Upland cotton (Gossypium hirsutum) is cultivated in many contrasting production environments and is often subjected to a combination of abiotic stresses such as high temperature (heat) and water deficit (drought) stress. In the present dissertation, two recombinant inbred line populations were constructed from heat-tolerant and -susceptible parental lines and evaluated in multiple environments under the presence of two treatments, well-watered (heat stress) and water-limited in the presence of high temperature (combination of heat and drought stresses). We assessed two agronomic traits, seed cotton yield and lint yield, as well as six fiber traits, lint percent, micronaire, length, strength, uniformity, and elongation. Fiber traits had moderate to very high broad-sense heritabilities, while heritabilities of agronomic traits were lower for both populations in each irrigation regime. Correlations between traits were not effected by the irrigation regimes. A stability analysis across the range of environments tested demonstrated that high seed cotton yield performance and greater stability may play a role in tolerance to the combination of heat and drought stresses. Additionally, we constructed linkage maps for both recombinant inbred line populations and mapped QTL controlling variation all eight traits. A total of 138 QTL were identified across populations for the eight traits. Climate change in the form of rising temperatures and reduced water availability will increase the occurrence of the combination of heat and drought stresses in a farmer's field. Thus, current cotton breeding programs will need to focus on the development of cotton varieties tolerant to heat, drought, and the combination of the two.

The cactophilic Drosophila mojavensis species group living in the deserts and dry tropical forests of the Southwestern United States and Mexico provides a valuable system for studies in diversification and speciation. My dissertation addresses a variety of evolutionary genetic questions using this system.Rigorous studies of the relationships between host races of D. mojavensis and the relationships among the members of the species group (D. mojavensis, D. arizona, and D. navojoa) are lacking. I used mitochondrial CO1 sequence data to address the phylogenetics and population genetics of this species group (Appendix A). In this study I have found that the sister species D. mojavensis and D. arizonae share no mitochondrial haplotypes and thus show no evidence for recent introgression. I estimate the divergence time between D. mojavensis and D. arizonae to be between 0.66 and 0.99 million years ago. I performed additional population genetic analyses of these species to provide a basis for future hypothesis testing.In Appendix B, I report the first example of substantial intraspecific polymorphism for genetic factors contributing to hybrid male sterility. I show that the occurrence of hybrid male sterility in crosses between Drosophila mojavensis and its sister species, D. arizonae is controlled by factors present at different frequencies in different populations of D. mojavensis. In addition, I show that hybrid male sterility is a complex phenotype; some hybrid males with motile sperm still cannot sire offspring.The large degree of variation between isofemale lines in producing sterile hybrid sons suggests a complex genetic basis to hybrid male sterility warranting quantitative genetic analysis. Since the genes underlying hybrid male sterility in these species are not yet fixed, I am able to perform explicit genetic analysis of this reproductive isolating mechanism. In Appendix C, I present the results of mapping QTL for hybrid male sterility within species. The genetic architecture underlying hybrid male sterility when analyzed directly in the F1 is highly complex. Thus, hybrid male sterility arises as a complex trait in this system and we propose a drift-based model for the evolution of this phenotype.

Maize (Zea mays L.) inbred lines for hybrid breeding are usually developed within distinct heterotic groups. Breeders impose strong selection and maintain relatively small population sizes that are adapted to local environments, where the aim is to identify the desired recombinant types in the progeny. However, linkages between loci that control a trait may not permit breeders to obtain the desirable genetic recombination in these populations. It is hypothesized that different favorable and unfavorable alleles accumulate within the lines from different heterotic groups. In addition, within each inbred line, favourable alleles are linked with unfavourable alleles. Two early-season maize inbreds, CG60 (Iodent) and CG102 (Stiff Stalk), were used to develop a selfed recombinant inbred line (SRIL) and an intermated recombinant inbred line (IRIL) populations. Furthermore, individuals from within these populations were testcrossed with an inbred tester from the Lancaster Sure Crop heterotic group, to give rise to selfed SRIL testcross (SRIL-TC) and IRIL testcross (IRIL-TC) populations. The inbred and inbred-testcross populations were evaluated for trait variation and QTL mapping. The genetic variance was high in inbred populations (SRIL and IRIL) with transgressive segregation for flowering time and agronomic traits. However, genetic variances and correlation coefficients did not significantly differ between the inbred populations. Results suggested that pleiotropic genes were prevalent for these traits. In addition, linkages between the loci that control these traits were not common within parental genomes. Genetic linkage maps developed from the IRIL population were larger than those of the SRIL population. In the inbred-testcross populations (SRIL-TC and IRIL-TC) high means and high levels of trait variation were observed for all traits. The genetic variances and correlation coefficients of hybrid traits did not significantly differ between the SRIL-TC and IRIL-TC populations. Twenty five significant small to moderate QTL were detected, but only one, for grain moisture, was shared between inbred-testcross populations. Overall, the two inbred parents from different heterotic groups have many distinct alleles that contribute to traits. The recombinant inbred line populations had high means and variances for grain yield and related traits, which opens the possibility of utilizing these lines for hybrid breeding.

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)

Early flowering is important for maize adaptation to short-season growing environments. Dwarfism, by preventing lodging, has the potential to increase grain yield. This thesis investigates three novel mutants of maize. The early flowering mutant (EarlyF) sheds pollen 1 to 5 days earlier than wild type plants. EarlyF, was shorter and developed fewer leaves than wild type plants, suggesting an earlier transition from vegetative to reproductive development. A candidate QTL for EarlyF maps to bin 7.03. The two allelic dwarf mutants, brachytic3-1 and brachytic3-2, have short internodes at maturity, resulting in severely reduced plant height. Despite being short, days to pollen shed and number of leaves were unchanged for both brachytic3-1 and brachytic3-2. brachytic3 maps to a ~ 7 Megabase region of bin 5.04. This thesis characterizes EarlyF, br3-1 and br3-2 and sets the stage for positionally cloning the mutations causing these mutants and has potential to contribute to maize improvement.

