Indiana University-Purdue University Indianapolis (IUPUI) / Brain imaging genetics is an emerging research field aimed at studying the underlying genetic architecture of brain structure and function by utilizing different imaging modalities. However, not all the changes in the brain are a direct result of the genetic effect. Furthermore, the imaging phenotypes are promising for genetic analyses are usually unknown. In this thesis, we focus on identifying highly heritable measures of structural brain networks derived from Diffusion Weighted Magnetic Resonance imaging data. Using data for twins that is made available by the Human Connectome Project (HCP), the reliability of edge-level measures, namely fractional anisotropy, fiber length, and fiber number in the structural connectome, as well as seven network-level measures, specifically assortativity coefficient, local efficiency, modularity, transitivity, cluster coefficient, global efficiency, and characteristic path length, were evaluated using intraclass correlation coefficients. In addition, estimates of the heritability of the reliable measures were also obtained. It was observed that across all 64,620 network edges between 360 brain regions in the Glasser parcellation, approximately 5% were significantly high heritability based on fractional anisotropy, fiber length, or fiber number. Moreover, all tested network level measures, that capture network integrity, segregation, or resilience, were found to be highly heritable, having a variance ranging from 59% to 77% that is attributable to an additive genetic effect.

Genetic control of resistance to H. contortus was assessed in 198 ewes and 386 lambs of 50% Dorset, 25% Rambouillet and 25% Finnsheep breeding in fall and spring over 2 yr. After deworming, lambs that were approximately 120 d old and ewes that had weaned their lambs at 60 d and dried off were individually dosed with approximately 10,000 infective larvae. After infection, body weight (BW), fecal egg counts (FEC) and packed cell volume (PCV) were measured weekly for 7 wk in lambs and fortnightly for eleven wk in ewes. Summary traits were defined as initial PCV, mean BW (MBW) across all times, and means for FEC, log-transformed FEC (MLFEC), and PCV (MPCV) at wk 3 to 7 post-infection for lambs and wk 3 to 11 post-infection for ewes. No consistent seasonal variation in FEC was observed. Younger ewes were more susceptible to infection than older ewes. Sex differences in FEC were not observed in lambs. Heritabilities for summary traits were estimated from a REML analysis that included fixed effects of year and season plus effects of either sex (for lambs) or age category (for ewes). Heritability estimates for MBW, MPCV, and MLFEC were 0.74, 0.57, and 0.27 respectively (all P < 0.01), in lambs, and 0.24 (P < 0.1), 0.25 (P < 0.05) and 0.55 (P < 0.01), respectively, in ewes. Across-year repeatability estimates in ewes for MBW, MPCV, and MLFEC were 0.83, 0.54 and 0.56, respectively (all P < 0.01). Resistance was antagonistically associated with estimated breeding values for growth in ewes but not in lambs. Fertility and prolificacy in ewes were not related to resistance. Breed differences in resistance to H. contortus were also evaluated in 4 to 6-mo-old crossbred Dorset and Dorper, straightbred Katahdin, and Barbados Blackbelly x St. Croix lambs. Dorpers were not more resistant than Dorsets but appeared to cope better, with higher PCV and similar BW during infection compared to Dorsets. Katahdin and Barbados Blackbelly x St. Croix lambs were more resistant with lower FEC. / Master of Science

