The region of eastern and southern Africa is very diverse in environments and agronomic practices. The region has one of the highest per capita consumption of maize (Zea mays. L), which is predominantly produced by smallholder farmers. Some important constraints facing these farmers include drought and low fertility. For decades, the International Center for Wheat and Maize Improvement (CIMMYT) has been involved in developing maize genotypes that have high grain yields and are tolerant to drought, low fertility and other important constraints. This germplasm is developed for wide adaptation. However, the development of superior germplasm is significantly affected by interaction between genotypes and the environment (i.e., genotype by environment interaction, GEI). To estimate and understand GEI maize genotypes are evaluated in a range of environments representing as much variability of the target growing areas as possible. Because of dwindling resources needed to conduct testing in the region, it may not be possible to test in all potential target areas. Therefore, a careful process of site selection for testing is essential to improve efficiencies in cultivar testing and deployment. The objective of this research was to characterize the maize testing locations of the eastern and southern Africa region. Historical data from CIMMYT Regional Trials from 1999 to 2003 was used to characterize the environments and estimate genetic parameters. Environmnent and GEI showed consistently high contributions to the total variation observed among genotypes for grain yield. Environment contributed over 60% and sometimes up to 85% of total variation observed. Sequential retrospective pattern analysis (Seqret) was conducted on the adjusted standardized grain yield. A total of 7 groups of environments were identified. Repeatabilites, a measure of the proportion of phenotypic variation that is due to genetic differences, was reduced under stress conditions. The relationship among traits showed that anthesis-silking interval (ASI) is an important selective trait, which can improve selection efficiency for grain yield under stress conditions. Stability analysis provided an opportunity to observe the response and adaptation of genotypes to a wide range of environments. Variety ZM621 was a stable and high yielding genotype.

Genotype by environment interactions (GxE) can form a potential source of inefficiency in animal breeding if selection decisions are made without accounting for their effects. The UK sheep industry covers an assorted range of farming systems and environments, with each flock having a unique and diverse set of resources and management styles. As a result, what may be the best performing genotype in one environment may not necessarily be the best performing genotype in another. This thesis reports on an investigation into the presence of GxE within the UK sheep industry. Pedigree and performance data, available from both hill and terminal sire breeds, were analysed using a number of different methods. When environments were defined as 2 individual hill farms, genetic correlations were estimated between farms, for a range of Scottish Blackface ewe and lamb traits. Those found to be significantly different from 1 (P<0.05), and therefore indicating the presence of GxE, were lamb birth weight and ewe premating weight. Following on from this, fine-scale information obtained by a farmer questionnaire, from 79 different terminal sire flocks was combined with nationally-available climatic data and analysed using principle coordinate analysis and non-hierarchical clustering methods. Three distinct clusters of farm environments were identified, with grazing type, climatic conditions and the use of vitamin/mineral supplements proving to be the most distinguishing factors. The presence of GxE was then investigated by estimating genetic correlations between the clusters identified, using performance data from Charollais lambs, for 21 week old weight (21WT), ultrasound back-fat (UFD) and muscle (UMD) depths. The correlations estimated between clusters 1 and 2, which had the highest number of common Charollais sires used, were all low and significantly different from 1 (P<0.05) suggesting GxE was evident in terms of both scaling and re-ranking. Finally, the relationship between the level of concentrate feed used in each flock, as obtained from the questionnaire, and performance and climatic information available nationally for all flocks was estimated using canonical correlation analysis. This allowed the development of a farm environment scale, applicable to all flocks within the UK, and the use of reaction norm analyses to investigate the presence of GxE. The reaction norm describes the phenotype of an individual animal as a function of the environment. The environment scale developed, using data from Texel flocks only, went from low performance averages and poorer weather conditions to high performance averages and improved weather conditions. The slope of the reaction norm measures the sensitivity of an animal to a change in the environment. For each trait, (21WT, UMD and UFD), evidence of both re-ranking and scaling of sires were observed. A number of “robust” sires, with a low level of environmental sensitivity, were also identified. The findings from these analyses may have implications for future sheep breeding programmes. Providing a suitable “measure of environment” can be agreed, the identification of sires that perform well in specific environments, as well as those who perform consistently across a number of different environments, would be beneficial for farmers. This would potentially remove any unwanted effects of GxE and allow the farmer to select animals best suited to their overall farm environment.

