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.

No description available.

An inter-specific linkage map of a backcross (BC1) population derived from a cross between C. tinctorius and C. oxyacanthus was developed using primarily microsatellite markers. A composite map, which aligned the inter-specific (C. tinctorius x C. oxyacanthus) map with an intra-specific linkage map previously developed from an F2 population of C. tinctorius, was created to search for syntenic regions. Results indicate that despite low marker saturation, there is substantial colinearity between the two linkage maps, and one translocation or inversion event. Upon subsequent self-fertilization events, phenotypes of the inter-specific backcross population were characterized in both the field (BC1S2 generation) and growth chamber (BC1S2 and BC1S3 generations), and identified several lines of agronomic interest. Introgression analysis was performed (BC1S3 generation) to assess the level of integration of C. oxyacanthus DNA into the C. tinctorius genome, and results are suggestive of less inter-specific recombination than expected. / Plant Biology

Chickens exhibit considerable variation in morphological traits, with some populations having undergone intensive selection for uniqueness and uniformity. These populations are a source of experimental material to study the genetics of morphological traits. An important first step in such studies is to map the genes and the causal mutations that influence these traits. This research focused on gene mapping of 12 morphological traits including 4 intra-feather color patterns (Pattern, Columbian, Melanotic, and mottling), 2 inter-feather color patterns (Blue and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Ten backcross and/or F2 populations were designed to produce 1,880 individuals. An additional 339 DNA samples from other populations were included. The procedures for gene mapping were: 1. Pooling of DNA samples of backcross or F2 individuals based on their shared phenotypes, followed by microarray assays for genotyping, a cost-effective initial screen for the candidate genomic regions, 2. Linkage mapping to narrow the range of candidate genes, 3. Sequencing to identify the candidate mutations, 4. Diagnostic tests to confirm the association between the candidate mutation and the phenotype. Of the 12 traits studied, 3 (mottling, Blue, and chocolate) made progress into step 4. Complexities due to genomic context, modifiers, and environmental factors precluded step 4 for the first form of the feathered-leg gene, step 3 for the mapping of Melanotic, and earlier stages for the mapping of Pattern, Columbian, dark brown egg, vulture hock, and the second form of feathered-leg. These findings provide insights of the complexity of how background genome can influence the phenotypic expression of single genes (gene genetic background interactions) and an understanding of cellular and molecular mechanisms involved in morphogenesis. / Ph. D. / Chickens, one of the major protein sources in diets for humans, have a long cultural, sport and religious history since their initial domestication during the neolithic period. Darwin wrote of the importance of variation, which today we see for example in size of body, length of shank, number of toes, distribution of feathers, comb types, and plumage color patterns resulting in a plethora of breeds of chickens that differ in appearance. Some of these traits are "simply" inherited, which in the molecular era facilitates the study of relationships between DNA sequences and phenotypes. This dissertation focuses on identification of differences in DNA sequences among chickens responsible for these "simply" inherited phenotypes. The 12 phenotypes that were studied included 6 plumage color patterns (Pattern, Columbian, Melanotic, mottling, Blue, and chocolate), 2 forms of feathered-legs, polydactyly, dark brown eggshell color, vulture hock, and creeper. Designed were ten 3-generation populations to produce 1,880 chickens. An additional 339 DNA samples from other populations were included. Of the 12 phenotypes, 8 involved genotyping of pooled DNA samples, a cost-effective initial screen to target DNA sequences. This was followed by genotyping individual samples in 5 of the more promising studies. Candidate genes identified as associated with these 5 phenotypes underwent further studies which identified differences in DNA sequences associated with 4 of them (mottling, feathered-leg, Blue, and chocolate). These findings provide insights of how DNA sequences contribute to the phenotypic appearance of animals.

Since 2000, stripe rust, caused by the fungal pathogen (Puccinia striiformis Westend. f.sp. tritici Eriks.) has resulted in yield losses of wheat (Triticum aestivium L.) in the United States, that exceeded the combined losses of leaf rust (Puccinia triticina Eriks.) and stem rust (Puccinia gramins Pers.:Pers f. sp. Tritici Eriks. E. Henn.). The objectives of this study are to identify and map adult plant stripe rust resistance quantitative trait loci (QTL) in soft red winter (SRW) wheat that are effective against race PST-100, which is the predominant race of the pathogen in the eastern U.S. Adult plant resistance (APR) was characterized in the resistant wheat lines "USG 3555", VA00W-38, and "Coker 9553". Resistance in each of the lines was evaluated in populations derived from crosses with susceptible lines "Neuse", Pioneer Brand "26R46", and VA01W-21, respectively. On chromosomes 1AS, 4BL, and 7D of USG 3555, QTL were identified that explain on average 12.8, 73.0, and 13.6 percent of the variation for stripe rust infection type (IT), and 13.5, 72.3, and 10.5 percent of the variation for stripe rust severity. A QTL from Neuse was identified on 3A that on average explains 10.9 percent of the variation for IT and 13.0 percent of the variation for severity. On chromosomes 2AS and 4BL of VA00W-38, QTL were identified that on average explain 58.9 and 19.3 percent of the variation for stripe rust IT, and 51.9 and 12.1 percent of the variation for severity. On chromosomes 6BL and 3BL of Pioneer 26R46, QTL were identified that on average explain 8.9 and 2.1 percent of the variation for IT and 11.7 and 3.9 percent of the variation for severity. Coker 9553 possesses the QTL on 4BL that is also present in USG 3555 and VA00W-38. The SSR markers, Xgwm296, Xbarc163, and Xwmc756 were tightly linked to QTL on chromosomes 2AS, 4BL, and 6BL, respectively, and their use and development of additional diagnostic markers will facilitate the incorporation and pyramiding of stripe rust resistance QTL into SRW wheat lines via marker-assisted selection. / Ph. D.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

