A produção de grãos e outros caracteres de importância econômica para a cultura do milho, tais como a altura da planta, o comprimento e o diâmetro da espiga, apresentam herança poligênica, o que dificulta a obtenção de informações sobre as bases genéticas envolvidas na variação desses caracteres. Associações entre marcadores e QTLs foram analisadas através dos métodos de mapeamento por intervalo composto (CIM) e mapeamento por intervalo Bayesiano (BIM). A partir de um conjunto de dados de produção de grãos, referentes à avaliação de 256 progênies de milho genotipadas para 139 marcadores moleculares codominantes, verificou-se que as metodologias apresentadas permitiram classificar marcas associadas a QTLs. Através do procedimento CIM, associações entre marcadores e QTLs foram consideradas significativas quando o valor da estatística de razão de verossimilhança (LR) ao longo do cromossomo atingiu o valor máximo dentre os que ultrapassaram o limite crítico LR = 11; 5 no intervalo considerado. Dez QTLs foram mapeados distribuídos em três cromossomos. Juntos, explicaram 19,86% da variância genética. Os tipos de interação alélica predominantes foram de dominância parcial (quatro QTLs) e dominância completa (três QTLs). O grau médio de dominância calculado foi de 1,12, indicando grau médio de dominância completa. Grande parte dos alelos favoráveis ao caráter foram provenientes da linhagem parental L0202D, que apresentou mais elevada produção de grãos. Adotando-se a abordagem Bayesiana, foram implementados métodos de amostragem através de cadeias de Markov (MCMC), para obtenção de uma amostra da distribuição a posteriori dos parâmetros de interesse, incorporando as crenças e incertezas a priori. Resumos sobre as localizações dos QTLs e seus efeitos aditivo e de dominância foram obtidos. Métodos MCMC com saltos reversíveis (RJMCMC) foram utilizados para a análise Bayesiana e Fator calculado de Bayes para estimar o número de QTLs. Através do método BIM associações entre marcadores e QTLs foram consideradas significativas em quatro cromossomos, com um total de cinco QTLs mapeados. Juntos, esses QTLs explicaram 13,06% da variância genética. A maior parte dos alelos favoráveis ao caráter também foram provenientes da linhagem parental L02-02D. / Grain yield and other important economic traits in maize, such as plant heigth, stalk length, and stalk diameter, exhibit polygenic inheritance, making dificult information achievement about the genetic bases related to the variation of these traits. The number and sites of (QTLs) loci that control grain yield in maize have been estimated. Associations between markers and QTLs were undertaken by composite interval mapping (CIM) and Bayesian interval mapping (BIM). Based on a set of grain yield data, obtained from the evaluation of 256 maize progenies genotyped for 139 codominant molecular markers, the presented methodologies allowed classification of markers associated to QTLs.Through composite interval mapping were significant when value of likelihood ratio (LR) throughout the chromosome surpassed LR = 11; 5. Significant associations between markers and QTLs were obtained in three chromosomes, ten QTLs has been mapped, which explained 19; 86% of genetic variation. Predominant genetic action for mapped QTLs was partial dominance and (four QTLs) complete dominance (tree QTLs). Average dominance amounted to 1,12 and confirmed complete dominance for grain yield. Most alleles that contributed positively in trait came from parental strain L0202D. The latter had the highest yield rate. Adopting a Bayesian approach to inference, usually implemented via Markov chain Monte Carlo (MCMC). The output of a Bayesian analysis is a posterior distribution on the parameters, fully incorporating prior beliefs and parameter uncertainty. Reversible Jump MCMC (RJMCMC) is used in this work. Bayes Factor is used to estimate the number of QTL. Through Bayesian interval, significant associations between markers and QTLs were obtained in four chromosomes and five QTLs has been mapped, which explained 13; 06% of genetic variation. Most alleles that contributed positively in trait came from parental strain L02-02D. The latter had the highest yield rate.

