Indiana University-Purdue University Indianapolis (IUPUI) / Forensic DNA phenotyping is an up and coming area in forensic DNA analyses that enables the prediction of physical appearance of an individual from DNA left at a crime scene. At present, there has been substantial work performed in understanding what genes/markers are required to produce a reliable prediction of categorical eye and hair color from the DNA of an individual of interest. These pigmentation markers (variants from HERC2, OCA2, TYR, SLC24A4, SLC45A2, IRF4 to name a few) are at the core of several prediction systems for eye and hair color such as IrisPlex, HIrisPlex, and the Snipper 2.5 suite. The contribution of these markers towards prediction in most cases however, only factors in an independent effect and do not take into account potential interactions or epistasis in the production of the final phenotypic color. Epistasis is a phenomenon that occurs when a gene’s effect relies on the presence of ‘modifier genes’, and can display different effects (enhance/repress a particular color) in genotype combinations rather than individually. In an effort to detect such epistatic interactions and their influence on hair color prediction models, for this current study, 872 individuals were genotyped at 61 associative and predictive pigmentation markers from several diverse population subsets. Individuals were phenotypically evaluated for eye and hair color by three separate independent assessments. Several analyses were performed using statistical approaches such as multifactor dimensionality reduction (MDR) for example, in an effort to detect if there are any SNP- SNP epistatic interactions present that could potentially enhance eye and hair color prediction model performances. The ultimate goal of this study was to assess what SNP-SNP combinations amongst these known pigmentation genes should be included as an additional variable in future prediction models and how much they can potentially enhance overall pigmentation prediction model performance. The second part of the project involved the analyses of several differentially expressed candidate genes between different hair color follicles of the same individual using quantitative Real Time PCR. We looked at 26 different genes identified through a concurrent non-human primate study being performed in the laboratory. The purpose of this study was to gain more insight on the level of differentially expressed mRNA between different hair color follicles within the same human individual. Data generated from this part of the project will act as a pilot study or ‘proof of principle’ on the mRNA expression of several pigmentation associated genes on individual beard hair of varying phenotypic colors. This analysis gives a first glimpse at expression levels that remain constant or differentiate between hairs of the same individual, therefore limiting the contribution of individual variation.

No description available.

No description available.

Plant hormones and their gene regulatory networks orchestrate a diverse array of metabolic and physiological changes crucial for growth, development, and environmental responses. Targeting the engineering of hormone signaling networks holds promise for enhancing plant health, crop productivity, and vigor. However, these networks are intricate, featuring negative feedback loops, extensive interconnections between pathways, pleiotropy, and overlapping gene expression. These complexities pose challenges in identifying candidate genes and parsing apart their isolated functions that could be strategically engineered to achieve desired plant phenotypes. Integration of comparative evolution, synthetic biology, and expression analysis facilitates the deconstruction of these networks. Through systems biology approaches data dimensionality can be reduced, enabling the attribution of specific phenotypes to associated genes. Here, I reviewed how the employment of these above-mentioned approaches can aid in the identification of candidate genes involved the regulation of growth and development within specific tissues, and how through synthetic biology we can explore the sequence-function space of candidate genes and their pathway modules. Candidate genes identified through this process can be evaluated through comparative evolutionary approaches, and efficiently tested in synthetic systems for engineering of their molecular functionalities in a high-throughput manner. Here, as a case study, I employ a systems biology approach to identify tissue-specific candidate genes within the auxin regulatory network in soybean shoot development. This method aims to minimize pleiotropy and off-target effects by utilizing expression analysis tissue-specificity score and principal component analysis. I primarily, focused on three pivotal components of the nuclear auxin signaling pathway: Aux/IAA transcriptional repressors, ARF