Bread wheat (Triticum aestivum L.) is an important cereal crop that provides over 20% of the global calorie intake. With the world population constantly growing, yield production must increase to meet food demands. Wheat plays a significant role on nutritional and food security especially in rural areas, however, bread wheat grains are known to be inherently deficient in micronutrients, particularly Fe and Zn, which makes them important biofortification targets. To date, South African wheat genotypes have not been explored for their nutritional micronutrient variation; hence there is a need to investigate the variation of nutritional quality and its association with yield components. Bread wheat cultivars, TugelaDN and Elands were used in this study based on their known high yield potential, resistance to insect pests and diseases as well as their good-to-excellent bread-making quality. The goal of this study was to use a doubled haploid (DH) mapping population, developed from a cross between cultivars Tugela-DN and Elands, to identify single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS)-based markers linked to high nutritional quality and yield-related traits. This was achieved by (i) determining grain micronutrient (Fe and Zn) concentration variation in 139 lines of a DH mapping population; (ii) evaluating the mapping population for yield-related traits; (iii) determining the correlation between micronutrient and yield-related traits among the genotypes; (iv) identifying SNP GBS-based markers linked to the high minerals and yield-related traits. The analysis of variance (ANOVA) showed significant (P<0.001) differences between genotypes for all traits evaluated. A wide variation was observed for both GFeC and GZnC. The statistical analysis revealed significant variation for Zn concentration (P < 0.001) among genotypes and not significant Fe concentration. DArT-Seq was used to genotype Tugela-DN and Elands cultivars and 139 DH genotypes. Quantitative trait loci (QTL) were detected using SNP GBS-based markers on chromosome 2D, 5B, 5D, 6A, and 6B for GZnC, and on chromosome 2D, 5B, 5D and 7D for GFeC. Most QTLs identified for GFeC and GZnC shared the genomic interval and some of them also co-located with few yield-related traits. The results of this study will contribute to breeding programmes to improve nutritional quality of bread wheat and food security of the country. / Life and Consumer Sciences

No description available.

Body colouration in tilapia is an important trait affecting consumer preference. In the Nile tilapia (Oreochromis niloticus), there are three colour variants which are normal (wild type), red and blond. In some countries, the red variant is important and reaches higher prices in the market. However, one major problem regarding red tilapia culture is their body colouration which is often associated with blotching (mainly black but also red) which is undesirable for the consumer. The overall aim of this work was to expand knowledge on various aspects of body colouration in Nile tilapia using genetic approaches. The results of this research are presented as four different manuscripts. The manuscripts (here referred as Papers) have either been published (Paper IV) or are to be submitted (Paper I, II and III) in relevant peer reviewed journals. Paper I and II investigated the inheritance of black blotching and other body colour components of the red body colour. Specifically, Paper I consisted of two preliminary trials (Trial 1 and 2), to look at the ontogeny of black blotching and body colour components over a period of six months. Trial 1 investigated the effect of tank background colour (light vs dark) on black blotching and other body colour components and was carried out using a fully inbred (all female) clonal red line. Trial 2 was carried out using mixed sex fish and was aimed to investigate the association of black blotching with the sex of the fish. The results from this study were used to guide the experiment described in Paper II. Sixteen red sires with various levels of black and red blotching were crossed to clonal females and the inheritance of blotching and other body colour components were investigated using parent-offspring regressions. The results showed no significant heritability for black blotching and body redness, but a significant correlation for body redness and black blotching was found in female offspring at one sampling point suggesting that attempts to increase body redness may increase black blotching, as had been hypothesized. Paper III was divided into two parts. The first objective was to map the blond locus onto the tilapia linkage map and the second was to investigate the interaction of the blond and red genes on black blotching using the blond-linked markers to distinguish different blond genotypes in heterozygous red fish (i.e. RrBlbl or Rrblbl). In the blond fish, the formation of melanin is almost blocked via much reduced melanophores and this feature may be able to help reducing the black blotching in red tilapia. Two intraspecific families (O. niloticus) and one interspecific family (O. aureus and O. niloticus) were used as mapping families and the blond locus was located in LG5. Four out of eight markers were successfully used to assess the interaction of blond on red blotched fish. The blond gene did not significantly reduce the area of blotching but did reduce the saturation (paler blotching) and enhanced the redness of body colour in the Rrblbl fish compared to the RrBlbl group. Finally, Paper IV aimed to find out the effect of male colouration on reproductive success in Nile tilapia. A choice of one wild type male and one red male was presented to red or wild type females and these fish were allowed to spawn under semi-natural spawning conditions. Eggs were collected from the female’s mouth after spawning and paternity was assessed using microsatellite genotyping and phenotype scoring. No significant departures from equal mating success were observed between the red and wild type males, however there was a significant difference between the red and wild type females in the frequency of secondary paternal contribution to egg batches. The results suggest that mating success of wild type and red tilapia is approximately equal. The results from this research help to broaden our knowledge and understanding on the aspects of body colouration in Nile tilapia and provide fundamental information for further research.