Fagus sylvatica L.), two phylogenetically related species to oak. Transferability rates of 28% and 56.6% were observed for beech and chestnut, respectively. A genetic map was then established for chestnut on the basis of orthologous SSRs already mapped in oak. The comparison between both maps clearly showed that the macro-synteny and the macro-colinearity were conserved across genus, opening interesting perspectives in respect to the transfer of genetic information (eg. QTLs, quantitative trait loci) from one species to another. This study will be soon completed by the mapping of orthologous markers derived from single nucleotide polymorphisms (SNPs). This will made it possible to better understand the evolution of the genome of these three major species of the Fagaceae family.

Submitted by (ana.araujo@ufrpe.br) on 2017-02-21T18:02:51Z No. of bitstreams: 1 Silvan Gomes de Brito.pdf: 841884 bytes, checksum: 6b8e147dd9071bbb1076ca5bcf2a438e (MD5) / Made available in DSpace on 2017-02-21T18:02:51Z (GMT). No. of bitstreams: 1 Silvan Gomes de Brito.pdf: 841884 bytes, checksum: 6b8e147dd9071bbb1076ca5bcf2a438e (MD5) Previous issue date: 2012-07-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Genetic mapping based on the planning and establishment of the linear distance between marks associated with genes responsible for controlling qualitative and quantitative characteristics. The construction of genetic maps is considered the most impact applications of the technology of molecular markers in genetic analysis of species, potentially in plant breeding. A genetic map of linkage may be low, medium and high resolution in accordance with the greater or lesser number of genes or ordered markers. A factor of considerable importance to obtain consistent data that result in more accurate maps is the sample size or population, level of saturation in the linkage groups and marker type to be used. Thus, the aim of this work was to estimate the optimum size of population and saturation of the genomes were generated with saturation levels of 5, 10 and 20 cM, containing 210, 110, and marks 60, respectively, and F2 populations double-haploid populations. Each genome was composed of 10 linkage groups, with a size of 100 cM each. For each level of saturation of the genome populations were generated at 100, 200, 300, 500, 800 and 1000 individuals, with 100 replicates, each codominant and dominant markers used when the type F2 populations were dominant and only double-haploid populations. These populations were mapped using LODmín 3 and a maximum frequency of recombination of 30%. From the maps obtained were extracted information regarding the number of linkage groups and marks for group, size of linkage group, distance between adjacent marks, variance of the distances between adjacent marks, marks inversion obtained by Spearman correlation and degree of agreement of distances on maps with the original genome, obtained by the stress. Populations of the same size tend to produce maps with greater accuracy in higher levels of genome saturation. The optimum size of F2 populations for genetic mapping must be of at least 200 individuals when codominant markers are of type and 300 when the markers are the dominant type, regardless of the saturation level of the genome. While double-haploid populations in the optimal size was 200, 500 and 1000 individuals when the saturation levels of the genome were 5, 10 and 20 cM, respectively. / O mapeamento genético baseia-se no ordenamento linear e estabelecimento da distância entre marcas associadas a genes responsáveis pelo controle de características qualitativas e quantitativas. A construção de mapas genéticos é considerada uma das aplicações de maior impacto da tecnologia de marcadores moleculares na análise genética de espécies, e potencialmente, no melhoramento de plantas. Um mapa genético de ligação pode ter baixa, média e alta resolução, de acordo com menor ou maior número de genes ou marcadores ordenados. Um fator de fundamental importância para se obter dados consistentes que resultem em mapas mais acurados é o tamanho da amostra ou da população, o nível de saturação nos grupos de ligação e tipo de marcador a ser utilizado. Desse modo, objetivou-se com este trabalho estimar o tamanho ideal de população e saturação do genoma para a obtenção de mapas de ligação confiáveis por meio de simulação de dados em computador. Foram gerados três genomas com níveis de saturação de 5, 10 e 20 cM, contendo 210, 110 e 60 marcas, respectivamente, para populações F2 e populações duplo-haplóide. Cada genoma foi composto por 10 grupos de ligação, com um tamanho de 100 cM cada. Para cada nível de saturação do genoma foram geradas populações com 100, 200, 300, 500, 800 e 1000 indivíduos, com 100 repetições cada, sendo utilizado marcadores codominantes e dominantes quando as populações eram do tipo F2 e apenas dominante para populações duplo-haplóide. Estas populações foram mapeadas utilizando um LODmín de 3 e frequência máxima de recombinação de 30%. Dos mapas obtidos foram extraídas informações referentes ao número de grupos de ligação e de marcas por grupo, tamanho de grupo de ligação, distância entre marcas adjacentes, variância das distâncias entre marcas adjacentes, inversão de marcas obtida pela correlação de Spearman e grau de concordância das distâncias nos mapas com o genoma original obtida pelo estresse. Populações de mesmo tamanho tendem a produzir mapas com maior acurácia em níveis de saturação do genoma mais elevados. O tamanho ideal de populações F2 para mapeamento genético é de no mínimo 200 indivíduos quando os marcadores forem do tipo codominante e de 300 quando os marcadores forem do tipo dominante, independente do nível de saturação do genoma. Enquanto que em populações duplo-haplóide o tamanho ideal é de 200, 500 e 1000 indivíduos quando os níveis de saturação do genoma forem de 5, 10 e 20 cM, respectivamente.