transcription factors, and TIR1/AFB auxin receptors. These components collectively modulate auxin signaling, influencing various growth and environmental responses. I identified genes within the three pivotal components of auxin signaling involved in early shoot architecture development, which has advantages from weed suppression to yield in soybean cultivation. I used a yeast chassis to investigate the function of pleiotropic auxin receptors, which primarily regulate Aux/IAA levels and orchestrate transcriptional changes in response to auxin. I explored whether these receptors modulate auxin response in a concerted fashion, as they are generally not tissue specific. Here, I reported that auxin receptors interact in an epistatic manner to modulate auxin response. This case of study serves as a foundation in engineering plant genotype-phenotype via auxin signaling. / Doctor of Philosophy / Plant hormones are essential for controlling various processes that drive plant growth, development, and responses to the environment. Scientists are exploring ways to engineer the networks that regulate these hormones to improve plant health, boost crop yields, and enhance plant strength. However, these networks are complex, with many interacting parts, making it difficult to identify which genes to modify to achieve specific outcomes in plants. To tackle this challenge, researchers use a combination of approaches, including studying how these networks have evolved, analyzing large amounts of biological data, and using synthetic biology to test and refine their findings. By breaking down the complexity of these networks, they can link specific genes to particular plant traits. Once these genes–trait links are identified, they can be further tested and engineered to optimize plant characteristics. In this study, I focused on the auxin hormone, which plays a key role in numerous aspects of plant growth including soybean shoot development and Arabidopsis root development. I looked at three main components of the auxin regulatory network: Aux/IAA proteins (which act as repressors), ARF transcription factors (which control gene expression), and TIR1/AFB receptors (which detect auxin levels). These components work together to regulate how plants grow and respond to their environment. I identified key genes within these main auxin components that are important for early development of soybean shoots and minimizes off-target effects. This can help improve soybean farming by enhancing weed control and enhancing crop yields Using a synthetic biology yeast system, I studied the function of TIR1/AFB auxin receptors and how this family of receptors interact to perceive auxin and control the levels of Aux/IAA proteins, consequently controlling the plant's growth in response to auxin. I found that auxin receptors work in concert in a way that reduces their overall effect on the plants response to auxin. This research lays the groundwork for future efforts to engineer plant traits by modifying the auxin signaling pathway, which could lead to improved crop performance and resilience.

Nos programas de melhoramentos de soja as progênies endogâmicas são frequentemente avaliadas como possíveis cultivares. O estudo da estrutura da variação genética entre progênies de diferentes gerações de autofecundação depende da ação dos locos envolvidos e da variação do caráter sob estudo. Em soja o caráter produção de grãos (PG) é considerado o de maior importância econômica e destaca-se por apresentar herança quantitativa e ser altamente influenciada pelo ambiente. As estratégias de seleção utilizadas para o desenvolvimento de cultivares em soja poderiam ser otimizadas através do estudo da importância relativa dos componentes de variância, particularmente a proporção de variação devida à interação não alélica (epistasia). Com o objetivo de estudar a variação epistática e sua interação com ambientes (locais) para a produção de grãos em soja utilizou-se o delineamento "Triple Test Cross Modificado" (TTC) de JINKS, PERKINS e BREESE (1969). Uma amostra de 32 linhagens (Pi) derivadas de um cruzamento biparental foi cruzada com duas linhagens divergentes (L1 e L2) contrastantes para PG, derivadas da mesma população (testadores). Os experimentos de avaliação foram conduzidos no ano agrícola de 2006/2007 em dois locais (Piraciacaba e Anhembi) em delineamentos em látice triplo 10 x 10. Os tratamentos correspondiam aos 32 cruzamentos Pi x L1, 32 cruzamentos Pi x L2, 34 linhas puras (32 Pi + 2 testadores) e duas testemunhas comerciais. De acordo com a metodologia utilizada foram estudados os contrastes ( i 2i 1i P L L - + ) para avaliar a ocorrência de epistasia. Os resultados das análises individuais mostraram que a epistasia afetou a expressão da produção de grãos em ambos os locais. A análise conjunta permitiu detectar significância para locais, epistasia e interação epistasia por locais, indicando que a produção