No description available.

Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr), is a major foliar disease in wheat. QTL mapping and meta-QTL analysis are effective methods to understand genetic basis of tan spot resistance, which can further facilitate resistant variety development. A number of QTL mapping studies have been conducted in hexaploid bread wheat whereas few mapping studies have been carried out in tetraploid wheat. Four interconnected tetraploid wheat mapping populations were evaluated for resistance to race 2 isolate 86-124. Twelve QTL were identified in three of the four mapping populations. To further extend understanding of tan spot resistance, meta-QTL analysis was conducted by using reported QTL from 14 previous QTL mapping studies. Three meta-QTL located on chromosomes 2A, 3B, and 5A showed large genetic effects in multiple populations and conferred resistance to multiple races. Integrating those race-nonspecific QTL could provide high and stable tan spot resistance in wheat.

No description available.

Wheat leaf rust, caused by Puccinia triticina Eriks. (= P. recondita Rob. Ex Desmaz. f. sp. tritici), is the most widespread disease of wheat worldwide and causes average annual yield losses of 5 to 25%. The emergence of a new predominant race of leaf rust, TDBG, in the 2004 Canadian virulence survey led to the identification of a second leaf rust resistance gene segregating in the Thatcher-Lr1 near-isogenic differential line, RL6003, which produced an unusual mesothetic infection type. This gene was subsequently isolated in a Thatcher background and temporarily designated as LrCen (Tc-LrCen). A cross was made with a susceptible parent (Tc-LrCen/ Sumai3-lr34) and a doubled haploid (DH) mapping population was generated from the hybrids. Parental lines and 180 double haploid (DH) individuals were phenotyped with race TDBG and a 1:1 ratio was observed in the DH population. Parental lines and 94 DH individuals were genotyped with the Illumina Infinium assay using a custom iSelect 90K wheat SNP array. Two-point linkage between the phenotype and polymorphic SNP markers identified linked markers. A BLAST search of linked SNP sequences was performed against the Wheat Survey Sequence providing a putative chromosomal location of 7AL. Subsequent mapping with microsatellite markers confirmed LrCen was located on the long arm of chromosome 7A flanked by gwm344 (9.5 cM) and cfa2240 (0.6 cM) as well as a group of co-segregating SNPs also at a genetic distance of 0.6 cM. When the SNP sequences were converted to the kompetitive allele specific PCR (KASP) markers they were found to be dominant, making them less useful for marker assisted selection in populations with heterozygotes. LrCen mapped distal to Lr20; the only other Lr gene previously identified on chromosome 7AL. / October 2016

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

Researchers interested in examining a given species of interest (or target species) that lacks complete sequence data can infer some knowledge of that species from one or more related species that has a complete set of data. To infer knowledge, it is desired to compare the available sequence data between the two species to find orthologs. However, without complete data sets, one cannot be certain of the validity of the detected orthologs. Using ortholog detection systems in concert with species’ mapping data, researchers can find regions of shared synteny, allowing for more certainty of the detected orthologs as well as allowing inference of some genetic information based on these regions of shared synteny. A pipeline software solution, Detection of Orthologs via Genetic Mapping Augmentation (DOGMA), was developed for this purpose. DOGMA’s functionality was tested using a target species, Phaseolus vulgaris, which only had partial sequence data available, and a closely related species, Glycine max, which has a fully se- quenced genome. On sequence similarity alone, which is the standard technique for detecting or- thologs, 205 potential orthologs were detected. DOGMA then filtered these results using mapping data from each species to determine that 121 of the 205 were quite likely true orthologs, referred to as putative orthologs, and the remaining 84 were categorized as reduced orthologs as there was either insufficient information present or were clearly outside a noted region of shared synteny. This provides evidence that DOGMA is capable of reducing false positives versus traditional techniques, such as applications based on Reciprocal Best BLAST Hits. If we interpret the output of the Or- tholuge program as the correct answer, DOGMA achieves 95% sensitivity. However, it is possible that some of the reduced orthologs classified by DOGMA are actually Ortholuge’s false positives, since DOGMA is using mapping data. To support this idea, we show DOGMA’s ability to detect false positives in the results of Ortholuge by artificially creating a paralog and removing the real ortholog. DOGMA properly classifies this data as opposed to Ortholuge.

