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Pinheiro, Cassia Renata. "Mapeamento de QTL (Quantitative Trait Loci) associados à resposta do maracujá-doce à bacteriose usando a abordagem de modelos mistos." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-23062015-161305/.
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O maracujazeiro-doce (Passiflora alata Curtis) é uma espécie de cruzamento e diploide (2n = 18) que vem se destacando no Brasil por alcançar melhores cotações no mercado de frutas. Apesar disso, é sensível às adversidades em monocultura, sendo extremamente afetada por variações climáticas, pragas e doenças, dentre elas, a bacteriose causada por Xanthomonas axonopodis pv. passiflorae. O patógeno é endêmico no país, apresentando considerável variabilidade genética nas populações naturais. O presente trabalho teve como objetivo contribuir para o melhoramento genético do maracujazeiro-doce por meio do mapeamento de QTL (Quantitative Trait Loci) relacionados à resistência à bacteriose de uma população F1 segregante, composta de 100 indivíduos e oriunda do cruzamento simples entre dois acessos não endogâmicos. A população foi mantida em casa de vegetação, em delineamento em blocos ao acaso, e foi inoculada com três isolados bacterianos, M129, PA8-2 e AP302, durante 2010, 2012 e 2013, respectivamente. Aos 14 dias após a inoculação, as folhas foram fotografadas e a partir das imagens digitalizadas foram mensuradas as áreas: sadia, de clorose, necrose e lesão (soma das áreas de clorose e necrose), além da área total da folha. Inicialmente, foi realizada uma análise exploratória dos dados e subsequentemente foram selecionados os caracteres área de necrose e de lesão foliar para fins de mapeamento de QTL. Para tanto foi usada uma estratégia desenvolvida para a detecção de QTL em F1 segregantes, com base em modelos mistos, considerando diferentes estruturas de variância e covariância, visando explicar os padrões de variação existentes. A herdabilidade variou de 14% a 64% para o carater necrose, e se manteve estável (28%) para o carater área de lesão, nos três anos de avaliação. Com base em um mapa de ligação integrado previamente construído, foi realizado o mapeamento de QTL por intervalo composto. Foram identificados 20 QTL, sendo 9 deles referentes à necrose e 11 referentes à lesão. Os efeitos individuais variaram de 0,2% a 15,7%, sendo que dois QTL de maior efeito (R² = 15,7%) foram identificados em resposta ao isolado PA8-2, um localizado no grupo de ligação III e o outro no IV do mapa genético integrado do maracujazeiro-doce. Essas informações, aliadas a outros estudos relacionados à produção de frutos, devem contribuir para o melhoramento do maracujazeiro-doce.The sweet passion fruit (Passiflora alata Curtis) is an outcrossing and diploid (2n = 18) species that is achieving a competitive advantage in the fruit markets in Brazil. Nevertheless, the crop is sensitive to monoculture, being greatly affected by weather changes, pests and diseases, among them the bacterial disease caused by Xanthomonas axonopodis pv. passiflorae. The pathogen is endemic in the country, with considerable genetic variability in natural populations. The present study aimed to contribute to genetic improvement of sweet passion fruit through QTL (Quantitative Trait Loci) mapping associated with bacterial resistance using a F1 segregating population containing 100 individuals, which resulted from a single cross between two outbred accessions. The population was kept in a greenhouse, arranged in a randomized block design, and innoculated with three bacterial isolates, M129, PA8-2 and AP302, during 2010, 2012 and 2013, respectively. At 14 days after inoculation, the inoculated leaves were photographed, and the following areas from the scanned images were measured: healthy, with chlorosis, necrosis and leaf lesion (sum of the areas with chlorosis and necrosis), in addition to the total area of the leaf. Initially all data were investigated trough an exploratory analysis and those relative to necrotic and leaf lesion areas were subsequently used for QTLmapping. For that we used a strategy developed for QTL detection in F1 segregating populations based on composite interval mapping and mixed models considering different variance and covariance structures in order to explain the existing patterns of variation. Heritabilities ranged from 14% to 64% for the trait necrosis, and remained stable (28%) for the trait leaf lesion for the three years of evaluation. Based on an integrated linkage map previously constructed, we performed a composite interval mapping of QTL. Twenty QTL were identified, 9 of them related to necrosis and 11 related to the leaf lesion. The individual effects ranged from 0,2% to 15,7%, and two large-effect QTL (R² = 15,7%) were identified in response to isolate PA8-2, one assigned to linkage group III and other to linkage group IV of the integrated genetic map of sweet passion fruit. This information combined with other studies related to fruit production may contribute to sweet passion fruit breeding.
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Sadeque, Abdus. "Genetic mapping of noodle quality characters and rust resistance in hexaploid wheat." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3795.
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Polyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.
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Sadeque, Abdus. "Genetic mapping of noodle quality characters and rust resistance in hexaploid wheat." University of Sydney, 2008. http://hdl.handle.net/2123/3795.