de grãos em soja é afetada pela interação não alélica (epistasia) e que esta não é consistente entre locais. O estudo do contraste ( i 2i 1i P L L - + ) das médias individuais nas análises por local e na análise conjunta indicou haver contribuição diferencial dos genótipos para a epistasia. Os resultados gerais indicam que a epistasia pode ser um componente importante para a expressão da produção de grãos de soja e, consequentemente, esta deveria ser incluída nos modelos para a decomposição dos componentes da variância genética. / In soybean breeding programs the selfing progenies are generally evaluated as possible cultivars. The study of the structure of the genetic variation among progenies in different generations of selfing depends upon the action of the loci involved and the variability of the trait under study. In soybeans, grain yield is the most important trait and it is characterized by a quantitative inheritance and highly influenced by the environment. The selection strategies used for the development of soybean cultivars could be optimized through the study of the relative importance of the variance components, in particular the proportion of the non-allelic interaction component (epistasis). In order to study the epistatic variation and its interaction with locations for grain yield in soybeans the "Modified Triple Test Cross" (TTC) method (JINKS, PERKINS e BREESE, 1969) was used. A sample of 32 inbred lines (Pi) derived from a single cross were crossed with two divergent inbred lines (L1 e L2) of the same population (testers). The experiments were carried out in the 2006/2007 growing season in two locations (Piracicaba and Anhembi) in a 10x10 triple lattice design. Entries consisted of the 32 Pi x L1 crosses, 32 Pi x L2 crosses, 34 lines (Pi + 2 testers) and 2 commercial checks. Following the methodology, the contrasts ( i 2i 1i P L L - + ) were studied in order to evaluate the occurrence of epistasis. General results showed that epistasis affected grain yield in soybeans in both locations. Significance for locations, epistasis and epistais by locations interactions were also detected in the joint analysis of variance, indicating that grain yield in soybeans is affected by the non-allelic interaction (epistasis) and that the epistasis is not consistent in different locations. A study of the contrast ( i 2i 1i P L L - + ) of individual means for each location and in the joint analyses indicated the occurrence of differential contribution of the genotypes for the epistasis. General results had demonstrated that epistasis could be an important component for the expression of grain yield in soybeans and consequently it should be included in the model for the partition of the genetic components of variance.

Nos programas de melhoramentos de soja as progênies endogâmicas são frequentemente avaliadas como possíveis cultivares. O estudo da estrutura da variação genética entre progênies de diferentes gerações de autofecundação depende da ação dos locos envolvidos e da variação do caráter sob estudo. Em soja o caráter produção de grãos (PG) é considerado o de maior importância econômica e destaca-se por apresentar herança quantitativa e ser altamente influenciada pelo ambiente. As estratégias de seleção utilizadas para o desenvolvimento de cultivares em soja poderiam ser otimizadas através do estudo da importância relativa dos componentes de variância, particularmente a proporção de variação devida à interação não alélica (epistasia). Com o objetivo de estudar a variação epistática e sua interação com ambientes (locais) para a produção de grãos em soja utilizou-se o delineamento "Triple Test Cross Modificado" (TTC) de JINKS, PERKINS e BREESE (1969). Uma amostra de 32 linhagens (Pi) derivadas de um cruzamento biparental foi cruzada com duas linhagens divergentes (L1 e L2) contrastantes para PG, derivadas da mesma população (testadores). Os experimentos de avaliação foram conduzidos no ano agrícola de 2006/2007 em dois locais (Piraciacaba e Anhembi) em delineamentos em látice triplo 10 x 10. Os tratamentos correspondiam aos 32 cruzamentos Pi x L1, 32 cruzamentos Pi x L2, 34 linhas puras (32 Pi + 2 testadores) e duas testemunhas comerciais. De acordo com a metodologia utilizada foram estudados os contrastes ( i 2i 1i P L L - + ) para avaliar a ocorrência de epistasia. Os resultados das análises individuais mostraram que a epistasia afetou a expressão da produção de grãos em ambos os locais. A análise conjunta permitiu detectar significância para locais, epistasia e interação epistasia por locais, indicando que a produção de grãos em soja é afetada pela interação não alélica (epistasia) e que esta não é consistente entre locais. O estudo do contraste ( i 2i 1i P L L - + ) das médias individuais nas análises por local e na análise conjunta indicou haver contribuição diferencial dos genótipos para a epistasia. Os resultados gerais indicam que a epistasia