Pre-harvest sprouting (PHS) in bread wheat (<i>Triticum aestivum</i> L.) is one of the major abiotic constraints influencing the production of high quality grain. The flour milled from sprouted wheat grains has increased Ñ-amylase activity as compared to non-sprouted grain. PHS negatively affects the properties of flour with deleterious effects on bread and noodle quality. White-grained wheat is generally more susceptible to PHS damage than red-grained wheat. The objectives of this study were to identify a suitable method for phenotyping PHS resistance and to identify PHS resistance genomic regions and markers that could be used for marker-assisted selection in wheat improvement programs. A doubled haploid (DH) mapping population from a cross between two white-grained spring wheat genotypes, Argent (non-dormant) and W98616 (dormant) was used in this study. Forty DH lines (20 dormant and 20 non-dormant) were evaluated for germination frequency, Falling Number, and Ñ-amylase activity in dry and water-imbibed seeds and spikes. The germination test was the most reliable method for measurement of PHS resistance, whereas the Falling Number and Ñ-amylase activity in dry harvested seeds could not be correlated to dormancy levels. However, a positive association (r = 0.60***) was detected between germination frequency and Ñ-amylase activity in imbibed seeds. To identify the genomic regions associated with PHS resistance, a genetic linkage map with a total genome coverage of 2,577 cM was developed. The map was constructed from 913 scored markers (356 SSR, 290 AFLP, 258 DArT and 9 EST) with an average marker density of 3.7 cM/marker. Five genomic regions on chromosomes 1A, 3A, 4A, 7A and 7D were associated with PHS resistance by interval mapping and all regions were contributed by the dormant parent W98616. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers, DuPw004, barc170 and wmc650, located under the major quantitative trait locus (QTL) on chromosome 4A. The SSR markers explained 60-75% of the total variation in germination frequency among different wheat genotypes. By using the DuPw004 marker in marker-assisted back crossing, the population size in the BC1F1 and BC2F1 generations were reduced by 41% and 59%, respectively. Thus, the 4A QTL markers have been proven useful for marker-assisted selection of PHS resistance for wheat improvement.

<p>In a mouse model of ischemic stroke, infarct volume is highly variable and strain dependent, but the natural genetic determinants responsible for this difference remain unknown. To identify genetic determinants regulating ischemic neuronal damage and to dissect apart the role of individual genes and physiological mechanisms in infarction in mice, we performed forward genetic mapping analyses of surgically induced cerebral infarct volume. We have identified multiple quantitative trait loci (QTL) that modulate infarct volume, with a major locus (<italic>Civq1 </italic>) on chromosome 7 accounting for over 50% of the variation, with a combined LOD score of 21.7. Measurement of infarct volume in chromosome substitution strains (CSS) and two additional intercrosses validate that <italic>Civq1</italic> on chromosome 7 is present in multiple inbred strains. Interval-specific ancestral SNP haplotype analysis for <italic>Civq1</italic> results in 5 candidate genes. A causative gene underlying <italic>Civq1</italic> may regulate collateral artery formation and genetic variations in the gene may result in the differential outcome of cerebral infarction. Additionally, we have identified a locus of large effect, <italic>Civq4</italic>, modulating infarct volume through a mechanism different from collateral circulation. In conclusion, the extent of ischemic tissue damage after distal middle cerebral artery occlusion (MCAO) in inbred strains of mice is regulated by genetic variation mapping to at least 4 different loci. A single locus on chromosome 7 determines the majority of the observed variation in the trait in multiple mouse strains. <italic>Civq1</italic> appears to be identical to <italic>Lsq1</italic>, a locus conferring limb salvage and reperfusion in hindlimb ischemia. The identification of the genes underlying these loci may uncover novel genetic and physiological pathways that modulate cerebral infarction and provide new targets for therapeutic intervention in ischemic stroke, and possibly other human vascular occlusive diseases.</p> / Dissertation

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.

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.