Video Image Analysis (VIA) is a digital camera based technology that extracts relevant information from images using purpose tailored image processing software. In the present work, the VSS2000 image analysis system from E+V Technology GmbH has been used in a large lamb abattoir to determine the value of carcasses in an objective, consistent and automated way. In this thesis results are reported of several experiments conducted within the framework of two UK-funded projects. The aims of the research were (i) the calibration and validation of the VIAtechnique for the evaluation of lamb carcasses under UK abattoir conditions, with the view to scientifically examine the accuracy and precision of information from the VIA systems as the basis for a value-based marketing system, (ii) to investigate the use of VIA measurements (weights of primal meat yields and carcass dimensional measurements) in sheep breeding programmes to improve carcass and meat quality and (iii) to evaluate the potential of this technology to reward increased carcass quality associated with the use of breeding strategies based on the inclusion of a quantitative trait locus (QTL) for improved muscularity. Accuracy, precision and consistency of The Meat and Livestock Commission (MLC) carcass classification scheme, currently used in UK abattoirs to evaluate carcass quality, was compared against the VIA system in the prediction of various primal joint weights. The results highlighted the advantage of the VIA system being on average 2% more accurate (measured as coefficient of determination: R2) and 12% more precise (measured as root meat squared error: RMSE) in predicting weight of primal meat yields (leg, chump, loin, breast and shoulder) of the lamb carcasses than the MLC carcass classification scheme. The genetic analysis of VIA-based predicted primal joint weights showed substantial additive genetic variance, suggesting that their use in sheep breeding programmes could improve carcass quality either by an improvement of conformation or by an increased weight of the most valuable primal cuts, without an increase in fatness. Favourable associations between VIA primal weights and performance traits indicate that selection based on VIA traits is possible without a negative effect on average daily gain, live weight and cold carcass weight. Although computer tomography (CT) and dissection found in related studies significant effects of a Texel muscling-QTL (TM-QTL) for increased muscularity in the loin region, in the present study they could not be identified by both, the current industry carcass evaluation system for conformation and fatness and the VIA system. A calibration of the VIA system against CT measurements resulted in improved VIA prediction equations for primal meat yields and also showed a moderate potential to estimate loin muscle traits measured by CT and to detect partially the effect of the TM-QTL on these traits. The results of the research demonstrated that VIA is a consistent method to measure carcass composition and that it improved the prediction (accuracy and precision) of primal meat yields compared to the present MLC scoring system. The estimated genetic parameters for VIA primal meat yields suggested that selection for increased lean meat yield from lamb carcass measured using VIA can contribute to genetic improvement of carcass quality without increasing carcass fatness. The results suggest that VIA technology installed in abattoirs could provide the means for the development of a value-based marketing system by paying for weights of the most valuable primal cuts measured using VIA.

Orientador: Eduardo Kokubun / Banca: Claudio Alexandre Gobatto / Banca: Dartagnan Pinto Guedes / Resumo: Baixa atividade física e aptidão cardiorrespiratória estão associadas diretamente a resistência a insulina que pode ser considerada como fator inicial para posteriores distúrbios, como aumento da adiposidade corporal, hipertensão, intolerância a glicose e dos teores de lipídios no sangue. Apesar destas anormalidades possuírem um componente herdado significativo, pouco se conhece sobre a relação entre as influências genéticas e ambientais para estas variáveis na população brasileira, muito menos em crianças e adolescentes. Portanto, o objetivo do presente estudo foi estabelecer a contribuição de fatores genéticos e ambientais na variância da aptidão cardiorrespiratória, atividade física e metabolismo de glicose em crianças e adolescentes gêmeos. Para realização do estudo gêmeos do mesmo sexo entre 11 e 18 anos matriculados em 19 escolas publicas e 5 particulares do município de Rio Claro- SP (6º ao 3º ano do ensino médio) foram cadastrados e convidados a participar. Aqueles que concordarem foram submetidos a medidas de pedometria para estimativa da AF diária, a um teste de esforço para determinação da capacidade aeróbia e a uma coleta de sangue periférico a fim de determinar a concentração de glicose e insulina, além de uma bateria de medidas antropométricas. A partir de um questionário aplicado aos pais e aos gêmeos, os pares foram classificados em monozigóticos (idênticos) e dizigóticos (fraternos). Para o tratamento estatístico inicialmente foi utilizada a estatística descritiva para agrupar os resultados, a análise de variância para estimar a similaridade dentro dos pares de gêmeos calculando a herdabilidade através da equação h2 = 2(rMZ - rDZ). Os resultados obtidos mostraram que as medidas antropométricas possuem um forte componente genético, principalmente para os meninos (40% a 100%), porém com moderado impacto do ambiente... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Low physical activity and cardiorespiratory fitness are associated directly with the insulin resistance that can be considered as initial factor for later disorders, such as increased adiposity, hypertension, impaired glucose tolerance and lipids in the blood. Despite these abnormalities have a significant inherited component, little is known about the relationship between genetic and environmental influences for these variables in our population, much less in children and adolescents. Therefore, the aim of this study was to establish the contribution of genetic and environmental variance in cardiorespiratory fitness, physical activity and glucose metabolism in children and adolescent twins. For the study of same-sex twins between 11 and 18 years enrolled in 19 public and 5 private schools in the municipality of Rio Claro-SP (6º to 3º year of high school) were registered and invited to participate. Those who agree underwent pedometrics measures to estimate daily AF, effort test to determine aerobic capacity and a collection of peripheral blood to determine the concentration of glucose and insulin, plus a battery of anthropometric measurements. From a questionnaire administered to parents and twins, the couple were classified as monozygotic (identical) and dizygotic (fraternal). The statistic was first used descriptive statistics to group the results, analysis of variance to estimate the similarity within pairs of twins calculated the heritability of the equation h2 = 2(rMZ - rDZ). The results showed that the anthropometric measures have a strong genetic component, especially for boys (40% to 100%), but with a moderate impact on the environment for girls (34% to 80%). Already AF weekly usual cardiorespiratory fitness and suffer a moderate impact of genetics for the boys (6% to 72%) and girls receiving a large influence of the environment (45% to 100%). The metabolism of glucose... (Complete abstract click electronic access below) / Mestre