pode ser um componente importante para a expressão da produção de grãos de soja e, consequentemente, esta deveria ser incluída nos modelos para a decomposição dos componentes da variância genética. / In soybean breeding programs the selfing progenies are generally evaluated as possible cultivars. The study of the structure of the genetic variation among progenies in different generations of selfing depends upon the action of the loci involved and the variability of the trait under study. In soybeans, grain yield is the most important trait and it is characterized by a quantitative inheritance and highly influenced by the environment. The selection strategies used for the development of soybean cultivars could be optimized through the study of the relative importance of the variance components, in particular the proportion of the non-allelic interaction component (epistasis). In order to study the epistatic variation and its interaction with locations for grain yield in soybeans the "Modified Triple Test Cross" (TTC) method (JINKS, PERKINS e BREESE, 1969) was used. A sample of 32 inbred lines (Pi) derived from a single cross were crossed with two divergent inbred lines (L1 e L2) of the same population (testers). The experiments were carried out in the 2006/2007 growing season in two locations (Piracicaba and Anhembi) in a 10x10 triple lattice design. Entries consisted of the 32 Pi x L1 crosses, 32 Pi x L2 crosses, 34 lines (Pi + 2 testers) and 2 commercial checks. Following the methodology, the contrasts ( i 2i 1i P L L - + ) were studied in order to evaluate the occurrence of epistasis. General results showed that epistasis affected grain yield in soybeans in both locations. Significance for locations, epistasis and epistais by locations interactions were also detected in the joint analysis of variance, indicating that grain yield in soybeans is affected by the non-allelic interaction (epistasis) and that the epistasis is not consistent in different locations. A study of the contrast ( i 2i 1i P L L - + ) of individual means for each location and in the joint analyses indicated the occurrence of differential contribution of the genotypes for the epistasis. General results had demonstrated that epistasis could be an important component for the expression of grain yield in soybeans and consequently it should be included in the model for the partition of the genetic components of variance.

A epistasia tem sido considerada como um componente importante da herança de caracteres quantitativos, estando presente nos componentes de variância e covariância genética. No entanto, por ser desconsiderada na maioria dos modelos genético-estatísticos, seu impacto nos programas de melhoramento ainda é pouco conhecido. Além disso, como os programas de melhoramento de milho, em especial no Brasil, têm realizado seleção sob condições de estresse hídrico, é importante analisar o efeito desse estresse sobre a epistasia. Assim, este trabalho teve como objetivo a análise genética de caracteres quantitativos em milho, incluindo epistasia e epistasia pleiotrópica, em ambientes contrastantes para estresse hídrico. Foi utilizado o delineamento triple test cross modificado com testadores, em que cem progênies F2:3 foram retrocruzadas com suas linhagens genitoras L-08-05F e L-38-05D e sua geração F1. Posteriormente, as 300 progênies de retrocruzamento foram cruzadas com duas linhagens testadoras, L-02-03D e L-04-05F. Os testecrosses foram avaliados em dez ambientes no município de Piracicaba/SP, sendo cinco ambientes sem estresse hídrico e cinco com estresse hídrico, utilizando o delineamento α-látice em esquema fatorial com duas repetições por ambiente. Os caracteres analisados foram produção de grãos (PG), acamamento e quebramento de plantas (ACQ), prolificidade (PROL), altura da planta (AP) e da espiga (AE), posição relativa da espiga (PRE), florescimento masculino (FM) e feminino (FF) e intervalo entre florescimentos (IF). A presença de epistasia foi detectada para todos os caracteres. No entanto, os grupos de ambientes, sem e com estresse hídrico, e os diferentes testadores afetaram a detecção de epistasia para todos os caracteres, com exceção de PG, PROL e AP em que a epistasia foi detectada em todas as análises de variâncias conjuntas. A interação epistasia x grupos de ambientes foi significativa apenas para os caracteres PG e PROL dos testecrosses provenientes do testador L-02-03D (TC1) e AP e AE dos testecrosses provenientes do testador L-04-05F (TC2), enquanto que, a interação epistasia x testadores foi significativa para todos os caracteres. Os efeitos epistáticos de testecrosses referentes às plantas F2 significativos foram bidirecionais, com exceção do caráter PROL do TC2 no grupo de ambientes com estresse hídrico, em que os efeitos foram unidirecionais e positivos. Além disso, para cada testador e grupo de ambientes foram detectados efeitos epistáticos significativos