Full textAbstract:
Doctor of PhilosophyPolyphenol oxidase (PPO) catalyses undesirable darkening in wheat products such as Asian noodles. Genetic variation for PPO activity is characterized in bread wheat. Australian wheat breeding programmes recognize that reduced PPO activity is an important quality target. Despite this interest from breeders, no varieties possessing extremely low and null PPO activity exist. The development of null PPO wheat varieties is dependant on an understanding of the genetic control of the null phenotype. Knowledge of these factors will accelerate efforts to develop them. The inheritance of PPO activity was investigated in two populations that were derived from hybrids between a null PPO genotype and Australian wheat varieties Lang and QAlBis. Observed genetic ratios were consistent with two and three gene control, respectively in these populations. QTL mapping was performed in the QALBis x VAW08-A17 population. The Diversity Array Technology (DArT) approach was employed to genotype the QALBis x VAW08-A17 population. Three highly significant QTLs that control PPO activity were identified on chromosomes 2AL, 2BS and 2DL. Close associations between PPO activity and DArT marker loci wPt-7024, wPt-0094 and wPt-2544 were observed, respectively. Collectively, these loci explained 74% of the observed variation in PPO activity across seasons. Significant QTLs on chromosomes 1B and 3B were also identified that together explained an additional 17% of variation in PPO activity. The relationship between PPO activity and yellow alkaline noodles (YAN) colour stability parameters was investigated in a DM5637*B8 x H45 doubled haploid population. PPO activity and changes in YAN brightness (ΔL* 0-24h) and yellowness (Δb* 0-24h) in both seasons were analysed. Quantitative trait analyses of PPO activity, flour yellowness (b*) and YAN colour stability was also conducted in this population. QTL mapping of variation in PPO activity in the DM5637*B8 x H45 DH population identified a highly significant QTL on chromosome 2AL, which explained 52% of the observed variation across seasons. Regression analysis identified that wPt-7024 was highly significantly associated with PPO activity in this population. A highly significant association between this marker and PPO was also identified in the QALBis x VAW08-A17 population. Collectively, the three identified QTLs (on chromosomes 2AL, 7A and 7B) explained 71% of variation in PPO activity across seasons. A highly significant (P<0.001) QTL on chromosome 2B along with significant (P<0.01) QTLs on the chromosomes 1A, 3B, 4B and 5B were found to control flour yellowness. The QTLs on 2B, 4B and 5B were detected in both seasons analysed and accounted for 90% of variation in flour b* across seasons. The study on YAN colour stability located two highly significant (P<0.001) QTLs and two significant (P<0.01) QTLs that controlled the change in brightness of yellow alkaline noodle. The 2A QTL accounted for 64% of observed variation across seasons. It was in the same location as the PPO QTL and shared a common closest marker wPt-7024. Only one significant QTL for YAN a* (0-24h) was identified. It accounted for 12% of variation across seasons and was only detected in one season. One highly significant (P<0.001) QTL and two significant (P<0.01) QTLs were identified that controlled the change in yellowness of yellow alkaline noodle. The 2A QTL accounted for 68% of observed variation across seasons. The location of this QTL corresponded with that of 2A QTLs for PPO activity and L* of YAN in this study. Furthermore, wPt-7024 was also identified as the marker with the most significant association with L*. The identification of a correlation between the characters and a common location of a highly significant QTL for each of these characters indicates that it is likely that PPO activity is directly responsible for a large proportion of the changes in brightness and yellowness of YAN. QTLs for L* and b* of YAN were detected in a common location on chromosome 1A. However, no corresponding QTL was identified that controls PPO activity, highlighting the complexity of the relationship between these traits. Resistance to three rust pathogens (Puccinia graminis, Puccinia striiformis, and Puccinia triticina) was also investigated in the DM5637*B8 x H45 DH population because they are major yield limiting diseases in wheat. Disease response data at the seedling stage were converted to genotypic scores for rust genes Sr24/Lr24, Sr36, Lr13 and Yr7 to construct a genetic linkage map. No recombination was observed between rust resistance genes Sr36, Lr13 and Yr7 in this DH population. Therefore, these genes mapped in the same position on chromosome 2B. The Lr24/Sr24 locus was incorporated into the chromosome 3D map. Interval mapping analysis identified QTLs on chromosomes 2B, 3B, 4B and 5B that control adult plant resistance (APR) to stripe rust. Two QTLs on chromosomes 2B and 3D were identified that controlled APR to leaf rust in this DH population.
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Logeswaran, Sayanthan. "Mapping quantitative trait loci in microbial populations." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/4881.
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Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual the extreme progeny may be selected by multiple generations of asexual reproduction and selection. In this thesis I will analyse this method of measuring phenotype in asexual cross progeny. The aim is to examine the behaviour of marker allele frequency due to selection over many generations, and also to identify statistically significant changes in frequency in the selected population. I will show that stochasticity in marker frequency in the selected population arises due the finite initial population size. For Mendelian traits, the initial population size should be at least in the low to mid hundreds to avoid spurious changes in marker frequency in the selected population. For quantitative traits the length of time selection is applied for, as well as the initial population size, will affect the stochasticity in marker frequency. The longer selection is applied for, the more chance of spurious changes in marker frequency. Also for quantitative traits, I will show that the presence of epistasis can hinder changes in marker frequency at selected loci, and consequently make identification of selected loci more difficult. I also show that it is possible to detect epistasis from the marker frequency by identifying reversals in the direction of marker frequency change. Finally, I develop a maximum likelihood based statistical model that aims to identify significant changes in marker frequency in the selected population. I will show that the power of this statistical model is high for detecting large changes in marker frequency, but very low for detecting small changes in frequency.
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Joehanes, Roby. "Multiple-trait multiple-interval mapping of quantitative-trait loci." Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1605.
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Joehanes, Roby. "Generalized and multiple-trait extensions to Quantitative-Trait Locus mapping." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1919.
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Lu, Yue. "Genetic mapping of quantitative trait loci for slow-rusting traits in wheat." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/32179.
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Doctor of PhilosophyDepartment of Agronomy
Guihua Bai
Allan K. Fritz
Wheat leaf rust, caused by Puccinia triticina, is an important fungal disease worldwide. Growing resistant cultivars is an effective practice to reduce the losses caused by the disease, and using slow-rusting resistance genes can improve the durability of rust resistance in the cultivars. CI13227 is a winter wheat line that shows a high level of slow-rusting resistance to leaf rust and has been studied extensively. In this research, two recombinant inbreed line (RIL) populations derived from CI13227 x Suwon (104 RILs) and CI13227 x Everest (184 RILs) and one doubled haploid (DH) population derived from CI13227 x Lakin with 181 lines were used to identify quantitative trait loci (QTLs) for slow leaf rusting resistance. Each population and its parents were evaluated for slow-rusting traits in two greenhouse experiments. A selected set of 384 simple sequence repeat markers (SSRs), single nucleotide polymorphism markers (SNPs) derived from genotyping-by-sequencing (GBS-SNPs) or 90K-SNP chip (90K-SNPs) were analyzed in the three populations. Six QTLs for slow-rusting resistance, QLr.hwwgru-2DS, QLr.hwwgru-7BL, QLr.hwwgru-7AL, QLr.hwwgru-3B_1, QLr.hwwgru-3B_2, and QLr.hwwgru-1D were detected in the three populations with three stable QTLs, QLr.hwwgru-2DS, QLr.hwwgru-7BL and QLr.hwwgru-7AL. These were detected and validated by Kompetitive Allele-Specific PCR (KASP) markers converted from GBS-SNPs and 90K-SNPs in at least two populations. Another three QTLs were detected only in a single population, and either showed a minor effect or came from the susceptible parents. The KASP markers tightly linked to QLr.hwwgru-2DS (IWB34642, IWB8545 and GBS_snpj2228), QLr.hwwgru-7BL (GBS_snp1637 and IWB24039) and QLr.hwwgru-7AL (IWB73053 and IWB42182) are ready to be used in marker-assisted selection (MAS) to transfer these QTLs into wheat varieties to improve slow-rusting resistance in wheat.