Facial recognition methodologies, widely used today in everything from automatic passport controls at airports to unlocking devices on mobile phones, has developed greatly in recent years. The methodologies vary from feature based landmark comparisons in 2D and 3D, utilising Principal Component Analysis (PCA) to surface-based Iterative Closest Point Algorithm (ICP) analysis and a wide variety of techniques in between. The aim of all facial recognition software (FCS) is to find or match a target face with a reference face of a known individual from an existing database. FCS, however, faces many challenges including temporal variations due to development/ageing and variations in facial expression. To determine any quantifiable heritability of facial morphology using this resource, one has to look for faces with enough demonstrable similarities to predict a possible genetic link, instead of the ordinary matching of the same individual’s face in different instances. With the exception of identical twins, this means the introduction of many more variables into the equation of how to relate faces to each other. Variation due to both developmental and degenerative aging becomes a much greater issue than in previous matching situations, especially when comparing parents with children. Additionally, sexual dimorphism is encountered with cross gender relationships, for example, between mothers and sons. Non-inherited variables are also encountered such as BMI, facial disfigurement and the effects of dental work and tooth loss. For this study a Trimmed Iterative Closest Point Algorithm (TrICP) was applied to three-dimensional surfaces scans, created using a white light scanner and Flexscan 3D, of the faces of 41 families consisting of 139 individuals. The TrICP algorithm produced 7176 Mesh-to-mesh Values (MMV) for each of seven sections of the face (Whole face, Eyes, Nose, Mouth, Eyes-Nose, Eyes-Nose-Mouth, and Eyes-Nose- Mouth-Chin). Receiver Operated Characteristic (ROC) analysis was then conducted for each of the seven sections of the face within 11 predetermined categories of relationship, in order to assess the utility of the method for predicting familial relationships (sensitivity/specificity). Additionally, the MMVs of three single features, (eyes, nose and mouth) were combined to form four combination areas which were analysed within the same 11 relationship categories. Overall the relationship between sisters showed the most similarity across all areas of the face with the clear exception of the mouth. Where female to female comparison was conducted the mouth consistently negatively affected the results. The father-daughter relationship showed the least similarity overall and was only significant for three of the 11 portions of the face. In general, the combination of three single features achieved greater accuracy as shown by Areas Under the Curve (AUC) than all other portions of the face and single features were less predictive than the face as a whole.