para um grupo específico de testecrosses, ocorrendo variações na magnitude e/ou sinais dos testecrosses coincidentes. A presença de epistasia pleiotrópica foi detectada entre diversos pares de caracteres e, além disso, foi observada a formação de agrupamentos de caracteres relacionados, indicando que a epistasia pleiotrópica é modular, porém sofre influência do ambiente, presença ou ausência de estresse hídrico, e dos testadores. Portanto, na população analisada, a epistasia é um componente importante tanto da variância genética de caracteres quantitativos como da covariância genética entre caracteres, indicando que não considerá-la nas análises pode resultar em interpretações que não refletem a real complexidade do controle genético destes caracteres. / Epistasis has been considered an important part of quantitative traits inheritance and it is present in the components of genetic variance and covariance. However, its impact on breeding programs is still little-known because it is disregarded in most statistical genetic models. In addition, maize breeding programs, especially in Brazil, have been practicing selection under water stress conditions, so it is important to analyze the effects of these environments on epistasis. In this context, the objective of this study was to perform a genetic analysis of quantitative traits in maize, including epistasis and pleiotropic epistasis, in contrasting environments for water stress. The modified triple test cross design with testers was used, in which 100 F2:3 progenies were backcrossed to their parental inbred lines, L-08-05F and L-38-05D, and their F1 generation. Thereafter, the 300 backcrossed progenies were testcrossed to the inbred lines testers L-02-03D and L-04-05F. The testcrosses were evaluated in Piracicaba, SP, Brazil, in ten environments, which five environments presented water stress and the other five not, in an α-lattice design on a factorial scheme with two replications by environment. The analyzed traits were grain yield (GY), root and stalk lodging (PL), ear per plant (EPP), plant height (PH), ear height (EH), ear placement (EP), days to anthesis (DA), days to silking (DS) and anthesis-silking interval (ASI). Epistasis was detected for all traits. However, the environmental groups and the different testers affected epistasis detection for all traits, except for GY, EPP and PH, in which epistasis was detected in all joint analysis of variance. The interaction epistasis x environments groups was significant only for GY and EPP of testcrosses from the tester L-02-03D (TC1) and PH and EH of testcrosses from the tester L-04-05F (TC2), whereas the interaction epistasis x testers was significant for all traits. The significant epistatic effects of testcrosses referring to F2 plants were bidirectional, except for EPP of TC2 in the water stress environmental group, where the effects were unidirectional and positives. Besides that, for each tester and environmental group, significant epistatic effects for a specific group of testcrosses were detected, occurring variation in magnitude and/or sign of coincident testcrosses. Pleiotropic epistasis was detected between many pairs of traits and it was observed formation of related traits clusters, suggesting that pleiotropic epistasis is modular, but the modules suffered influence of environments and testers. Therefore, in the population analyzed, epistasis is an important component of genetic variance of quantitative traits and also of genetic covariance between traits, showing that disregarding epistasis in analyses may result in interpretations that do not reflect the real complexity of the genetic control of these traits.

A epistasia tem sido considerada como um componente importante da herança de caracteres quantitativos, estando presente nos componentes de variância e covariância genética. No entanto, por ser desconsiderada na maioria dos modelos genético-estatísticos, seu impacto nos programas de melhoramento ainda é pouco conhecido. Além disso, como os programas de melhoramento de milho, em especial no Brasil, têm realizado seleção sob condições de estresse hídrico, é importante analisar o efeito desse estresse sobre a epistasia. Assim, este trabalho teve como objetivo a análise genética de caracteres quantitativos em milho, incluindo epistasia e epistasia pleiotrópica, em ambientes contrastantes para estresse hídrico. Foi utilizado o delineamento triple test cross modificado com testadores, em que cem progênies F2:3 foram retrocruzadas com suas linhagens genitoras L-08-05F e L-38-05D e sua geração F1. Posteriormente, as 300 progênies de retrocruzamento foram cruzadas com duas linhagens testadoras, L-02-03D e L-04-05F. Os testecrosses foram avaliados em dez ambientes no município de Piracicaba/SP, sendo cinco ambientes sem estresse hídrico e cinco com estresse hídrico, utilizando o delineamento α-látice em esquema fatorial com duas repetições por