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.

Wheat is infected by leaf rust disease (Puccinia triticina Eriks.) almost everywhere it is cultivated. The dynamic nature of P. triticina populations affects the effective life span of genes conferring leaf rust resistance (Lr genes). Genetic diversity and combinations of Lr genes should be used to achieve durable resistance. Toropi, a Brazilian wheat cultivar, has maintained leaf rust resistance since its release in 1965, suggesting that it is a good candidate for durable resistance. Two recessive complementary adult plant genes were previously described in Toropi. The objective of this study was to characterize and map the sources of resistance present in Toropi. Double haploid (DH) populations developed by crossing the susceptible leaf rust cultivar Thatcher with Toropi were analysed in Canada (Glenlea – 2010 and Portage La Prairie – 2011), New Zealand (Lincoln – 2010 and 2011) and in Brazil (Parana – 2011), and in greenhouse. The leaf rust reactions indicated the presence of at least four leaf rust resistance genes in Toropi: one seedling gene and three adult plant genes. The seedling resistance gene Trp-Se, responsible for immune response in New Zealand, was mapped on chromosome 3D. QTL analyses identified a QTL associated with leaf rust resistance (QLr.crc-5AL.1) on chromosome 5AL, which overlapped with a QTL for stripe rust (QStr.crc-5AL.1) in the same population. This gene, designated Trp1, is believed to be one of the two adult plant complementary partial resistance genes. The position of the Trp-2 is not confirmed yet. One minor race specific adult plant gene, temporarily designated Trp-3, was mapped on 4BL chromosome. The Lr genes in Toropi confer minor effects against leaf rust, except for Trp-Se, which conditioned immunity in New Zealand. However, when the Toropi Lr genes were combined an almost immune response resulted. Toropi had a very good leaf rust resistance in South and North America, and in New Zealand. The molecular markers identified during this project could facilitate the incorporation of the Toropi genes in new cultivars, helping to achieve more diverse and durable wheat.

USA soybean germplasm has a narrow genetic base that could be augmented by alleles from the wild species Glycine soja which positively influence agronomic traits. The objective of this study was to identify such alleles for yield and yield component QTL (quantitative trait loci). Two populations of 150 BC2F4 lines were generated from a mating between recurrent parent Glycine max 7499 and donor parent Glycine soja PI 245331 with one line in each population tracing back to the same BC2 plant. Population A was used for the QTL identification analysis and population B was used for the QTL verification test. The population A lines were genotyped at 120 SSR marker loci and one phenotype marker, covering a total map length of 1506 cM in 20 linkage groups with an average interval size of 12.5 cM. There were nine putative QTL significantly (Pandlt;0.0001, LODandgt;3.0) associated with yield and yield component traits across 3 environments. One QTL for seed yield was identified using the combined data; the G. soja allele at satt511 on LG-A1 was associated with increased seed yield (LOD=4.3) with an additive yield effect of 190 235 kg ha-1 depending on the QTL analysis method. The phenotypic variance accounted for by the QTL at satt511 was 12%. This QTL also provided a significant yield increase across environments in the validation population; lines that were homozygous for the G. soja allele at satt511 demonstrated a 6.3% (P=0.037) yield increase over lines that were homozygous for the G. max allele. One seed filling period QTL was identified at satt335 (LOD=4.0) on LG-F with an additive effect of +1 day. This QTL also provided a +1 day additive effect (LOD=3.3) on maturity. These results demonstrate the potential of using exotic germplasm to improve soybean yield.

Wheat is infected by leaf rust disease (Puccinia triticina Eriks.) almost everywhere it is cultivated. The dynamic nature of P. triticina populations affects the effective life span of genes conferring leaf rust resistance (Lr genes). Genetic diversity and combinations of Lr genes should be used to achieve durable resistance. Toropi, a Brazilian wheat cultivar, has maintained leaf rust resistance since its release in 1965, suggesting that it is a good candidate for durable resistance. Two recessive complementary adult plant genes were previously described in Toropi. The objective of this study was to characterize and map the sources of resistance present in Toropi. Double haploid (DH) populations developed by crossing the susceptible leaf rust cultivar Thatcher with Toropi were analysed in Canada (Glenlea – 2010 and Portage La Prairie – 2011), New Zealand (Lincoln – 2010 and 2011) and in Brazil (Parana – 2011), and in greenhouse. The leaf rust reactions indicated the presence of at least four leaf rust resistance genes in Toropi: one seedling gene and three adult plant genes. The seedling resistance gene Trp-Se, responsible for immune response in New Zealand, was mapped on chromosome 3D. QTL analyses identified a QTL associated with leaf rust resistance (QLr.crc-5AL.1) on chromosome 5AL, which overlapped with a QTL for stripe rust (QStr.crc-5AL.1) in the same population. This gene, designated Trp1, is believed to be one of the two adult plant complementary partial resistance genes. The position of the Trp-2 is not confirmed yet. One minor race specific adult plant gene, temporarily designated Trp-3, was mapped on 4BL chromosome. The Lr genes in Toropi confer minor effects against leaf rust, except for Trp-Se, which conditioned immunity in New Zealand. However, when the Toropi Lr genes were combined an almost immune response resulted. Toropi had a very good leaf rust resistance in South and North America, and in New Zealand. The molecular markers identified during this project could facilitate the incorporation of the Toropi genes in new cultivars, helping to achieve more diverse and durable wheat.

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