Camundongos foram selecionados geneticamente para alta (AIRmax) ou baixa (AIRmin) resposta inflamatória aguda, sendo utilizados em experimentos de regeneração tecidual. Foi observado que AIRmax apresentam uma regeneração rápida do tecido da orelha em relação aos AIRmin, sugerindo a existência de loci reguladores comuns para ambos fenótipos de inflamação e regeneração do tecido. Neste estudo investigamos o fenótipo inflamatório e o perfil de expressão gênica global em AIRmax e AIRmin durante a fase inicial da regeneração do tecido da orelha. A análise histológica mostrou que AIRmax apresentam uma regeneração completa, com formação de ilhas de cartilagem e glândulas sebáceas no centro da área regenerada. Os AIRmin não apresentam regeneração. Os dados obtidos sobre edema de orelha e níveis de MPO foram maiores em AIRmax quando comparados com AIRmin (P <0,001). A análise de expressão gênica global mostrou 794 genes ativados e 528 genes reprimidos em AIRmax, enquanto 1.086 genes ativados e 1.145 genes reprimidos nos AIRmin, 48 horas após a lesão. AIRmax e AIRmin apresentaram alta modulação de genes sobrerrepresentados em temas biológicos para resposta inflamatória, adesão celular e quimiotaxia (Gene Ontology). No entanto, foi observado uma baixa modulação de genes sobrerrepresentados para o transporte em AIRmax e para taxia, contração muscular e ciclo de ubiquitina em AIRmin. Nas regiões próximas ao QTL anteriormente encontrado no cromossomo 1, foram observados genes diferencialmente expressos como Stat1, Casp8, Hspe1 e Il1r2, enquanto Lect1, Fndc3 e Egr3 foram detectados no cromossomo 14. Os experimentos com qPCR mostram uma alta expressão de Il-1<font face=\"Symbol\">b, Il-8rb e Mmp9 em AIRmax e Cxcl2, Tnfa e Tgfb em AIRmin. Concluímos que os animais AIRmax e AIRmin apresentam (nos cromossomos 1 e 14) genes inflamatórios diferencialmente expressos que podem estar envolvidos nos fenótipos de resposta inflamatória aguda e regeneração do tecido da orelha. / Mice selected for high (AIRmax) or low (AIRmin) acute inflammatory response were used in tissue regeneration experiments. It was observed that AIRmax present faster ear tissue regeneration than AIRmin mice, suggesting the involvement of common regulatory loci for both inflammation and ear tissue regeneration phenotypes. In the study we investigated some inflammatory phenotypes and global gene expression profiles in AIRmax and AIRmin mice during the initial phase of the ear tissue regeneration. The histological analyses showed that AIRmax regeneration was complete, and cartilage islands and sebaceous glands were formed in the middle of the regenerated area. AIRmin mice displayed not regeneration. Ear thickness oedema and MPO levels were higher in AIRmax than AIRmin mice (P< 0.001). Global expression analysis showed 794 activated and 528 repressed genes in AIRmax, while 1086 activated and 1145 repressed genes were observed in AIRmin mice 48 hours after injury. AIRmax and AIRmin mice presented up-regulated genes over-represented in inflammatory response, cell adhesion and chemotaxis biological themes (Gene ontology). However, down-modulated genes were significant over-represented for transportation in AIRmax and for taxis, muscle contraction and cycle ubiquitin in AIRmin mice. In the previously QTL regions detected on chromosome 1 differentially-expressed Stat1, Casp8, Hspe1 and Il1r2 genes were found, while Lect1, Fndc3 and Egr3 were detected on chromosome 14. qPCR experiments showed high expression of Il-1<font face=\"Symbol\">b, Il-8rb and Mmp9 in AIRmax and Cxcl2, Tnfa, and Tgfb1 in AIRmin mice. We conclude that AIRmax and AIRmin mice presented several (some on chromosomes 1 and 14) differentially-expressed inflammatory genes which could be involved in the acute inflammatory response and ear tissue regeneration phenotypes.