ambiente. Os caracteres analisados foram produção de grãos (PG), acamamento e quebramento de plantas (ACQ), prolificidade (PROL), altura da planta (AP) e da espiga (AE), posição relativa da espiga (PRE), florescimento masculino (FM) e feminino (FF) e intervalo entre florescimentos (IF). A presença de epistasia foi detectada para todos os caracteres. No entanto, os grupos de ambientes, sem e com estresse hídrico, e os diferentes testadores afetaram a detecção de epistasia para todos os caracteres, com exceção de PG, PROL e AP em que a epistasia foi detectada em todas as análises de variâncias conjuntas. A interação epistasia x grupos de ambientes foi significativa apenas para os caracteres PG e PROL dos testecrosses provenientes do testador L-02-03D (TC1) e AP e AE dos testecrosses provenientes do testador L-04-05F (TC2), enquanto que, a interação epistasia x testadores foi significativa para todos os caracteres. Os efeitos epistáticos de testecrosses referentes às plantas F2 significativos foram bidirecionais, com exceção do caráter PROL do TC2 no grupo de ambientes com estresse hídrico, em que os efeitos foram unidirecionais e positivos. Além disso, para cada testador e grupo de ambientes foram detectados efeitos epistáticos significativos para um grupo específico de testecrosses, ocorrendo variações na magnitude e/ou sinais dos testecrosses coincidentes. A presença de epistasia pleiotrópica foi detectada entre diversos pares de caracteres e, além disso, foi observada a formação de agrupamentos de caracteres relacionados, indicando que a epistasia pleiotrópica é modular, porém sofre influência do ambiente, presença ou ausência de estresse hídrico, e dos testadores. Portanto, na população analisada, a epistasia é um componente importante tanto da variância genética de caracteres quantitativos como da covariância genética entre caracteres, indicando que não considerá-la nas análises pode resultar em interpretações que não refletem a real complexidade do controle genético destes caracteres. / Epistasis has been considered an important part of quantitative traits inheritance and it is present in the components of genetic variance and covariance. However, its impact on breeding programs is still little-known because it is disregarded in most statistical genetic models. In addition, maize breeding programs, especially in Brazil, have been practicing selection under water stress conditions, so it is important to analyze the effects of these environments on epistasis. In this context, the objective of this study was to perform a genetic analysis of quantitative traits in maize, including epistasis and pleiotropic epistasis, in contrasting environments for water stress. The modified triple test cross design with testers was used, in which 100 F2:3 progenies were backcrossed to their parental inbred lines, L-08-05F and L-38-05D, and their F1 generation. Thereafter, the 300 backcrossed progenies were testcrossed to the inbred lines testers L-02-03D and L-04-05F. The testcrosses were evaluated in Piracicaba, SP, Brazil, in ten environments, which five environments presented water stress and the other five not, in an α-lattice design on a factorial scheme with two replications by environment. The analyzed traits were grain yield (GY), root and stalk lodging (PL), ear per plant (EPP), plant height (PH), ear height (EH), ear placement (EP), days to anthesis (DA), days to silking (DS) and anthesis-silking interval (ASI). Epistasis was detected for all traits. However, the environmental groups and the different testers affected epistasis detection for all traits, except for GY, EPP and PH, in which epistasis was detected in all joint analysis of variance. The interaction epistasis x environments groups was significant only for GY and EPP of testcrosses from the tester L-02-03D (TC1) and PH and EH of testcrosses from the tester L-04-05F (TC2), whereas the interaction epistasis x testers was significant for all traits. The significant epistatic effects of testcrosses referring to F2 plants were bidirectional, except for EPP of TC2 in the water stress environmental group, where the effects were unidirectional and positives. Besides that, for each tester and environmental group, significant epistatic effects for a specific group of testcrosses were detected, occurring variation in magnitude and/or sign of coincident testcrosses. Pleiotropic epistasis was detected between many pairs of traits and it was observed formation of related traits clusters, suggesting that pleiotropic epistasis is modular, but the modules suffered influence of environments and testers. Therefore, in the population analyzed, epistasis is an important component of genetic variance of quantitative traits and also of genetic covariance between traits, showing that disregarding epistasis in analyses may result in interpretations that do not reflect the real complexity of the genetic control of these traits.

