Osteoporosis is a disease that leads to decreased bone mineral density (BMD), an altered bone micro-architecture and fragile bones. The disease is highly heritable and numerous genes are thought to be involved, making it difficult to identify the causative genetic elements. Animal models, mainly intercrosses between laboratory strains of mice, have been succesfully used to map genes affecting these traits, but may not mirror the multifactorial genetic etiology of highly complex traits such as osteoporosis. Over the course of tens of thousand years humans have kept domestic animals whose phenotypic repertoires have been tailored to meet our needs. Wild-type red junglefowl (RJ) and domestic White Leghorn (WL) chicken differ for several bone traits. In this thesis Quantitative Trait Loci (QTL) mapping was used to trace the inheritance of bone traits in two separate intercrosses between RJ and WL. In these studies we identified several QTL that contributed to differences in BMD, bone size and biomechanical strength of bone. In a comparison of QTL identified in the two intercrosses it was observed that nine QTL had overlapping genomic positions, implicating these loci as important to bone phenotypic variation in chicken. In two separate studies, microarray technology was used to compare global gene expression in bone tissue from RJ and WL. In these studies, differential expression was observed for 779 and 560 genes, respectively. Many differentially expressed genes were co-localized with QTL, which implicates them as QTL-candidates. Results presented in this thesis link several genomic regions and genes to variation in bone traits. Increased knowledge about these identified genes and regions will contribute to a better understanding of the mechanisms underlying inter-individual differences in bone metabolism, both in chicken and man.

Sorghum (Sorghum bicolor (L). Moench) is used for human consumption in parts of Africa and Asia and as an animal feed mainly in the U.S. Though sorghum grain contains higher amounts of protein than other cereal grains such as wheat and corn, it is not as readily available for enzyme degradation in humans and animals. Protein body matrices called kafirins surround the starch granules in sorghum. Because the protein is less digestible, the starch is also less digestible for biofuel production. However variation for this trait exists and the line P850029 has a higher protein digestibility compared to other normal grain sorghum lines. This increase in digestibility of protein is due to the rearrangement of the kafirins in the prolamin protein bodies where, the γ-kafirins are rearranged in the seed endosperm and the amount of γ-kafirin in the grain is also reduced. The assay to phenotype the HD trait is time consuming and unpredictable. So identifying a quantitative trait loci (QTL) controlling the protein digestibility trait in sorghum would be beneficial in breeding. A recombinant inbred lines (RILs) population derived from P850029 x ‘Sureno’, were developed and used to map QTL regulating the protein digestibility trait. A single QTL was identified on chromosome 1 between Xtxp43 and Xtxp329. Validation of the identified QTL was done on heterogenous inbred families (HIFs). The results validate the same QTL identified on the RIL population on chromosome 1. Later the high digestibility trait (HD) was integrated with the Waxy trait in sorghum. The Waxy (WX) sorghums have starch completely in the form of amylopectin. The effect of endosperm type on ethanol yield and fermentation efficiencies was studied among HD, WX and HD-WX lines. The HD-WX lines fermented in a shorter time i.e. completed fermentation in 48 h and their fermentation efficiencies were also higher around 90%. The DDGS of the HD-WX lines also had lower residual starch content and 50% higher amino acid lysine content when compared to wildtype sorghum. Moreover, the relation between endosperm traits and grain yield in sorghum has not been fully explored. In this study, we compared the yield and yield components of four unique endosperm phenotypes, HD, WX, HD-WX and wildtype lines. A total of 100 F2:4 derived recombinant inbred lines population from a cross between Tx2907/P850029 were selected with 25 lines from each HD, WX, HD-WX and wild-type line were included in the study. These lines were grown in three replications in College Station and Halfway, Texas in a randomized complete block design. The results show that there are no significant differences in the grain yield.

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

<p>An unresolved problem in evolutionary biology is the nature of forces that maintain standing variation for quantitative traits. In this study we take advantage of newly developed genomic resources to understand how variation is maintained for flower size and fitness components in a natural population of annual Mimulus guttatus in the Oregon Cascades. Extensive inbreeding depression has been documented in this population for fertility and viability (Willis 1999 a,b), while previous biometric experiments have demonstrated that some of the floral variation in this site is due to common alleles perhaps maintained by balancing selection (Kelly and Willis 2001, Kelly 2003). Detailed comparison of the genetic architecture of these two categories of traits can clarify the relative contributions of mutation versus selection in maintaining trait variation within populations as well as the relevance of standing variation for trait diversification. </p><p>We present here the results from a large scale effort to dissect variation for flower size and a suite of genetically correlated traits. In 3 independent F2 mapping populations we mapped QTLs for floral morphology (flower width and length, pistil length, and stamen length), flowering time, and leaf size. We also mapped segregation distortion loci and QTLs for fertility components (pollen viability and seed set) that exhibit inbreeding depression. We compare the genetic architecture of these two sets of traits and find clear differences. Morphological traits and flowering time are polygenic and QTLs are generally additive. In contrast, deleterious QTLs associated with segregation distortion or fertility are partially recessive and include major QTLs. There is also little co-localization between morphological/flowering time and fertility QTLs. The analysis suggests that the genetic basis of segregating variation in morphology is fundamentally different from traits exhibiting inbreeding depression. Further, there is considerable variation in the extant of pleiotropy exhibited by QTLs for morphological traits as well as flowering time and we report that epistasis contributes to the standing variation for these traits. The analysis suggests that the standing variation is relevant for trait diversification and that the variation in floral allometry, plant form, and life history observed in the guttatus species complex could have readily evolved from the standing variation.</p> / Dissertation

No description available.