Camundongos AIRmax e AIRmin homozigotos para os alelos R e S do gene Slc11a1 foram avaliados para susceptibilidade à artrite induzida por pristane (PIA). A presença do alelo S aumentou a incidência e a gravidade nos AIRmax, sugerindo que o gene Slc11a1, ou outro próximo, esteja interagindo com os loci de resposta inflamatória na modulação de PIA. Para identificar estes loci foram realizados estudos de associação genótipo-fenótipo e de expressão gênica global. Os RNAs das patas dos animais foram isolados após 180 dias da indução por pristane. As análises de expressão gênica global foram realizadas usando a plataforma Codelink (36k genes), cujos resultados foram validados por PCR em tempo real. Os estudos de associação foram realizados através da análise de polimorfismo de microssatélites pelo programa MapManager. Foram identificadas duas regiões nos cromossomos 1 e 11. Um número grande de genes diferencialmente expressos foi verificado nos animais AIRmax SS cujos temas biológicos significativamente sobre-representados foram a resposta inflamatória e quimiotaxia. Os camundongos AIRmax SS também possuem uma ativação maior dos genes Ccl3, Ccl7, C3ar1, Il10, Stat3, Tirap, Trem 1, Trem 3, Mefv, Ptx3, Chi3l3 e Kras. Alguns desses genes co-localizam com regiões previamente mapeadas nos cromossomos 1 e 11. / AIRmax and AIRmin mice homozygous for Slc11a1 R and S allele were evaluated for pristane-induced arthritis (PIA) susceptibility. The presence of S allele increased the incidence and the arthritis severity in ARmax mice, suggesting that Slc11a1 or other closed-linked gene interacts with inflammatory loci to modulate PIA. In order to identify inflammatory modifier loci modulating experimental arthritis development, genotype-phenotype association studies and global gene expression analyses were performed. Mice received i.p. injections of pristane and the paw RNAs were isolated at day 180. Global gene expression analysis was performed on Codelink bioarrays (36k genes) and validated by real time PCR. The microsatellite polymorphism analyses were performed using MapManager program. Two regions on chromosomes 1 and 11 were identified. Higher number of differentially-expressed genes were detected in AIRmax SS subline, which significant over-represented biological themes were related to inflammatory response and chemotaxis. Susceptible AIRmax SS mice also display high up-regulation of Ccl3, Ccl7, C3ar1, Il10, Stat3, Tirap, Trem 1, Trem 3, Mefv, Ptx3, Chi3l3 e Kras genes. Some of them co-localize with previously identified regions mapped on chromosomes 1 and 11.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

<p>The purpose of gene mapping is to understand the underlying genetics of simple and complex traits like plumage colour and growth. This thesis is based on a cross between the wild ancestor of the modern chicken, the red junglefowl, and a White Leghorn line selected for high egg mass. There are obvious phenotypic differences between these two breeds in several aspects such as growth, egg production and behaviour. These complex traits are often influenced by a number of genes or Quantitative Trait Loci (QTL) as well as environmental factors.</p><p>Identification of QTL regions involves testing of association between genetic markers and the phenotype of interest. The QTL identified in this study explain most of the difference in adult body weight between the red junglefowl and the White Leghorn, but less of the difference at earlier age. By applying a different method for detection of QTL, including gene interactions, epistasis, we can understand more of the genetics behind early growth. The allele coming from the red junglefowl is generally associated with lower weight, egg production and food consumption.</p><p>In this study we have also identified two genes explaining the difference in plumage colour in the cross. The <i>Extension</i> locus, encoded by the melanocortin receptor 1 (<i>MC1R</i>), controls the amount of pigment produced has shown to be associated with plumage colour. A mutation in the <i>MC1R</i> gene causes black pigmentation of the plumage. </p><p>We have also found association between the <i>PMEL17</i> gene, known to be involved in normal pigmentation, and the <i>Dominant white</i> phenotype present in the White Leghorn. After comparison of sequences from different alleles at the <i>Dominant white</i> locus, amino acid alteration caused by insertion and deletion in the transmembrane region of the <i>PMEL17</i> protein has been revealed. These mutations are associated with alleles representing different plumage colour variants.</p>