Master of Science / Department of Agronomy / Jianming Yu / Tannin, a second metabolic product in sorghum, has been directly related to resistance to insects and birds. Tannin also impacts sorghum nutritional value. Previous studies have shown tannin content has a positive correlation with early season cold tolerance, an important agronomic trait. Sorghum contains condensed tannins in testa layer below the pericarp. The testa layer tannin is controlled by two complementary genes B1 and B2: tannins are present when both genes are dominant but absent when only one or none of these two is dominant. The purpose of this research is to identify and map QTLs associated with the presence of condensed tannins, analyze interaction of QTLs, and provide a potential path to dissect the more complex trait of early season cold tolerance in future studies. A population of 109 F6:7 recombinant inbred lines (RILs) developed from the cross of a high tannin sorghum Shan Qui Red (SQR) and non-tannin line Tx430 was used in the mapping study. Two QTLs related to condense tannin presence in testa layer were mapped to chromosome 2 and 4, respectively. Strong epistatic interaction of these two QTLs was detected. The two QTLs together with their interaction explained 74% of the phenotypic variation. Sorghum grain quality traits, including kernel size, kernel hardness, protein and starch content, are complex traits which are directly related to sorghum nutritional value and market value. Association mapping is a promising method for complex quantitative traits analysis and dissection in plant science. Sorghum grain quality trait association analysis research is purposed to analyze large amount of grain quality data based on a diversity panel. A sorghum bicolor panel of 300 lines including germplasm derived from sorghum conversion program and elite commercial lines were established and served as diversity population for the association study. Phenotypic data of grain quality traits were collected by single kernel characterization system (SKCS) and near infrared reflectance spectroscopy (NIRS). Data analysis proved high diversity within the SB panel. A correlation between tannin presence and kernel hardness was also observed. Quality traits showed high consistence across years and environments.

Of central importance in the dissection of the components that govern complex traits is understanding the architecture of natural genetic variation. Genetic interaction, or epistasis, constitutes one aspect of this, but epistatic analysis has been largely avoided in genome wide association studies because of statistical and computational difficulties. This thesis explores both issues in the context of two-locus interactions. Initially, through simulation and deterministic calculations it was demonstrated that not only can epistasis maintain deleterious mutations at intermediate frequencies when under selection, but that it may also have a role in the maintenance of additive variance. Based on the epistatic patterns that are evolutionarily persistent, and the frequencies at which they are maintained, it was shown that exhaustive two dimensional search strategies are the most powerful approaches for uncovering both additive variance and the other genetic variance components that are co-precipitated. However, while these simulations demonstrate encouraging statistical benefits, two dimensional searches are often computationally prohibitive, particularly with the marker densities and sample sizes that are typical of genome wide association studies. To address this issue different software implementations were developed to parallelise the two dimensional triangular search grid across various types of high performance computing hardware. Of these, particularly effective was using the massively-multi-core architecture of consumer level graphics cards. While the performance will continue to improve as hardware improves, at the time of testing the speed was 2-3 orders of magnitude faster than CPU based software solutions that are in current use. Not only does this software enable epistatic scans to be performed routinely at minimal cost, but it is now feasible to empirically explore the false discovery rates introduced by the high dimensionality of multiple testing. Through permutation analysis it was shown that the significance threshold for epistatic searches is a function of both marker density and population sample size, and that because of the correlation structure that exists between tests the threshold estimates currently used are overly stringent. Although the relaxed threshold estimates constitute an improvement in the power of two dimensional searches, detection is still most likely limited to relatively large genetic effects. Through direct calculation it was shown that, in contrast to the additive case where the decay of estimated genetic variance was proportional to falling linkage disequilibrium between causal variants and observed markers, for epistasis this decay was exponential. One way to rescue poorly captured causal variants is to parameterise association tests using haplotypes rather than single markers. A novel statistical method that uses a regularised parameter selection procedure on two locus haplotypes was developed, and through extensive simulations it can be shown that it delivers a substantial gain in power over single marker based tests. Ultimately, this thesis seeks to demonstrate that many of the obstacles in epistatic analysis can be ameliorated, and with the current abundance of genomic data gathered by the scientific community direct search may be a viable method to qualify the importance of epistasis.