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Lisec, Jan. "Identification and characterization of metabolic Quantitative Trait Loci (QTL) in Arabidopsis thaliana." Phd thesis, Universität Potsdam, 2008. http://opus.kobv.de/ubp/volltexte/2008/2590/.
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Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach.
This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL).
Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis.
The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.
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Huq, Md Nazmul. "The genetic basis of a domestication trait in the chicken: mapping quantitative trait loci for plumage colour." Thesis, Linköpings universitet, Biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-78393.
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Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.
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Podisi, Baitsi Kingsley. "Quantitative trait loci mapping of sexual maturity traits applied to chicken breeding." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5561.
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Many phenotypes are controlled by factors which include the genes, the environment, interactions between genes and interaction between the genotypes and the environment. Great strides have been made to understand how these various factors affect traits of agricultural, medical and environmental importance. The chicken is regarded as a model organism whose study would not only assist efforts towards increased agricultural productivity but also provide insight into the genetic determination of traits with potential application in understanding human health and disease. Detection of genomic regions or loci responsible for controlling quantitative traits (QTL) in poultry has focussed mainly on growth and production traits with limited information on reproductive traits. Most of the reported results have used additive-dominance models which are easy to implement because they ignore epistatic gene action despite indications that it may be important for traits with low heritability and high heterosis. The thesis presents results on the detection of loci and genetic mechanisms involved in sexual maturity traits through modelling both additive-dominance gene actions and epistasis. The study was conducted on an F2 broiler x White Leghorn layer cross for QTL detection for age, weight, abdominal fat, ovary weight, oviduct weight, comb weight, number of ovarian yellow follicles, a score for the persistence of the right oviduct and bone density. In addition, body weight QTL at 3, 6, 12, 24, 48 and 72 weeks of age, QTL for growth rate between the successive ages and QTL for the parameters of the growth curve were also detected. Most of the QTL for traits at sexual maturity acted additively. A few of the QTL explained a modest proportion of the phenotypic variation with most of the QTL explaining a small component of the cumulative proportion of the variation explained by the QTL. Body weight QTL were critical in determining the attainment of puberty. The broiler allele had positive effects on weight at first egg and negative effects on age at first egg. Most QTL affecting weight at first egg overlapped with QTL for age at first egg and for early growth rate (6-9 weeks) suggesting that growth rate QTL are intimately related to the onset of puberty. Specific QTL for early and adult growth were detected but most QTL had varying influence on growth throughout life. Chromosome 4 harboured most of QTL for the assessed traits which explained the highest proportion of the phenotypic variation in the traits confirming its critical role in influencing traits of economic importance. There was no evidence for epistasis for almost all the studied traits. Evidence for role of epistasis was significant for ovary weight and suggestive for both growth rate and abdominal fat.
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Ritchey, Brian Michael. "Quantitative Trait Loci Mapping Of Macrophage Atherogenic Phenotypes." Cleveland State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=csu1510080975338565.
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Lee, Yi-Chen. "MENDELIZING QUANTITATIVE TRAIT LOCI THAT UNDERLIE RESISTANCE TO SOYBEAN SUDDEN DEATH SYNDROME." OpenSIUC, 2016. https://opensiuc.lib.siu.edu/theses/1999.
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Soybean (Glycine max [L.] Merr.) cultivars differ in their resistance to sudden death syndrome (SDS). The syndrome is caused by root colonization by Fusarium virguliforme (ex. F. solani f. sp. glycines). Breeding for improve SDS response has proven challenging, possible due to interactions among the 18 known loci for resistance. Four loci for resistance to SDS (cqRfs to cqRfs3) were found clustered within 20 cM of the rhg1 locus underlying resistance to soybean cyst nematode (SCN) on chromosome 18. Another locus on chromosome 20 (cqRfs5) was reported to interact with this cluster. The aims of this study were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for resistance to SCN but still segregated at 2 of the 4 loci (cqRfs1 and cqRfs) for resistance to SDS on chromosome 18; to examine the interaction with the locus on chromosome 20; and to identify candidate regions underlying quantitative trait loci (QTL). Used were a near isogenic line population derived from residual heterozygosity in an F5:7 recombinant inbred line EF60 1-40; SDS response data from 2 locations and years; four microsatellite markers and six thousand SNP markers. Polymorphic regions were found from 2,788 to 8,938 Kbp on chromosome 18 and 33,100 to 34,943 Kbp on chromosome 20. Both regions were significantly (0.005 < P > 0.0001) associated with resistance to SDS. A fine map was constructed that Mendelized the three loci. Substitution maps suggested the two loci on chromosome 18 were actually 3 loci (cqRfs, cqRfs1 and cqRfs19). Candidate genes for cqRfs19 were identified in a small region of the genome sequence of soybean. An epistatic interaction was inferred where the allele of loci on chromosome 18 determined the value of the locus on chromosome 20. It was concluded that SDS loci are both complex and interacting which may explain the slow progress in breeding for resistance to SDS.
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Ishikawa, Akira. "Mapping an Overdominant Quantitative Trait Locus for Heterosis of Body Weight in Mice." Oxford University Press, 2009. http://hdl.handle.net/2237/20573.
