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

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

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 4 uppsatser.

Thesis (Ph.D. in Pharmacology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 121-149). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

Thesis (Ph.D.)--University of Alabama at Birmingham, 2008. / Title from first page of PDF file (viewed on June 23, 2009). Includes bibliographical references.

Thesis (Ph. D.)--Case Western Reserve University, 2005. / [School of Medicine] Department of Epidemiology and Biostatistics. Includes bibliographical references. Available online via OhioLINK's ETD Center.

Background Atlantic salmon (Salmo Salar) is a key aquaculture species in several countries. Since its critical role in economic sector and scientific research, this species has been relatively extensively investigated, in comparison with other farmed and wild aquatic species. However, the genetic components associated with growth and fillet-related traits are lack consistency, and the issue of sea louse disease in both wild and famed salmon is still unsolved. Objectives Overall aim of this project was to understand the genetic basis of growth-related traits and host resistance to sea lice using three large commercial farmed salmon populations. Specifically, the method of quantitative trait loci (QTL) mapping, genome-wide association study (GWAS), and genomic prediction (GS) were utilized to dissect the genetic architectures associated with traits of interest in our experimental populations. Prior to this, linkage mapping was performed to construct a high-density linkage map for Atlantic salmon. Results Linkage map A linkage map was firstly constructed underlying a SNP array containing 132 K validated SNPs. 96,396 SNPs were successfully assigned to 29 chromosomes that correspond to the linkage group number of European Atlantic salmon. 6.5 % of unassigned contigs, which was equal to 1 % of recent whole genome reference assembly (GCA_000233375.4) anchored to exist chromosomes by referring to linkage mapping result. Genetic components associated with growth traits Heritabilities of growth-related traits were about 0.5 to 0.6 in adult and juvenile farmed salmon. The QTL mapping and GWAS suggested the growth-related traits are likely a polygenic genetic architecture with no major QTL segregating. The prediction accuracy estimated by genomic prediction showed that approximately 5,000 SNP markers could achieve the highest accuracy in body weight and length in juvenile salmon within population. Genetic components associated with lice resistance The heritability of lice resistance was 0.22 to 0.33 using pedigree and genetic relationship matrices respectively. GWAS indicated that the host resistance to sea lice was likely polygenic with no individual SNP surpassed the genome-wide significance threshold. Genomic prediction showed that about 5 to 10 K SNPs was able to achieve the asymptote of accuracy in closely related animals, while the greatest advantage of genomic prediction was observed in non-sibling test within population. Conclusions As the growth-related traits and lice resistance are both likely polygenic and population-specific, the genomic prediction is an efficient approach to capture the genetic variances of the traits in selection candidates in experimental population, especially for traits with low heritability such as flesh colour and lice resistance. Family-based selection method is the better choice than mass selection to accumulate the genetic effects in corresponding SNP platform. Given the high cost of genotyping and field data collection, the genotyping-by-sequencing and genotype imputation are likely the way to make significant improvements in relevant research.

Doctor of Philosophy / Department of Statistics / Weixing Song / In this dissertation, we proposed a new robust estimation procedure for two multivariate mixture regression models and applied this novel method to functional mapping of dynamic traits. In the first part, a robust estimation procedure for the mixture of classical multivariate linear regression models is discussed by assuming that the error terms follow a multivariate Laplace distribution. An EM algorithm is developed based on the fact that the multivariate Laplace distribution is a scale mixture of the multivariate standard normal distribution. The performance of the proposed algorithm is thoroughly evaluated by some simulation and comparison studies. In the second part, the similar idea is extended to the mixture of linear mixed regression models by assuming that the random effect and the regression error jointly follow a multivariate Laplace distribution. Compared with the existing robust t procedure in the literature, simulation studies indicate that the finite sample performance of the proposed estimation procedure outperforms or is at least comparable to the robust t procedure. Comparing to t procedure, there is no need to determine the degrees of freedom, so the new robust estimation procedure is computationally more efficient than the robust t procedure. The ascent property for both EM algorithms are also proved. In the third part, the proposed robust method is applied to identify quantitative trait loci (QTL) underlying a functional mapping framework with dynamic traits of agricultural or biomedical interest. A robust multivariate Laplace mapping framework was proposed to replace the normality assumption. Simulation studies show the proposed method is comparable to the robust multivariate t-distribution developed in literature and outperforms the normal procedure. As an illustration, the proposed method is also applied to a real data set.