Post-harvest seedcoat darkening is a major problem in many pulses, including common bean (</i>Phaseolus vulgaris</i> L.). In some bean market classes, such as pinto, beans that have a darkened seedcoat are discounted in the market place as it is assumed that the beans are old and will be hard-to-cook (HTC). Pinto genotypes that darken more slowly than conventional pinto beans would be more desirable and have been identified in the bean breeding program at the University of Saskatchewan. <p>To study the slow-darkening trait, a quick, reliable, and inexpensive screening method that would not affect seed germination would be beneficial. Three potential protocols to accelerate seedcoat darkening were examined. The greenhouse protocol was conducted in the greenhouse by placing the bean seeds in polybags with a 1 cm2 piece of moistened felt. For the UV light protocol, bean seeds were placed 10 cm below an UV lamp which had a wavelength of 254 nm. For the cabinet protocol, bean seeds were placed in a cabinet set at 30¢ªC, 80% relative humidity, and full fluorescent lights. Color measurements were taken routinely using a Hunter Lab colorimeter. All three methods were successful in distinguishing darkening beans from slow-darkening beans although the UV light protocol was considered to be superior to the greenhouse and cabinet protocol as the UV light protocol was quick, consistent over years, and the most economical. Unlike the greenhouse and the cabinet protocols, the UV light protocol did not affect seed germination following accelerated darkening. <p>The stability of the slow-darkening trait was further investigated in genotype by environment (g x e) studies across different indoor and outdoor environments. In the g x e study across different field environments, it was found that prior to accelerated seedcoat darkening the g x e interaction was significant. Following accelerated seedcoat darkening, environment and genotype were both significant and g x e was not. The slow-darkening genotypes had lighter seedcoats than the darkening genotypes and those field sites that had more favorable weather had lighter seedcoats. For the g x e study across indoor and outdoor environments, when the genotypes were split into either slow-darkening or darkening, the g x e interaction was not significant and the slow-darkening genotypes had lighter seedcoats. <p>Genetic control of the slow darkening trait was determined. For crosses between slow-darkening genotypes and CDC Pintium, the F2 populations segregated 3 darkening : 1 slow-darkening with distinct bimodal distribution. This indicated that seedcoat darkening was controlled by a single gene and darkening was dominant over slow-darkening. For both slow-darkening by slow-darkening crosses, the F2 populations¡¯ L* values were unimodal, normal distributions, indicating there may be modifying genes for the slow-darkening trait.

Post-harvest seedcoat darkening is a major problem in many pulses, including common bean (</i>Phaseolus vulgaris</i> L.). In some bean market classes, such as pinto, beans that have a darkened seedcoat are discounted in the market place as it is assumed that the beans are old and will be hard-to-cook (HTC). Pinto genotypes that darken more slowly than conventional pinto beans would be more desirable and have been identified in the bean breeding program at the University of Saskatchewan. <p>To study the slow-darkening trait, a quick, reliable, and inexpensive screening method that would not affect seed germination would be beneficial. Three potential protocols to accelerate seedcoat darkening were examined. The greenhouse protocol was conducted in the greenhouse by placing the bean seeds in polybags with a 1 cm2 piece of moistened felt. For the UV light protocol, bean seeds were placed 10 cm below an UV lamp which had a wavelength of 254 nm. For the cabinet protocol, bean seeds were placed in a cabinet set at 30¢ªC, 80% relative humidity, and full fluorescent lights. Color measurements were taken routinely using a Hunter Lab colorimeter. All three methods were successful in distinguishing darkening beans from slow-darkening beans although the UV light protocol was considered to be superior to the greenhouse and cabinet protocol as the UV light protocol was quick, consistent over years, and the most economical. Unlike the greenhouse and the cabinet protocols, the UV light protocol did not affect seed germination following accelerated darkening. <p>The stability of the slow-darkening trait was further investigated in genotype by environment (g x e) studies across different indoor and outdoor environments. In the g x e study across different field environments, it was found that prior to accelerated seedcoat darkening the g x e interaction was significant. Following accelerated seedcoat darkening, environment and genotype were both significant and g x e was not. The slow-darkening genotypes had lighter seedcoats than the darkening genotypes and those field sites that had more favorable weather had lighter seedcoats. For the g x e study across indoor and outdoor environments, when the genotypes were split into either slow-darkening or darkening, the g x e interaction was not significant and the slow-darkening genotypes had lighter seedcoats. <p>Genetic control of the slow darkening trait was determined. For crosses between slow-darkening genotypes and CDC Pintium, the F2 populations segregated 3 darkening : 1 slow-darkening with distinct bimodal distribution. This indicated that seedcoat darkening was controlled by a single gene and darkening was dominant over slow-darkening. For both slow-darkening by slow-darkening crosses, the F2 populations¡¯ L* values were unimodal, normal distributions, indicating there may be modifying genes for the slow-darkening trait.