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Banerjee, Samprit. "Bayesian genome-wide QTL mapping for multiple traits." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2009r/banerjee.pdf.
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Pita, Fabiano Veraldo da Costa. "Construction of the gametic covariance matrix for quantitative trait loci analyses in outbred populations." Universidade Federal de Viçosa, 2003. http://www.locus.ufv.br/handle/123456789/10501.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico
A aplicação de análises de “Quantitative Trait Loci” (QTL) em populações exogâmicas é desafiadora porque pressuposições simplificadoras não podem ser aplicadas (por exemplo, os alelos QTL não podem ser assumidos fixados em diferentes famílias, o número de alelos QTL segregantes não é conhecido a priori, não há desequilíbrio de ligação entre um dado alelo marcador e um dado alelo QTL). Quando o efeito genotípico do QTL é assumido aleatório no modelo de análise, a matriz de covariância gamética deve ser calculada para a realização das análises em populações exogâmicas. A acurácia dessa matriz é importante para a obtenção de estimativas confiáveis da posição ou efeito do QTL em análises de mapeamento, ou de valores genotípicos em avaliação genética assistida por marcadores. O objetivo do primeiro estudo foi avaliar diferente estratégias já implementadas em programas computacionais (SO- LAR, LOKI, ESIP e MATVEC) para calcular a matriz de coeficientes Idênticos por Descendência (IBD), que é necessária para o mapeamento de QTL em populações exogâmicas. SOLAR utiliza um método baseado em regressão linear, LOKI e ESIP são ambos baseados em “reverse peeling” e o amostrador implementado em MAT VEC amostra indicadores de segregação. Um pedigree com estrutura F2 típica foi simulado com uma família F2 pequena (2 indivíduos) ou grande (20 indivíduos) e marcadores flanqueadores localizados a 2 cM, 5 cM ou 10 cM de distância um do outro, com o QTL localizado no meio do intervalo. A habilidade dessas estratégias em lidar com informações de marcadores perdidas foi avaliada assumindo um dos pais da geração F2 com ou sem informação de marcador. SOLAR nao estimou os coeficientes IBD corretamente para a maior parte das situações simuladas, enquanto que LOKI apre- sentou problemas quando o tamanho da família F2 era grande. ESIP e o amostrador em MATVEC apresentaram bom desempenho em todas as situacões simuladas, com estimativas de coeficientes IBD próximas aos coeficientes verdadeiros. Portanto, ESIP e MATVEC são os softwares mais indicados quando analises genéticas são realizadas em pedigrees com estruturas complexas. O objetivo do segundo estudo foi avaliar o efeito da utilização de uma melhor aproximação da inversa da matriz de covariância gamética para a avaliação genética de grandes populações de animais domésticos. Algoritmos eficientes, baseados no rastreamento dos alelos QTL de um indivíduo em relação aos de seus avós (Probabilidade de Descendência de um QTL - PDQ), podem ser usados para construir a inversa da matriz de covariância gamética diretamente. Mas essa inversa é uma aproximação quando há informação incompleta de marcador. Também, o calculo exato de PDQºs torna-se difícil quando a informação de marcador é incompleta. Nesse estudo, a inversa da matriz de covariãncia gamética para uma pop- ulação exogãmica simulada foi calculada usando o algoritmo eficiente, mas as PDQ's foram calculadas usando um algoritmo Monte Carlo Cadeia de Markov (MCMC). Essa inversa foi utilizada para predizer o valor genético dos indivíduos através de BLUP assistido por marcadores (MABLUP). O efeito dos cálculos de PDQ usando o algoritmo MCMC sobre a acurãcia da MABLUP foi avaliado com base na resposta a seleção realizada, calculada para o pedigree simulado. Os resultados mostraram que quando as PDQ’S foram estimadas usando MCMC a perda em resposta devido ao uso da inversa aproximada pode ser reduzida em aproximadamente 20%, enquanto que em estudos anteriores essa redução foi de 50%. Ainda, quando quatro marcadores bi-alélicos foram utilizados a resposta para MABLUP foi maior e a perda em re- sposta devido a marcadores com informação perdida foi menor, quando comparadas a situação onde apenas dois marcadores bi-alélicos foram utilizados.
The application of Quantitative Trait Loci (QTL) analyses in outbred population is challenging because simplified assumptions do not hold for these populations (e.g., the QTL alleles cannot be assumed fixed in different families, the number of QTL alleles segregating is not known a priori, there is not gametic phase disequilibrium between a given genetic marker allele and a QTL allele). When the QTL genotypic effect is assumed random, the gametic covariance matrix must be calculated to per- form QTL analyses in outbred populations. The accuracy of this matrix is important to obtain reliable estimates of QTL position or effect when applying QTL mapping, or QTL genotypic values when applying Marker Assisted Genetic Evaluation. The objective of the first study was to evaluate the different strategies already imple- mented in softwares (SOLAR, LOKI, ESIP and MATVEC) to calculate the matrix of identical by descent (IBD) coefficients, which is required for QTL mapping anal- ysis in outbred populations. SOLAR uses a regression method, LOKI and ESIP are both based on reverse peeling, and the MAT VEC sampler samples segregation in- dicators. A typical F2 pedigree was simulated with a small (2 offspring) or a large (20 offspring) F2 family, and the flanking markers were simulated 2 CM, 5 CM, or 10 CM apart, with the QTL located in the middle. The ability of these strategies to deal with missing genetic marker information was evaluated assuming one of the F2 parents with or without marker information. SOLAR failed to estimate the correct coefficients at almost all situations simulated, while LOKI showed problems when a large family was present in the pedigree. ESIP and MATVEC sampler performed well at all situations, providing IBD coefficients closed to the true ones. Therefore, ESIP and MATVEC are more indicated when genetic analysis are carried out on complex pedigree structures. The objective of the second study was to evaluate the effect of using a better approximation of the inverse of the gametic covariance matrix on the genetic evaluation of large livestock populations. Efficient algorithms, based on trac- ing the QTL alleles of an individual to its grandmother or grandfather (probability of descent a QTL - PDQ’s), can be used to construct the inverse of the gametic covari- ance matrix directly. But this inverse is an approximation when incomplete marker information is available. Also, computing the exact PDQ’s becomes difficult when marker information is incomplete. In this study, the inverse of the gametic covariance matrix for a simulated outbred pedigree was calculated using the efficient algorithm, but the PDQ’s were calculated using a Markov chain Monte Carlo (MCMC) algo- rithm. This inverse was used to calculate the predicted genetic value of individuals through Marker Assisted Best Linear Unbiased Prediction (MABLUP). The effect of PDQ calculations using the MCMC algorithm on MABLUP accuracy was evaluated based on the realized response to selection for the simulated pedigree. The results showed that by estimating the PDQ’s by MCMC the loss in response because of using an approximate inverse could be reduced to about 20%, while in previous studies this reduction was of 50%. Further, response to MABLUP was greater when four bi-allelic markers were used, and the loss in response due to missing markers was smaller in the case with four markers compared to when only two bi-allelic markers were used.
