Detecting both the majors genes that control the phenotypic mean and those controlling phenotypic variance has been raised in quantitative trait loci analysis. In order to mapping both kinds of genes, we applied the idea of the classic Haley-Knott regression to double generalized linear models. We performed both kinds of quantitative trait loci detection for a Red Jungle Fowl x White Leghorn F2 intercross using double generalized linear models. It is shown that double generalized linear model is a proper and efficient approach for localizing variance-controlling genes. We compared two models with or without fixed sex effect and prefer including the sex effect in order to reduce the residual variances. We found that different genes might take effect on the body weight at different time as the chicken grows.

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.

Co-variation in the genetic architecture, and co-localization of quantitative trait loci (QTL), for embryonic developmental rate and age at maturation in male rainbow trout (Oncorhynchus mykiss) was examined. Two lots (September and December spawning) of 2 x 5 (male x female) diallel crosses were performed and the resulting progeny were raised to maturity. Higher incidences of precocious maturation were observed in the September lot fish compared to December lot fish, which was uncoupled to developmental rate. However, precocious maturation and body size was higher in early hatching December lot fish. A genome scan was also completed across 4 linkage groups previously reported to possess embryonic developmental rate QTL and/or age at maturation QTL. No evidence of co-localization of QTL for the two traits was detected. However, the presence of QTL for embryonic developmental rate on RT-8 and RT-24 and one for age at maturation on RT-17 supports previous results.

The main goal of soybean breeding is to increase yield with improved seed quality characters. The objectives of this thesis were: i) to identify yield quantitative trait loci (QTL) across different mega-environments (ME); ii) to evaluate the relationship between yield and yield components and the co-localization of QTL; iii) to analyze environmental factors that affect QTL expression and identify different ME. Two Canadian x Chinese soybean populations were tested across Canada, northern United States and China. Yield QTL were identified at one, two and three hypothetical ME. Most of them were co-localized with agronomic trait QTL. These results give strong evidence that Canada, northern United States and China are different ME. Novel alleles from plant introductions can favorably contribute directly or indirectly to seed yield and the use of QTL would facilitate their introgression into breeding populations in both North America and China. / National Science and Engineering Research Council of Canada (NSERC) and the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)

I examined the influence of cyclic feeding regime on fillet yield and quality and their genetic architecture in rainbow trout (Oncorhynchus mykiss). Two lots of half-sib families produced in September and December were exposed to periods of reduced ration followed by increased ration. Fish fed cyclically reduced rations weighed less and had smaller fillets and body proportions relative to controls. They also had less estimated muscle and visceral lipid but also more proportional visceral mass. Lots and families within lots differed significantly for the majority of traits. Genotypic analysis with 23 microsatellite markers spanning 19 linkage groups detected QTL for all traits over multiple linkage groups that were not necessarily consistent between feeding regime and parental lot. Linkage groups RT-9 and 29 had the largest QTL effects for fillet composition traits and overall body size across the greatest number of parents sampled.

Soybean [Glycine max (L.) Merr.] seed is a major source of edible oil in the world and the main renewable raw material for biodiesel production in North America. Oil, which on average accounts for 20% of the soybean seed weight, is a complex quantitative trait controlled by many genes with mostly minor effects and influenced by environmental conditions. Because of its quantitative nature, the seed oil concentration may have an indirect effect on other economically important and agronomic traits such as seed yield and protein concentration. Increasing the oil concentration in soybean has been given more attention in recent years due to increasing demand for both edible oil and feedstock. To achieve this objective, it is important to understand the genetic control of the oil accumulation and its relationship with other traits. The main objectives of this thesis were to identify quantitative trait loci (QTL) and genes involved in oil biosynthesis in soybean. Two recombinant inbred line (RIL) populations were developed from crosses between moderately high oil soybean cultivars with high seed yield and protein concentration. In a population of 203 F3:6 RILs from a cross of ‘OAC Wallace’ and ‘OAC Glencoe’, a total of 11 genomic regions located on nine different chromosomes were identified as associated with oil concentration using multiple QTL mapping (MQM) and single-factor ANOVA. Among the 11 oil-associated QTL, four QTL were also validated in a population of 211 F3:5 RILs from a cross of ‘RCAT Angora’ and ‘OAC Wallace’. There were six oil QTL identified in this study that were co-localized with seed protein QTL and four for seed yield QTL. The oil-beneficial allele of the QTL tagged by marker Sat_020, on Chromosome 9, was positively associated with seed protein concentration. The oil-enhancing alleles at markers Satt001 and GmDGAT2B were positively correlated with seed yield. In this study, three sequence mutations were also discovered in either the coding or non-coding regions of three DGAT soybean genes (GmDGAT2B, GmDGAT2C, and GmDGAT1B) between ‘OAC Wallace’ and ‘OAC Glencoe’ that showed significant effects on some of the traits evaluated. GmDGAT2B showed significant association with seed oil and yield across different environments. The oil-favorable allele of the gene GmDGAT2B from ‘OAC Glencoe’ was also positively correlated with seed yield. GmDGAT2C was associated with seed yield, whereas GmDGAT1B showed significant effects on seed yield and protein concentration. However, neither of these two genes showed any association with seed oil. The yield-enhancing allele of GmDGAT1B showed negative association with protein concentration. The identification of oil QTL that were either positively associated with seed yield and protein or neutral to both traits and the development of new gene-based markers will facilitate marker-assisted breeding to develop high oil soybean cultivars with high yield and minimal effect on protein concentration. / Generous funding to conduct this research was provided by the Alternative Renewable Fuels II Program of the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) and by the Grain Farmers of Ontario.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2006. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 135-137).

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