No description available.

Master of Science / Division of Biology / Michael A. Herman / Caenorhabditis elegans are free-living bacterivorous nematodes that naturally consume bacteria as food source. As an excellent genetic model, C. elegans has proven to be a successful system to study innate immune responses to human pathogens, which resulted in identification of many evolutionarily conserved defense pathways. Most of these studies examined innate immune pathway mutants in a single genetic background in response to monoculture of human pathogens that worms might not necessarily encounter in the wild. While this has led to the successful genetic dissection of these defense pathways, in order to fully understand their biological functions, the relevant ecological and evolutionary context needs to be taken into account. The bacterial environment C. elegans naturally encounter is likely to be highly heterogeneous. While many bacteria are mainly considered as dietary resource for worms, some could be potential pathogens. Worms thus constantly face the challenge to defend against the pathogens mixed in the food. Stenotrophomonas maltophilia is one such bacterium. S. maltophilia is a ubiquitous bacterium that has been found associated with native nematodes. But it can also cause nosocomial infections in human, especially in immune-compromised individuals. Due to its natural resistance to multiple antibiotics, it has been emerging as an opportunistic human pathogen. Our lab isolated a S. maltophilia strain, JCMS, which was found being pathogenic to C. elegans. Both C. elegans strains, N2 (Bristol, England) and CB4856 (Hawaii), showed decreased survivorship when fed on S. maltophilia JCMS compared to E. coli OP50. However, more interestingly, the specific responses towards bacteria are different between strains. This indicates that survivorship of C. elegans is determined by not only genetic and environmental factors, but also genotype by environment (G×E) interactions (GEI). In order to identify the underlying genetic basis, we mapped quantitative trait loci (QTL) in a N2×CB4856 recombinant inbred panel for the survivorship in response to E. coli OP50 and S. maltophilia JCMS.

Children who are more fearful and inhibited during early childhood are at greater risk for social problems (e.g., loneliness, social isolation) and clinically significant internalizing disorders during adolescence and adulthood (e.g., Rubin, Chen, McDougall, Bowker, & McKinnon, 1995; Williams et al., 2009). While the impact of fearful temperament on adjustment indices are regularly the focus of study, less well understood are biological and social processes that may affect the development of fearful temperament. The present study considered the role of the 5-HTTLPR polymorphism and parenting on change in fearful and inhibited temperamental characteristics during early childhood. The s/s genotype was expected to be associated with elevated and sustained levels of fearful temperament. Moreover, supportive parenting was expected to be associated with less fearful temperament while more harsh parenting would be associated with more fearful temperamental characteristics, especially for children with the s/s 5-HTTLPR genotype. Study hypotheses were tested using 165 families (i.e., biological mothers and fathers, 3-5 year old children) who participated in the Family Transitions Project (FTP: R. D. Conger & K. J. Conger, 2002). Children were genotyped using cheek swabs. Parents reported on children’s temperamental characteristics at ages 3, 4, and 5. Independent observations of mothers and fathers completing a puzzle with their 3 and 4 year old children were used to measure parenting. Results were partially supportive of predictions. Parenting interacted with the 5-HTTLPR genotype to predict trajectories of shyness and soothability dimensions of fearful temperament, but the pattern of findings varied for mothers and fathers. Results are discussed in terms of differential susceptibility and the conceptualization of risk and resilience.

Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.

In this thesis, the relationships between 17 traits including starch, fibre, culinary quality and agronomic parameters of potato were investigated. In two studies, 12 genotypes were grown at three locations in Ontario and 18 genotypes were grown at four locations in Manitoba, Ontario and New Brunswick. Genotype by environment interactions were significant for fibre and agronomic traits, except bake score and specific gravity. Correlations were found between some, but not all, starch, fibre and agronomic parameters. Several genotypes containing desirable starch, fibre and agronomic profiles with high stability were identified. Although no single genotype was superior in all analyzed traits, certain genotypes excelled in specific attributes. CV96044-3 had the best starch and fibre profile, but low yields compared to other cultivars. Three genotypes, CV96044-3, F04037 and Goldrush, may be useful parents in a breeding program to improve starch and fibre characteristics, producing cultivars containing all desirable traits. / AAFC, Agricultural Bioproducts Innovation Program, BioPotato Network

Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.