Tese importada do Alexandria
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Brasier, Kyle Geoffrey. "Physiological Traits and Quantitative Trait Loci Associated with Nitrogen Use Efficiency in Soft Red Winter Wheat." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/89216.
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Development of winter wheat (Triticum aestivum L.) cultivars capable of more efficient uptake and utilization of applied nitrogen (N) has the potential to increase grower profitability and reduce negative environmental consequences associated with N lost from the plant-soil system. The first study sought to evaluate genotypic variation for N use efficiency (NUE) and identify lines consistently expressing high or low NUE under two or more N rates in a total of 51 N-environments. The results indicated that significant genotype by N rate interactions were frequently observed when trials utilized at least three N rates and identified wheat lines with high and stable yield potential that varied in performance under low N conditions. In addition, NUE was associated with above-ground biomass at physiological maturity were found to be both highly heritable across multiple N supplies. In the second study, two bi-parental mapping populations having a common low ('Yorktown') and two high (VA05W-151 and VA09W-52) NUE parents were characterized to dissect the genetics underlying N response. The populations were evaluated in eight N-environments and genotyped using single-nucleotide polymorphism data derived from a genotyping-by-sequencing protocol to identify quantitative trait loci (QTL) associated with high NUE. Six QTL for NUE were identified on chromosomes 1D, 2D, 4A, 6A, 7A, and 7D that were associated with N use efficiency. The QTL on 2D and 4A co-localized with known loci governing photoperiod sensitivity and resistance to Fusarium head blight (caused by the fungal pathogen Fusarium graminearum Schwabe), respectively. Three of the identified QTL (6A, 7A, and 7D) were associated with NUE in previous investigations, while the QTL on 1D was novel. The final experiment employed a small panel of soft red winter wheat lines to study the effects of photoperiod alleles on chromosome 1D (Ppd-D1) on yield-related traits under three or five N rates that were variably split over two growth stages in eight environments. The results validated the effect of a photoperiod sensitive allele (Ppd-D1b) that was associated with increased grain yield across N rates in half of the Virginia testing environments and under low N rates in all Ohio testing sites at the expense of grain N content. Yield advantages conferred by the Ppd-D1b allele were attributable to increased floret fertility and kernel number per spike. The findings from these studies have direct application for winter wheat breeding programs targeting NUE improvements.Doctor of Philosophy
Wheat (Triticum aestivum L.) products account for a significant percentage of the total dietary calories and protein consumed globally. To meet production demands, wheat requires efficient nitrogen (N) management to ensure continued grower profitability and to reduce negative environmental impacts of N lost from agricultural systems. This dissertation sought to evaluate variation among wheat lines for N use efficiency (NUE), assess the performance of wheat lines under multiple N supplies, validate traits that are associated with NUE, investigate the role of photoperiod sensitivity genes on N response, and identify regions of the wheat genome associated with high N use efficiency. These studies were conducted using panels of winter wheat lines grown under two or more N conditions over a combined 32 location-years. Results of Chapter I identified variation in cultivar response to N rates was more frequently observed when a greater number of N rates were used in trials of wheat N response. The first chapter also identified variation among wheat lines for NUE and identified lines that consistently produce high grain yields over N-location-years. In addition, above-ground biomass at physiological maturity was found to be strongly associated with grain yield under all N rates and was highly heritable in both studies. Chapter II utilized a combination of genetic and observable trait data to perform genetic analysis in two bi-parental populations grown in eight Nlocation-years. The study identified reproducible and significant genetic markers associated with NUE for application in wheat breeding programs. Upon analysis of photoperiod sensitive versus insensitive wheat lines in Chapter III, photoperiod sensitive wheat lines had a significant yield advantage under N-limited conditions in Ohio and across N treatments in half of the Virginia testing location-years. This resulted from an increased number of kernels per spike and fertile florets in photoperiod sensitive wheat lines. Results from this dissertation suggest that active breeding and selection for N response may be achieved through the employment of high NUE genes and the continued identification of adapted high NUE wheat parental lines.
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Moran, Maradiaga Jorge Luis. "Quantitative trait loci affecting the agronomic performance of a Sorghum bicolor (L.) Moench recombinant inbred restorer line population." Diss., Texas A&M University, 2003. http://hdl.handle.net/1969/465.
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Wang, Ziyi. "QTL mapping for Caenorhabditis elegans survivorship in response to Escherichia coli and Stenotrophomonas maltophilia." Kansas State University, 2016. http://hdl.handle.net/2097/32624.
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Master of ScienceDivision 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.
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Steinhoff, Jana [Verfasser], and Jochen C. [Akademischer Betreuer] Reif. "Quantitative trait loci (QTL) mapping in multi-line crosses of European maize / Jana Steinhoff. Betreuer: Jochen C. Reif." Hohenheim : Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim, 2013. http://d-nb.info/1044645253/34.
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O'Shea, Marie. "Fine mapping of quantitative trait loci (QTL) and identification of candidate genes for prion disease incubation in mice." Thesis, University College London (University of London), 2008. http://discovery.ucl.ac.uk/1446322/.