Lately the rate of genetic gain in most agronomic crop species has been reduced due to several factors that limit breeding efficiency and genetic gain. New genetic tools and more powerful statistical analyses provide an alternative approach to enhance genetic improvements through the identification of molecular markers linked to genomic regions or QTLs controlling quantitative traits. The main objective of this research was to identify genomic regions associated with enhanced agronomic performance in lines per se and hybrid combination in Sorghum bicolor (L.) Moench. A population composed of 187 F5:6 recombinant inbred lines (RIL) was derived from the cross of restorer lines RTx430 and RTx7000. Also, a testcross hybrid population (TCH) was developed by using each RIL as a pollinator onto ATx2752. A linkage map was constructed using 174 marker loci generated from AFLP and SSR primer combinations. These markers were assigned to 12 different linkage groups. The linkage map covers 1573 cM with marker loci spaced at an averaged 9.04 cM. In this study, 89 QTL that control variation in seven different morphological traits were identified in the recombinant inbred line population, while in the testcross hybrid population, 79 QTL were identified. These traits included grain yield, plant height, days to mid-anthesis, panicle number, panicle length, panicle exsertion and panicle weight. These putative QTL explained from 4 to 42% of the phenotypic variation observed for each trait. Many of the QTL were not consistent across populations and across environments. Nevertheless, a few key QTL were identified and the source of the positive additive genetics isolated. RTx7000 was consistently associated with better agronomic performance in RIL, while in testcrosses, RTx430 was. Some genomic regions from RTx7000 may be utilized to improve RTx430 as a line per se. However, it is very unlikely that such regions will have a positive effect on the combining ability of RTx430 since testcross results did not reveal any transgressive segregants from the RIL population.

A quantitative trait locus (QTL) is the location of a gene that affects a trait that is measured on a quantitative (linear) scale. Many important agricultural traits such as weight gain, milk fat content and intramuscular fat in cattle are quantitative traits. There is a need to integrate genomic sequence data with QTL data and to develop an analytical tool to visualize the data. Without integration, application of this data to agricultural enterprise productivity will be slow and inefficient. My thesis presents a web-accessible tool called the Bovine QTL Viewer developed to solve this problem. It consists of an integrated database of bovine QTL and the QTL viewer to view the QTL and their relative chromosomal position. This tool generates dynamic and interactive images and supports research in the field of genomics. For this tool, the data is modeled and the QTL viewer is developed based on the requirements and feedback of experts in the field of bovine genomics.

Melanin pigmentation is a complex trait governed by many genes. Variation in melanin pigmentation within, and between, populations makes it an important trait for assisting in physical identification of an individual in forensic investigations. Utilizing a training sample (n=789) comprised of various ethnicities and SNPs (75) in 24 genes previously implicated in human or animal pigmentation studies, I determined three-SNP multiple linear regression models that accounted for large proportions of pigmentation variation in skin (45.7%), eye color (76.4%), and hair [eumelanin-to-pheomelanin (43.2%) and total melanin (76.3%)], independent of ethnic origin. Rather than implementing stepwise regression, to ascertain the three-SNP predictive models, I devised an algorithm that is likely more robust than stepwise regression. The algorithm consisted of two steps: the first step reduced the pool of 75 SNPs to a pool of 40 by selection of SNPs that were significant (p<0.05) by one-way ANOVA; the second step enabled selection of SNPs for model incorporation based on their frequency in the best-fitted models of all possible combinations of three-SNP models (i.e., 40 choose 3).Prediction models were validated utilizing an independent cohort (n=242, test sample) that was very similar in ethnic composition to the training sample. Relative shrinkage was moderate for skin reflectance (23.4%), eye color (19.4%), and eumelanin-to-pheomelanin (37.3%) of hair, and largest for total melanin (67%) of hair. Additionally, we refined our model-building algorithm, enabling visual comparison of the frequency and co-linearity due to linkage or co-inheritance of SNPs of the best-fitted models. Application of our algorithm to the test sample yielded the same or similar models as the training sample. Two of the three SNPs composing the models were the same, with some variability in the third SNP of the model.

Behavioral differences among closely related species can result from adaptation via natural selection, and this is especially true of innately expressed behavior that shows evidence of complex design or function. A major goal of biologists is to understand how and why complex, adaptive behavior evolves. To this end, I investigated the evolution, ecology and genetics of innate burrowing differences in deer mice (genus Peromyscus). First, I show that several species of deer mice recapitulate their natural burrowing habits under laboratory conditions. When I compare these behaviors in a phylogenetic context, I find that burrowing is species-specific and the complex burrows of the oldfield mouse (P. polionotus) likely arose from simple behavior similar to that expressed by two closely related species. Second, I examine the influences of soil composition and genetics on the burrowing behavior of oldfield mice. Although burrow length variation is relatively constant in nature, burrow depth is negatively associated with the silt content of soils. To determine the genetic architecture of complex burrowing, I crossed the oldfield mouse and its sister species, the deer mouse (P. maniculatus), which builds a relatively simple burrow. My results suggest that complexity results from the integration of several component behaviors: the lengthening of entrance tunnels and the construction of an escape tunnel. Additionally, complex burrowing segregates as a dominant trait and I identify four quantitative trait loci that influence burrow variation--three affect tunnel length and a single locus influences escape tunnel construction. Last, I test whether Peromyscus burrow socially. Specifically, I measure burrows constructed by both pairs of mice and individuals across three Peromyscus species with different social systems. Only in the monogamous species (P. polionotus), which is also the only species that builds complex burrows, do pairs of mice coordinate their behavior to build longer burrows. This effect of pairing increases burrow length in same-sex pairs of unrelated individuals, but it is most pronounced in male-female pairs, suggesting that oldfield mice invest most heavily in burrows constructed for the purpose of reproduction.