The Dalmatian is affected by deafness more than any other breed of domestic dog, with 30% of the United States population suffering from unilateral or bilateral deafness. The genetic origin of deafness in the Dalmatian is unknown. The objective of this work was to identify, using linkage analysis, any chromosomal region(s) in which the gene(s) responsible for deafness in the Dalmatian may be located. To achieve this objective it was necessary to 1) develop multiplexed microsatellite markers for an efficient whole genome scan, 2) assemble a multigenerational Dalmatian kindred segregating deafness, 3) estimate the heritability of deafness and perform complex segregation analysis, and 4) perform linkage analysis of deafness, and other phenotypic traits, in the Dalmatian kindred. A set of 172 microsatellite markers, termed Minimal Screening Set 1 (MSS1), was characterized, prior to this work, for whole genome scans of the domestic dog. 155 of the MSS1 markers were multiplexed into 48 multiplex sets. Amplification of the multiplex sets was achieved using a single thermal cycling program. The markers were labeled with fluorescent dyes and optimized for resolution on an ABI 310 Genetic Analyzer or ABI 377 Sequencer. A kindred of 266 Dalmatians was assembled, of which 199 had been diagnosed using the brainstem auditory evoked response to determine auditory status. Of these, 74.4% (N = 148) had normal hearing, 18.1% (N = 36) were unilaterally deaf, and 7.5% (N = 15) were bilaterally deaf. A heritability of 0.73 was estimated considering deafness a dichotomous trait and 0.75 as a trichotomous trait. Although deafness in the Dalmatian is clearly heritable, the evidence for the presence of a major gene affecting the disorder was not persuasive. Dalmatians (N = 117) from the assembled kindred were genotyped for the MSS1 markers (149 were polymorphic). Linkage analysis was performed for deafness, eye color, and spot color. The maximum LOD scores for deafness were found with markers Cos15 on CFA17 (LOD = 1.69) and FH2585 on CFA28 (LOD = 1.34). No significant linkage was found with eye color. Significant linkage for spot color was found with marker FH2319 (LOD = 9.7) on CFA11.

The Dalmatian is affected by deafness more than any other breed of domestic dog, with 30% of the United States population suffering from unilateral or bilateral deafness. The genetic origin of deafness in the Dalmatian is unknown. The objective of this work was to identify, using linkage analysis, any chromosomal region(s) in which the gene(s) responsible for deafness in the Dalmatian may be located. To achieve this objective it was necessary to 1) develop multiplexed microsatellite markers for an efficient whole genome scan, 2) assemble a multigenerational Dalmatian kindred segregating deafness, 3) estimate the heritability of deafness and perform complex segregation analysis, and 4) perform linkage analysis of deafness, and other phenotypic traits, in the Dalmatian kindred. A set of 172 microsatellite markers, termed Minimal Screening Set 1 (MSS1), was characterized, prior to this work, for whole genome scans of the domestic dog. 155 of the MSS1 markers were multiplexed into 48 multiplex sets. Amplification of the multiplex sets was achieved using a single thermal cycling program. The markers were labeled with fluorescent dyes and optimized for resolution on an ABI 310 Genetic Analyzer or ABI 377 Sequencer. A kindred of 266 Dalmatians was assembled, of which 199 had been diagnosed using the brainstem auditory evoked response to determine auditory status. Of these, 74.4% (N = 148) had normal hearing, 18.1% (N = 36) were unilaterally deaf, and 7.5% (N = 15) were bilaterally deaf. A heritability of 0.73 was estimated considering deafness a dichotomous trait and 0.75 as a trichotomous trait. Although deafness in the Dalmatian is clearly heritable, the evidence for the presence of a major gene affecting the disorder was not persuasive. Dalmatians (N = 117) from the assembled kindred were genotyped for the MSS1 markers (149 were polymorphic). Linkage analysis was performed for deafness, eye color, and spot color. The maximum LOD scores for deafness were found with markers Cos15 on CFA17 (LOD = 1.69) and FH2585 on CFA28 (LOD = 1.34). No significant linkage was found with eye color. Significant linkage for spot color was found with marker FH2319 (LOD = 9.7) on CFA11.

Switchgrass (Panicum virgatum L.) is a warm-season perennial bunchgrass native to North America. In addition to its importance as a forage grass, it has promise as a biofuel crop. However, its use is limited because the grass is difficult to establish. Improving seedling vigor is one approach for improving establishment. The objectives of this study were to: 1) select for increased seedling mass through half-sib family selection; 2) calculate an estimate of heritability for seedling mass; and 3) determine the mode of pollination of switchgrass. One cycle of selection was completed using a half-sib methodology. Seedling mass was determined in a series of growth chamber studies. The seed was produced in different space planted field nurseries in the College Station, TX area. Mean seedling weight of the base population (C0) was 0.014 gm seedling-1, while the mean seedling weight from the C1 cycle of selection was 0.029 gm seedling-1. Unfortunately, bulked seed from the base population was old and did not germinate well. Therefore, a new base population was recreated, and the C0 seedlings from this population were heavier than the C1 seedlings, 0.020 and 0.016 gm seedling-1, respectively. The calculated heritability estimate was H2 = 0.6. Since the C0 and C1 nurseries were not grown on the same soil type, the lack of a positive response for seedling weight may be due to the different soil types. However, it may require another cycle of selection to determine if seedling mass can be positively impacted via half-sib selection. The mode of pollination of the species was determined by 1) observing pollen germination and tube growth in the pistils using fluorescent microscopy and 2) determining seed set with selfed plants. When self-pollinated, the pollen tubes never grew into the ovaries but when cross-pollinated the tubes readily grew to the micropyle. Also, when switchgrass plants were self-pollinated, viable seed were not produced. These findings indicate that switchgrass is highly self-sterile because a self-incompatibility mechanism prevents the pollen tubes from growing into the ovary of the same genotype.