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Prion diseases are progressive neurodegenerative diseases which show characteristic prolonged incubation periods. Polymorphisms in the prion protein gene are known to influence incubation time but additional genetic loci have also been identified by quantitative trait locus mapping studies in mice. Genome-wide screening approaches using two-way crosses have identified broad regions of linkage with large confidence intervals on several mouse chromosomes. In order to reduce and fine map the regions, a genetically diverse heterogenous stock (HS) of mice has been utilized which provides a powerful tool for fine mapping at centimorgan (cM) intervals. Linkage analysis in the HS mice identified small (l-2cM), highly significant regions of linkage on chromosomes 8, 9 and 11. The predicted regulatory regions and entire mRNA transcript of candidate genes within these regions have been sequenced to identify polymorphisms between the parental strains of the cross. This variation may be indicative of genetic differences that influence prion disease incubation time. Linkage analysis was used to determine if identified polymorphisms correlated with the strain effects observed in the cross and resulting candidates were genotyped in the cross to assess association with incubation time. The expression of candidate genes was quantified in the parental strains of the cross to assess the regulatory control of polymorphisms identified. Attention on chromosome 11 has focused on Trans-acting Transcription Factor 6 (Sp6) and Monocyte Chemoattractant Protein 1 (Mcp-1), the latter having been assessed in a mouse model. A small group of genes on chromosome 8 have also been implicated as promising candidates. The identification of modifier genes influencing susceptibility to prion diseases will provide further insights into the pathogenesis of prion disease and identify ligands and pathways for the design of rational therapeutics.
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Clinesmith, Marshall. "Genetic mapping of QTL for Fusarium head blight resistance in winter wheat cultivars Art and Everest." Thesis, Kansas State University, 2016. http://hdl.handle.net/2097/32563.
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Master of ScienceAgronomy
Allan Fritz
Fusarium head blight (FHB) is a fungal disease, mostly commonly associated with F. graminearum, which affects cereal crops such as wheat resulting in substantial yield losses and reductions in grain quality. The onset of the disease can occur rapidly when warm, wet or humid weather coincides with flowering in the spring. The pathogen also produces mycotoxins such as deoxynivalenol (DON) that accumulate in the grain and can be toxic to humans and animals. This results in additional economic losses as contaminated grain must be discarded or blended to reduce the amount of toxin in order to meet federal regulatory limits. Development and deployment of resistant cultivars has proved to be an effective method to combat the disease, and many resistant sources have been reported in the literature with the majority of major resistance coming from Chinese landraces. Transferring resistance from these sources into cultivars adapted to the U.S. has been a slow process due to linkage of FHB resistance genes with poor agronomic traits. Therefore, it is important for breeders to search for sources of resistance in native material adapted to their local conditions. In this study, we aimed to identify quantitative trait loci (QTL) for resistance to spread of FHB within the head (Type II resistance), accumulation of DON toxin in grain (Type III resistance), and resistance to kernel infection (Type IV resistance). Plant material consisted of 148 doubled haploid (DH) lines from a cross between the two moderately resistant hard red winter wheat (HRWW) cultivars Art and Everest. The study was conducted for two years using a point inoculation technique in a greenhouse in Manhattan, KS. Three QTL conferring resistance to FHB traits were detected on chromosomes 2D, 4B, and 4D. The QTL on chromosomes 4B and 4D overlapped with the major height genes Rht1 and Rht2, respectively. Plant height has shown previous associations with FHB, though the underlying cause of these associations is not well understood. The majority of results have reported increased susceptibility associated with shorter plant types; however, in this study, the haplotype analysis for the Rht-B1 and Rht-D1 loci showed an association between the dwarfing alleles and increased resistance to FHB. This suggests either pleiotropic effects of these loci or perhaps linkage with nearby genes for FHB resistance. Markers close to the peaks of the FHB resistance QTL have the potential for Kompetitive Allele Specific PCR (KASP) marker development and subsequent use in marker assisted selection (MAS) to help improve overall FHB resistance within breeding programs.
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Wittwer, Catherine Elisabeth. "Mapping quantitative trait loci (QTL) and comparative analysis of positional candidate genes for osteochondrosis in South German Coldblood horses." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=983637571.
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Liu, Hang. "QTL (quantitative trait loci) mapping for nitrogen use efficiency (NUE) based on a high–density consensus map of wheat." Thesis, Liu, Hang (2022) QTL (quantitative trait loci) mapping for nitrogen use efficiency (NUE) based on a high–density consensus map of wheat. PhD thesis, Murdoch University, 2022. https://researchrepository.murdoch.edu.au/id/eprint/66033/.
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Nitrogen is not only an essential element for wheat growth, but also a major determinant for wheat yield and protein quality. Nitrogen use efficiency (NUE) is therefore a key factor in determining profit in wheat production, either through enhancing grain yields (GY) and grain protein content (GPC) or reducing fertilizer costs. NUE is defined as GY*GPC/N supply so both GY and GPC are targeted. To date, QTL mapping on NUE related traits has been using recombined inbred lines (RIL) and double haploid (DH) populations grown at different nitrogen levels. As most of the QTL mapping has been based on a single mapping population with limited genetic background, genetic regions identified are less abundant and of lower effects, whereas consensus maps generated from multiple genetic populations with wider genetic coverage are more efficient in QTL mapping. The Murdoch University wheat research group has developed six DH populations and using 90K SNP array analysis, a high–density consensus map was constructed containing 11,643 markers. Combined with two–year field trials, six major QTL clusters for NUE and related traits were detected on six chromosomes, explaining 4.7 – 20.8% of the phenotypic variances across environments. Two major QTL clusters (CI–2D and CI–4D) showed favourable relationships between GY and GPC, suggesting it is feasible to improve the grain yield and NUE simultaneously. A total of 176 potential candidate genes were associated with these six major QTL clusters. The use of consensus mapping based on six genetic populations varying in NUE is unprecedented, allowing identification and validation of candidate genes, target alleles and gene–based SNP haplotypes in the QTL clusters which can be used to accelerate the improvement of NUE in wheat breeding programs.
