Doctor of Philosophy / Department of Agronomy / Jianming Yu / Knowledge of the genetic bases of grain quality traits will complement plant breeding efforts to improve the end use value of sorghum (Sorghum bicolor (L.) Moench). The objective of the first experiment was to assess marker-trait associations for 10 grain quality traits through candidate gene association mapping on a diverse panel of 300 sorghum accessions. The 10 grain quality traits were measured using the single kernel characterization system (SKCS) and near-infrared reflectance spectroscopy (NIRS). The analysis of the accessions through 1,290 genome-wide single nucleotide polymorphisms (SNPs) separated the panel into five subpopulations that corresponded to three major sorghum races (durra, kafir, and caudatum), one intermediate race (guinea-caudatum), and one working group (zerazera/caudatum). Association analysis between 333 SNPs in candidate genes/loci and grain quality traits resulted in eight significant marker-trait associations. A SNP in starch synthase IIa (SSIIa) gene was associated with kernel hardness (KH) with a likelihood ratio–based R[superscript]2 (R[subscript]L[subscript]R[superscript]2) value of 0.08. SNPs in starch synthase (SSIIb) gene (R[subscript]L[subscript]R[superscript]2 = 0.10) and loci pSB1120 (R[subscript]L[subscript]R[superscript]2 = 0.09) was associated with starch content. Sorghum is a crop well adapted to the semi arid regions of the world and my harbor genes for drought tolerance. The objective of second experiment was to identify quantitative trait loci (QTLs) for yield potential and drought tolerance. From a cross between Tx436 (food grain type) and 00MN7645 (drought tolerant) 248 recombinant inbred lines (RILs) was developed. Multi-location trials were conducted in 8 environments to evaluate agronomic performance of the RILs under favorable and drought stress conditions. The 248 RILs and their parents were genotyped by genotyping-by-sequencing (GBS). A subset of 800 SNPs was used for linkage map construction and QTL detection. Composite interval mapping identified a major QTLs for grain yield in chromosome 8 and QTL for flowering time in chromosome 9 under favorable conditions. Three major QTLs were detected for grain yield in chromosomes 1, 6, and 8 and two flowering time QTLs on chromosome 1 under drought conditions. Six QTLs were identified for stay green: two on chromosome 4; one each on chromosome 5, 6, 7, and 10 under drought conditions.

Master of Science / Department of Agronomy / Allan Fritz / Fusarium head blight (FHB) is one of the most devastative diseases in wheat. Growing resistant cultivars is one of the most effective strategies to minimize the disease damage. Huangcandou (HCD) is a Chinese wheat landrace showing a high level of resistance to FHB spread within a spike (type II). To identify quantitative traits loci (QTL) for resistance in HCD, a population of 190 recombinant inbred lines (RILs) were developed from a cross between HCD and Jagger, a susceptible hard winter wheat (HWW) released in Kansas. The population was evaluated for type II resistance at the greenhouses of Kansas State University. After initial marker screening, 261 polymorphic simple-sequence repeats (SSR) between parents were used for analysis of the RIL population. Among three QTL identified, two from HCD were mapped on the short arms of chromosomes 3B (3BS) and 3A (3AS). The QTL on the distal end of 3BS showed a major effect on type II resistance in all three experiments. This QTL coincides with a previously reported Fhb1, and explained 28.3% of phenotypic variation. The QTL on 3AS explained 9.7% of phenotypic variation for mean PSS over three experiments. The third QTL from chromosome 2D of Jagger explained 6.5% of phenotypic variation. Allelic substitution using the closest marker to each QTL revealed that substitution of Jagger alleles of two QTL on 3AS and 3BS with those from HCD significantly reduced the PSS. HCD containing both QTL on 3AS and 3BS with a large effect on type II resistance can be an alternative source of FHB resistance for improving FHB type II resistance in wheat. Besides, meta-analyses were used to estimate 95% confidence intervals (CIs) of 24 mapped QTL in five previously mapped populations derived from Chinese landraces: Wangshuibai (WSB), Haiyanzhong (HYZ), Huangfangzhu (HFZ), Baishanyuehuang (BSYH) and Huangcandou (HCD). Nineteen QTL for FHB type II resistance were projected to 10 QTL clusters. Five QTL on chromosomes 1A, 5A, 7A, and 3BS (2) were identified as confirmed QTL that have stable and consistent effects on FHB resistance and markers in these meta-QTL regions should be useful for marker-assisted breeding.

Drosophila is involved in a wide range of interactions with parasites and pathogens (parasitoid wasps, bacteria, fungi, viruses). Drosophila hosts vary greatly at the species, population and individual level, in their response against such organisms, and much of this variation has a genetic basis. In this thesis I explored three aspects of this variation. First, using recombination mapping based on SNPs and a variation of bulk segregant analysis, I identified a QTL region on the right arm of the third chromosome of D. melanogaster associated with resistance to at least some of the parasitoid species / strains used in the experiments. The location of the QTL was further explored with deficiency complementation mapping and was narrowed down to the 96D1-97B1 region. The success of the deficiency mapping suggests that the resistant allele is not completely dominant. Second, I investigated patterns of molecular evolution in a set of immunity-related genes, using sequences from a D. melanogaster and a D. simulans population and a set of genes without known involvement in immunity for comparison. I found evidence that several of these genes have evolved under different selection pressure in each species, possibly indicating interactions with different parasites. The immunity genes tested appear to be evolving faster compared to non-immunity genes, supporting the idea that the immune system is evolving under strong selective pressure from parasites. Finally, in a D. melanogaster – sigma virus system, I measured genetic variation in the transmission of different virus genotypes, in different environments. There was poor correlation between temperatures, suggesting that environmental heterogeneity could constraint evolution of resistance (to virus transmission). The correlation between viral genotypes was also low, although relatively stronger for more closely phylogenetically related viral strains. Such interactions between host genotypes, virus genotypes and environmental conditions can maintain genetic variation in virus transmission.