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

The purpose of gene mapping is to understand the underlying genetics of simple and complex traits like plumage colour and growth. This thesis is based on a cross between the wild ancestor of the modern chicken, the red junglefowl, and a White Leghorn line selected for high egg mass. There are obvious phenotypic differences between these two breeds in several aspects such as growth, egg production and behaviour. These complex traits are often influenced by a number of genes or Quantitative Trait Loci (QTL) as well as environmental factors. Identification of QTL regions involves testing of association between genetic markers and the phenotype of interest. The QTL identified in this study explain most of the difference in adult body weight between the red junglefowl and the White Leghorn, but less of the difference at earlier age. By applying a different method for detection of QTL, including gene interactions, epistasis, we can understand more of the genetics behind early growth. The allele coming from the red junglefowl is generally associated with lower weight, egg production and food consumption. In this study we have also identified two genes explaining the difference in plumage colour in the cross. The Extension locus, encoded by the melanocortin receptor 1 (MC1R), controls the amount of pigment produced has shown to be associated with plumage colour. A mutation in the MC1R gene causes black pigmentation of the plumage. We have also found association between the PMEL17 gene, known to be involved in normal pigmentation, and the Dominant white phenotype present in the White Leghorn. After comparison of sequences from different alleles at the Dominant white locus, amino acid alteration caused by insertion and deletion in the transmembrane region of the PMEL17 protein has been revealed. These mutations are associated with alleles representing different plumage colour variants.

Identifying reliable screening tools and characterizing tolerant germplasm sources is essential for developing wheat (Triticum aestivum L.) varieties suited for the hot areas of the world. Our objective was to evaluate heat tolerance of promising wild tetraploid wheat (Triticum turgidum L.) accessions that could be used as sources of heat tolerance in common- and durum-wheat (Triticum durum) breeding programs. We screened 109 wild tetraploid wheat accessions collected by the International Center for Agriculture Research in the Dry Areas (ICARDA) from the hottest wheat growing areas in Africa and Asia, as well as, two common wheat checks for their response to heat stress by measuring damage to the thylakoid membranes, flag leaf temperature depression (FLTD), and spike temperature depression (STD) during exposure to heat stress for 16 beginning at anthesis. Measurements were taken on the day of anthesis then 4, 8, 12, and 16 days post anthesis (DPA) under controlled optimum and heat-stress conditions. Individual kernel weight (IKW) and heat susceptibility index (HSI) measurements were also obtained. Prolonged exposure to heat stress was associated with increased damage to thylakoid membranes, as indicated by the high ratio of constant fluorescence (O) to peak variable fluorescence (P). A positive and significant correlation was found between O/P ratio and both FLTD and STD under heat-stress conditions. A negative and significant correlation was found between FLTD and HSI and between STD and HSI based on the second and third measurements (4 and 8 DPA). Correlations obtained after the third measurement were not significant because heat-stress accelerated maturity and senescence. For a pedigree-based mapping strategy a family approach was then developed by crossing and back-crossing heat-tolerant and heat-susceptible germplasm. A set of 800 lines resulting from the pedigree-based family approach was phenotyped using FLTD, chlorophyll content and yield and its components under heat stress. Genotyping of these lines was accomplished using simple sequence repeat (SSRs) markers. Some QTLs associated with heat stress tolerance were identified. This study identified potential heat-tolerant wild tetraploid wheat germplasm and QTL conditioning heat tolerance that can be incorporated into wheat breeding programs to improve cultivated common and durum wheat.

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).