Araucaria cunninghamii is an ancient tropical conifer with substantial value as a forestry species in Australia and Papua New Guinea, and has been subject to a genetic improvement program for more than 50 years. This study was undertaken to demonstrate the utility of quantitative genetic analysis in describing the genetic architecture of commercial traits in A. cunninghamii. Linkage maps were prepared using the pseudotestcross strategy in what was believed to be a wide interprovenance cross using microsatellites and AFLP. A very low rate of marker polymorphism and limited differentiation between the parental provenances was identified, resulting in low mapping efficiency. The population genetic structure of A. cunninghamii was assessed to establish the underlying causes for the limited differentiation and low marker heterozygosity and assess the implications for future analysis of quantitative traits. Despite the limited mapping efficiency, genetic maps were generated for both parents. The maternal map for individual H15 contained 14 linkage groups comprising of 51 AFLP and one microsatellite. The map covered 1290 cM, representing 89% of the estimated genome size. The paternal map for individual Gil24 was 633 cM, consisting of eight linkage groups. Genetic architecture of quantitative traits was examined with putative QTL identified for height, DBH and stem straightness; one was highly significant (p<0.01), three significant (0.01<p<0.05) and 13 suggestive (p<0.10). Significant QTL each accounted for 7-11% of the phenotypic variance with a high allele substitution effect (0.63-0.81). These QTL were likely to be associated with genes of moderate effect. The suggestive QTL each accounted for 3-6% of the phenotypic variance with an allele substitution effect of 0.40-0.63. Three genomic regions contributed to the expression of multiple traits at multiple ages. Stable QTL had decreasing phenotypic effects with increasing age. The population genetic survey characterised low levels of allelic diversity across the geographic range. Three broad regions were characterised; Papua New Guinea, Cape York and northern Queensland to NSW. There was limited differentiation between provenances within these regions, and high diversity within provenances. Limited genetic differentiation between provenances seems to be the result of genetic stability due to long overlapping generations, limited founder effects and a very low mutation rate. The latter may also contribute the low heterozygosity. Limited marker polymorphism and limited differentiation between provenances within broad regions are common features in A. cunninghamii. Therefore careful parental selection and alternative experimental approaches will be required before undertaking further analysis of quantitative traits.

This thesis presents results from genetic studies conducted in the chicken (Gallus gallus). The domestication of chicken is believed to have been initiated approximately 7,000 – 9,000 years ago in Southeast Asia. Since that time, selective breeding has altered the appearance of the wild ancestor, creating highly specialized chicken lines developed for egg and meat production. The first part of this thesis describes a detailed genetic analysis conducted on an F2 intercross between two phenotypically diverse chicken lines. The two parental lines used in this experiment originated from the same base population and have been developed by divergent selection for juvenile body-weight. Selection during forty generations has resulted in an eight-fold difference in body-weight between the High-Weight Selected (HWS) and Low-Weight Selected (LWS) line. In an attempt to identify the genetic factors differentiating the two lines, a large intercross population was bred to map Quantitative Trait Loci (QTL) affecting body-weight traits. A linkage map was constructed which included 434 genetic markers covering 31 of the 38 chicken autosomes. Although there is a dramatic phenotypic difference between the two founder lines, the QTL analysis for marginal effect could only identify seven QTL, each with small additive effects, influencing body-weight. We extended the genetic analysis to also include a model testing for pair-wise interactions between loci (epistasis). The analysis revealed 15 QTL pairs that affect body-weight and several of those formed a network of interacting loci. These results suggest that the genetic basis for the large difference in body-weight is most likely a result of a combined effect of multiple genetic factors, including QTL with small additive effects in combination with pair-wise interactions between QTL. The second part of this thesis presents two linkage maps. The first map constructed was of the chicken Z chromosome, the second used a genome-wide marker set, including 12,945 SNP markers, to build an updated consensus map of the chicken genome. The resulting consensus map includes 9,268 genetic markers and covers 33 chromosomes, still leaving five microchromosomes without marker coverage. The genome average rate of recombination was estimated to 3.1 cM/Mb, but varied considerably between and within chromosomes. A general trend of elevated recombination rates towards telomeric ends and lower rates near centromeres was observed. This was in concordance to previous reports from mammalian species. Recombination rates in chicken were also found to be highly positively correlated with GC-rich sequences.