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Yu, Jianbin. "Identification of new sources and mapping of QTL for FHB resistance in Asian wheat Germplasm." Diss., Manhattan, Kan. : Kansas State University, 2007. http://hdl.handle.net/2097/258.
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Saunders, Garret. "Family-Wise Error Rate Control in Quantitative Trait Loci (QTL) Mapping and Gene Ontology Graphs with Remarks on Family Selection." DigitalCommons@USU, 2014. https://digitalcommons.usu.edu/etd/2164.
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The main aim of this dissertation is to meet real needs of practitioners in multiple hypothesis testing. The issue of multiplicity has become a signicant concern in most elds of research as computational abilities have increased, allowing for the simultaneous testing of many (thousands or millions) statistical hypothesis tests. While many error rates have been dened to address this issue of multiplicity, this work considers only the most natural generalization of the Type I Error rate to multiple tests, the family-wise error rate (FWER). Much work has already been done to establish powerful yet general methods which control the FWER under arbitrary dependencies among tests. This work both introduces these methods and expands upon them as is detailed through its four main chapters. Chapter 1 contains general introductions and preliminaries important to the remainder of the work, particularly a previously published graphical weighted Bonferroni multiplicity adjustment. Chapter 2 then applies the principles introduced in Chapter 1 to achieve a substantial computational improvement to an existing FWER controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs. This improvement to the Focus Level procedure, which we call the Short Focus Level procedure, is achieved by extending the reach of graphical weighted Bonferroni testing to closed testing situations where restricted hypotheses are present. This is accomplished through Theorem 1 of Chapter 2. As a result of the improvement, the full top-down approach to the Focus Level procedure can now be performed, overcoming a signicant disadvantage of the otherwise powerful approach to multiple testing. Chapter 3 presents a solution to a multiple testing diculty within quantitative trait loci (QTL) mapping in natural populations for QTL LD (linkage disequilibrium) mapping models. Such models apply a two-hypothesis framework to the testing of thousands of genetic markers across the genome in search of QTL underlying a quantitative trait of interest. Inherent to the model is an unidentiability issue where a parameter of interest is identiable only under the alternative hypothesis. Through a second application of graphical weighted Bonferroni methods we show how the multiplicity can be accounted for while simultaneously accounting for the required logical structuring of the testing such that identiability is preserved. Finally, Chapter 4 details some of the diculties associated with the distributional assumptions for the test statistics of the two hypotheses of the LDbased QTL mapping framework. A novel bivariate testing strategy is proposed for these test statistics in order to overcome these distributional diculties while preserving power in the multiplicity correction by reducing the number of tests performed. Chapter 5 concludes the work with a summary of the main contributions and future research goals aimed at continual improvement to the multiple testing issues inherent to both the elds of genetics and genomics.
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Saunders, Garrett. "Family-Wise Error Rate Control in Quantitative Trait Loci (QTL) Mapping and Gene Ontology Graphs with Remarks on Family Selection." DigitalCommons@USU, 2014. https://digitalcommons.usu.edu/etd/7021.
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One of the great aims of statistics, the science of collecting, analyzing, and interpreting data, is to protect against the probability of falsely rejecting an accepted claim, or hypothesis, given observed data stemming from some experiment. This is generally known as protecting against a Type I Error, or controlling the Type I Error rate. The extension of this protection against Type I Errors to the situation where thousands upon thousands of hypotheses are examined simultaneously is known as multiple hypothesis testing. This dissertation presents an improvement to an existing multiple hypothesis testing approach, the Focus Level method, specific to gene set testing (a branch of genomics) on Gene Ontology graphs. This improvement resolves a long standing computational difficulty of the Focus Level method, providing more than a 15.000-fold increase in computational efficiency. This dissertation also presents a solution to a multiple testing problem in genetics where a specific approach to mapping genes underlying quantitative traits of interest requires a multiplicity adjustment approach that both corrects for the number of tests while also ensuring logical consistency. The power advantage of the solution is demonstrated over the current standard approach to the problem. A side issue of this model framework led to the development of a new bivariate approach to quantitative trait marker detection, which is presented herein. The overall contribution of this dissertation to the statistics literature is that it provides novel solutions that meet real needs of practitioners in genetics and genomics with the aim of ensuring both that truth is discovered and that discoveries are actually true.
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Aryamanesh, Nader. "Chickpea improvement through genetic analysis and quantitative trait locus (QTL) mapping of ascochyta blight resistence using wild Cicer species." University of Western Australia. School of Plant Biology, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0072.