The heritability of frontal EEG asymmetry, a potential endophenotype for depression, was investigated using a large set of adolescent and young adult twins. Additionally, the relationship between polymorphisms within three serotonin genes, two receptor genes and one transporter gene, and frontal EEG asymmetry was also investigated. Using Falconer's estimate, frontal EEG asymmetry was shown to be more heritable at lateral compared to medial cites across nearly all reference montages, and greater in males compared to females. Using structural equation modeling (SEM), and investigating both additive (ACE) and non-additive (ADE) models of genetic heritability, males displayed consistently greater additive genetic contributions to heritability, with greater lateral contributions than medial ones. For female twins pairs, the additive genetic model data provided a mixed picture, with more consistent heritability estimates observed at medial sites, but with larger estimates shown at lateral channels. For non-additive genetic models, male twin pairs demonstrated exclusive non-additive contributions to heritability across channels within AVG and CZ referenced data, with metrics in the CSD and LM montages more mixed between additive and non-additive contributions. However, consistent with Falconer's estimates, lateral channels were nearly always estimated to be more heritable than medial channels regardless of gender. These models demonstrate some combination of additive and non-additive contributions to the heritability of frontal EEG asymmetry, with the CSD and AVG montages showing greater lateral compared to medial heritability and CZ and LM montages showing mixed contributions with additive heritability at lateral channels and non-additive primarily at medial channels. The complex interaction of gender and reference montage on the heritability estimates highlight the subtle yet important roles of age, gender, and recording methodology when investigating proposed endophenotypes. However, no association was found between the proposed polymorphisms in serotonin receptor 1a, 2a or serotonin transporter genes and frontal EEG asymmetry. Although the results support modest heritability of frontal EEG asymmetry, the proposed link to underlying serotonergic genetic markers remains an open question. Overall, these results indicate that frontal asymmetry may be a useful endophenotype for depressive risk with modest heritability, but is one that taps more environmental risk.

Guayule (Parthenium argentatum Gray) is a rubber producing plant native to the Chihuahuan Desert, which is currently being investigated as a source of hypoallergenic latex. Current efforts are focusing on increasing latex/rubber production in the plant by either manipulating the rubber biosynthetic pathway, altering agronomic practices to take advantage of environmental conditions that increase rubber synthesis, or both. Field and greenhouse studies were conducted to more fully understand the effect of genetic and environmental manipulation on rubber production in guayule. Three guayule breeding lines were transformed in order to increase the availability of the initiators of rubber synthesis. The tissue-culture-derived transgenic plants and their seed-generated progeny were grown in separate field experiments. Transformation with the genes for the initiators of rubber synthesis did not increase rubber concentration or yield. Height and width had high heritability estimates in the transgenic progeny and were the traits most correlated with rubber yield, while rubber concentration was poorly correlated with height and width. Greenhouse studies were conducted to understand why water stress and low night temperatures increase rubber concentration. Water stress increased the contribution of the stems to the total rubber in the plant and increased the bark to wood ratio of the stem. Most rubber is accumulated in the stems and these two effects of water stress contributed to the increased rubber concentration in water-stressed plants. Low night temperature reduced plant growth without a decrease in carbon exchange. Allocation of carbon fixation products to rubber synthesis rather than growth, contribute to the high rubber production under low night temperatures. Contributions from both breeders and agronomists are needed to further improve guayule rubber/latex yield.