Congenital heart disease is the most common form of birth defect, affecting approximately 1% of liveborn babies. Secundum atrial septal defect (ASD) is the second most common form of congenital heart disease (CHD). Most cases have no known cause. Chromosomal, syndromal and teratogenic causes account for a minority of cases. The hypothesis that mutations in the ASD genes NKX2-5 and GATA4 may cause apparently sporadic ASD was tested by sequencing them in unrelated probands with ASD. In this study, 1/102 individuals with ASD had an NKX2-5 mutation, and 1/129 had a deletion of the GATA4 gene. The cardiac transcription factor TBX20 interacts with other ASD genes but had not previously been associated with human disease. Of 352 individuals with CHD, including 175 with ASD, 2 individuals, each with a family history of CHD, had pathogenic mutations in TBX20. Phenotypes included ASD, VSD, valvular abnormalities and dilated cardiomyopathy. These studies of NKX2-5, GATA4 and TBX20 indicate that dominant ASD genes account for a small minority of cases of ASD, and emphasize the considerable genetic heterogeneity in dominant ASD (also caused by mutations in MYH6 and ACTC). A new syndrome of dominant ASD and the Marcus Gunn jaw winking phenomenon is reported. Linkage to known loci was excluded, extending this heterogeneity, but a whole genome scan did not identify a candidate locus for this disorder. Previous studies of inbred laboratory mice showed an association between patent foramen ovale (PFO) and measures of atrial septal morphology, particularly septum primum length (???flap valve length??? or FVL). In humans, PFO is associated with cryptogenic stroke and migraine, and is regarded as being in a pathological contiuum with ASD. Twelve inbred strains, including 129T2/SvEms and QSi5, were studied, with generation of [129T2/SvEms x QSi5] F1, F2 and F14 mice. Studies of atrial morphology in 3017 mice confirmed the relationship between FVL and PFO but revealed considerable complexity. An F2 mapping study identified 7 significant and 6 suggestive quantitative trait loci (QTL), affecting FVL and two other traits, foramen ovale width (FOW) and crescent width (CRW). Binary analysis of PFO supported four of these.

L'objectif de la thèse est la cartographie fine de QTL de fertilité femelle (FF) chez les races bovines Françaises : la Prim'Holstein (PH), la Normande (NO) et la Montbéliarde (MO). La première étape du projet consiste en une primo-localisation, sur un dispositif de 78 familles, de QTL de FF dans 12 régions génomiques. Six QTL de FF ont été détectés chez la PH et deux chez la NO. La deuxième étape consiste en une cartographie des QTL détectés sur les chromosomes BTA01, BTA02, BTA03 et BTA21 sur un échantillon de 41 familles des trois races. La localisation de ces QTL a été confirmée et précisée pour les QTL détectés sur les chromosomes BTA01 et BTA03. Le QTL sur le chromosome BTA03 a été finement cartographié en utilisant 437 SNP ce qui a permis de réduire son intervalle de localisation à quelques centimorgans et de sélectionner six gènes candidats. Les régions flanquant les exons de ces six gènes ont été séquencées sur quatre pools d'ADN d'individus de phénotypes extrêmes afin de trouver des polymorphismes intéressants dans les régions séquencées qui pourront ensuite être validés sur l'ensemble du dispositif. La mise à disposition récente d'une puce de 54000 SNP situés dans tout le génome bovin a changé la stratégie de cartographie de QTL de FF. Des gènes pouvant influencer la FF ont été sélectionnés et suggérés comme étant des gènes candidats positionnels et fonctionnels responsables de la dégradation de la FF chez les bovins laitiers.

<p>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.</p><p>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.</p><p>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. </p><p>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.</p><p>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. </p><p>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.</p>

The incidence of infectious diseases in livestock is a major concern for animal breeders as well as for consumers. As a alternative approach to the use of prophylactic measures or therapeutic agents, infectious diseases can be contended by increasing the disease resistance of animals by genetic improvement. Animals can be selected either on a measure of their resistance (indicator trait) or on the presence or absence of some specific resistance genes in their genotype. A prerequisite to the latter approach is the identification of the genes, or QTL for quantitative trait loci, underlying the trait of interest. By means of sophisticated statistical tools, the QTL mapping strategy combines the information from genetic markers and phenotypic values to dissect quantitative traits into their individual genetic components. Some of the methodological aspects of this strategy are studied in the present thesis in the context of disease resistance in livestock. Indicator traits of the resistance (such as bacteria or parasites counts) are not always satisfying the normality assumption underlying most of the QTL mapping methods. In this context, the ability of statistical tests to identify the underlying genes (i.e. the statistical power) can be considerably reduced. We show that compared to the use of a non-parametric method, the use of the least-squares-based parametric method on mathematically transformed phenotypes gives always the best results. In the context of high number of ties (equal values) as observed when measuring resistance to bacterial or parasitic diseases, the non-parametric test is a good alternative to this approach, as far as midranks are used for ties instead of random ranks. The efficiency of QTL mapping methods can also be increased by use of simple combinations of repeated measurements of the same trait. As a result of analyses performed on real data sets in chicken and sheep, we show that much attention should be paid to obtaining good quality measurements, reflecting at best differences in terms of resistance between animals, before performing a QTL search. The appropriate choice of resistance traits as well as of the time of their measurement are, beside the choice of the method and the quality of marker information, among the most preponderant factors to guarantee satisfying results.

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.

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.

No description available.