Submitted by MARCOS LEANDRO TEIXEIRA DE OLIVEIRA (marcosteixeira@ufv.br) on 2018-08-24T12:59:01Z No. of bitstreams: 1 texto completo.pdf: 3178737 bytes, checksum: 5041c62a2f0856a630f7f0f0865ee43b (MD5) / Made available in DSpace on 2018-08-24T12:59:01Z (GMT). No. of bitstreams: 1 texto completo.pdf: 3178737 bytes, checksum: 5041c62a2f0856a630f7f0f0865ee43b (MD5) Previous issue date: 2016-08-12 / Fundação de Amparo à Pesquisa do Estado de MInas Gerais / Para identificar regiões genômicas envolvidas na regulação de processos fisiológicos fundamentais, como fotossíntese, respiração e aqueles relacionados, uma população de ILs de Solanum pennellii em fundo genético de S. lycopersicum (M82) foi analisada. Foram estudados parâmetros fisiológicos, metabólicos e de crescimento, que vão desde troca gasosa (por exemplo, taxa de assimilação de CO 2 e condutância estomática), fluorescência da clorofila (por exemplo, taxa de transporte de elétrons e de extinção fotoquímica), bem como parâmetros de crescimento (por exemplo, taxa de crescimento relativo, matéria seca da raiz e parte aérea). Em paralelo, nós também analisamos, por meio de uma plataforma robotizada, os principais intermediários metabólicos (por exemplo, açúcares, amido, nitrato, aminoácidos e proteínas), e a atividade de nove enzimas representativas do metabolismo central do C e N. O objetivo do estudo foi: (1) combinar informações sobre as atividades enzimáticas e os níveis de metabólitos de caule, pecíolo e folha com a biomassa e rendimento de frutos; (2) através do estudo desses três órgãos interligados, examinar o quanto há de conectividade entre a atividade das enzimas e os níveis de metabólitos; (3) fornecer informações preditivas sobre as diferenças de particionamento do C e assimilação N inorgânico; (4) investigar a diversidade genética natural e identificar QTLs relacionados ao metabolimo central e a atividade enzimática no caule, pecíolo e folha. As análises dos dados permitiram a identificação de 67 QTL relacionados à parametros fisiológicos e metabólicos. Além disso, uma anotação abrangente e detalhada destas regiões permitiu apontar um total de 87 genes candidatos que possam controlar as características investigadas. Desses, 70 genes apresentou variantes alélicas relacionadas inserções de elementos transponíveis entre os dois genótipos parentais. As análises metabólicas e enzimática revelaram alta frequência de correlações positivas entre as enzymas, frequência moderada de correlações entre metabólitos relacionados, e baixa correlações entre a atividade das enzimas e os níveis de metabólitos. Tomados em conjunto, vapresentamos o maior estudo de parâmetros de fotossíntese e crescimento em plantas de tomate até à data. Os resultados permitiram a identificação de genes candidatos que podem estar envolvidos na regulação da fotossíntese, metabolismo primário e crescimento da planta, e fornece um recurso genético valioso para a compreensão dos mecanismos bioquímicos envolvidos na regulação do metabolismo primário em tomateiro. / To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis, respiration and underlying traits, a population of 71 Solanum pennellii introgression lines (ILs) in the genetic background of S. lycopersicum (M82) was analyzed. We determined IL phenotypes physiological, metabolic and growth related traits, ranging from gas- exchange parameters (e.g. CO 2 assimilation rates and stomatal conductance), chlorophyll fluorescence parameters (e.g. electron transport rate and photochemical quenching) as well as growth related traits (e.g. relative growth rate, shoot and root dry matter accumulation). In parallel, we also analyzed by robotized platform the major metabolic intermediates (e.g. sugars and starch), and the activities of nine representative enzymes from central C and N metabolism. We aimed: (1) combine information about enzyme activities and metabolite levels from stem, petiole and leaf with biomass and fruit yield; (2) by studying these three interconnected organs, examine how much connectivity exists between enzyme activities and metabolite levels; (3) provide predictive information about differences in C partitioning and inorganic N assimilation; (4) investigate the natural genetic diversity and identify QTL controlling variation of enzyme activities and metabolite levels in stem, petiole and leaf. Data analyses allowed identification of 67 physiological and metabolic QTL. Additionally, a comprehensive and detailed annotation of these regions allowed to point out a total of 87 candidate genes that might control the investigated traits. Out of those, 70 genes showed allelic variants related to differentially transposable element insertions pattern between both parental genotypes. Furthermore, the results revealed high frequency of positive correlations between enzyme activities, moderate frequency of correlations between related metabolites, and few correlations between enzyme activities and metabolite levels. Taken together, we present the largest study of photosynthetic and growth parameters in tomato plants to date. Our results allowed the identification of candidate genes that might be involved in the regulation of photosynthesis, primary metabolismo and plant growth, and provide an valuable genetic resource to understanding of the biochemical mechanisms involved in the regulation of primary metabolism in tomato plants.