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[Truncated abstract] The genetics of ascochyta blight resistance was studied in five 5 x 5 half-diallel cross sets involving seven genotypes of chickpea (ICC 3996, Almaz, Lasseter, Kaniva, 24B-Isoline, IG 9337 and Kimberley Large), three accessions of Cicer reticulatum (ILWC 118, ILWC 139 and ILWC 184) and one accession of C. echinospermum (ILWC 181) under field conditions. Both F1 and F2 generations were used in the diallel analysis. Almaz, ICC 3996 and ILWC 118 were the most resistant genotypes. Estimates of genetic parameters, following Hayman's method, showed significant additive and dominant gene actions. The analysis also revealed the involvement of both major and minor genes. Susceptibility was dominant over resistance to ascochyta blight. The recessive alleles were concentrated in the two resistant chickpea parents ICC 3996 and Almaz, and one C. reticulatum genotype ILWC 118. High narrow-sense heritability (ranging from 82 to 86% for F1 generations, and 43 to 63% for F2 generations) indicates that additive gene effects were more important than non-additive gene effects in the inheritance of the trait and greater genetic gain by breeding resistant chickpea cultivars using carefully selected parental genotypes. Current simple leaf varieties are often susceptible to ascochyta blight disease whereas varieties of other leaf types range from resistant to susceptible. The inheritance of ascochyta blight resistance and different leaf types and their correlation were investigated in intraspecific progeny derived from crosses among two resistant genotypes with normal leaf type (ICC 3996 and Almaz), one susceptible simple leaf type (Kimberley Large) and one susceptible multipinnate leaf type (24 B-Isoline). ... An interspecific F2 mapping population derived from a cross between chickpea accession ICC 3996 (resistant to ascochyta blight, early flowering, and semi-erect plant growth habit) and C. reticulatum accession ILWC 184 (susceptible to ascochyta blight, ii late flowering, and prostrate plant growth habit) was used for constructing a genetic linkage map. F2 plants were cloned through stem cuttings taken at pre-flowering stage, treated with plant growth regulator powder (0.5 mg/g indole butyric acid (IBA) and 0.5 mg/g naphthalene acetic acid (NAA)) and grown in a sand + potting mix substrate. Clones were screened for ascochyta blight resistance in controlled environment conditions using a 19 scale. Three quantitative trait loci (QTLs) were found for ascochyta blight resistance in this population. Two linked QTLs, located on linkage group (LG) 4, explained 21.1% and 4.9% of the phenotypic variation. The other QTL, located on LG3, explained 22.7% of the phenotypic variation for ascochyta blight resistance. These QTLs explained almost 49% of the variation for ascochyta blight resistance. LG3 had two major QTLs for days to flowering (explaining 90.2% of phenotypic variation) and a major single QTL for plant growth habit (explaining 95.2% of phenotypic variation). There was a negative correlation between ascochyta blight resistance and days to flowering, and a positive correlation between days to flowering and plant growth habit. The flanking markers for ascochyta blight resistance or other morphological characters can be used in marker-assisted selections to facilitate breeding programs.
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Aryamanesh, Nader. "Chickpea improvement through genetic analysis and quantitative trait locus (QTL) mapping of ascochyta blight resistence using wild Cicer species /." Connect to this title, 2007. http://theses.library.uwa.edu.au/adt-WU2008.0072.
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Li, Jingzhao. "Mapping of new microsatellite markers and molecular identification of quantitative trait locus (QTL) for agronomically important traits in barley." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=97412141X.
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Lopez-Gerena, Jershon. "Mapping QTL controlling durable resistance to rice blast in the cultivar Oryzica Llanos 5." Diss., Manhattan, Kan. : Kansas State University, 2006. http://hdl.handle.net/2097/163.
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Moraes, Michel Choairy de. "Mapas de ligação e mapeamento de QTL ("Quantitative Trait Loci") em maracujá-amarelo (Passiflora edulis Sims f. flavicarpa Deg.)." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-25012006-135856/.
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A despeito da importância comercial da cultura do maracujá-amarelo para o Brasil, estudos genéticos e de melhoramento são bastante escassos. Neste trabalho, foi conduzido um experimento visando construir mapas de ligação e mapear QTL para caracteres relacionados à produção e qualidade de frutos. Foi utilizada uma população composta por 160 indivíduos, proveniente do cruzamento de duas plantas dos acessos IAPAR-06 e IAPAR-123. Devido à alogamia da espécie, optou-se pela abordagem de mapeamento conhecida por pseudocruzamento teste para a construção de dois mapas de ligação, sendo um para cada genitor, utilizando marcadores moleculares do tipo AFLP, com segregação 1:1 e 3:1. No mapa do acesso IAPAR-06 foram obtidos 10 grupos de ligação, enquanto que no mapa do IAPAR-123, nove grupos foram obtidos. Os locos bi-parentais foram alocados como marcas acessórias nos mapas de ligação e serviram para o estabelecimento da homologia entre os grupos de ligação de cada genitor. Um total de oito grupos de ligação foi alinhado com base nesses locos. Em paralelo, procedeu-se a avaliação fenotípica de 100 indivíduos dessa mesma população, os quais foram avaliados em campo, na primeira safra de produção da cultura, para uma série de caracteres, quais sejam: velocidade de crescimento; produção total; número total de frutos; peso médio de frutos; comprimento e largura média de frutos; porcentagem de polpa; teor de sólidos solúveis totais; e formato médio de frutos. As análises genético-estatísticas dos dados fenotípicos indicaram que a população é amplamente variável para os caracteres avaliados, com exceção da velocidade de crescimento, apresentando coeficientes de herdabilidade entre médias que variaram de 52,6 a 83,0%. O mapeamento de QTL, utilizando o método de mapeamento por intervalo composto, identificou várias regiões associadas ao controle desses caracteres nos mapas individuais. Foram mapeados QTL para todos os caracteres que apresentaram variabilidade genética na população. A proporção da variação fenotípica explicada pelos QTL detectados variou de 4,6 até 21,8%.Although the yellow passion-fruit plays an important commercial role in Brazil, breeding and genetics studies are insipient. The present study was conducted aiming the construction of linkage maps and mapping of QTL for traits related to yield and fruit quality. It was used a population, composed of 160 individuals, derived from a cross from two plants of the IAPAR-06 and IAPAR-123 accessions. Since this is an allogamous species, the pseudo testcross mapping strategy was used for the construction of two linkage maps, one for each parent, using AFLP markers segregating in 1:1 and 3:1 configuration. The IAPAR-06 map was composed of 10 linkage groups, while in IAPAR-123 map, nine linkage groups were obtained. The bi-parental loci were located as accessory markers and served to establish the homology between the groups of each parent. Eight linkage groups were aligned using these markers. For the phenotypic evaluation, 100 individuals were evaluated in the field, during the first harvest of the culture, for various traits, including: growth increment, total yield, total number of fruits, average fruit weight, average fruit length, average fruit width, percentage of pulp, soluble solids content and fruit shape. The results of the phenotypic data indicated that the population had a wide genetic variance for all the traits, with the exception of growth increment, presenting broad-sense heritability varying from 52.6% to 83.0%. The analysis of QTL, using the composite interval method, has mapped various regions associated with the traits evaluated in both maps. It was mapped QTL for all the traits that exhibited genetic variation. The proportion of the phenotypic variation explained by the QTL identified ranged from 4.6 to 21.8%.
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Burgio, Gaëtan. "Etude [i. E. , Ettude] des QTL (quantitative trait loci) affectant la variation de la forme du crâne à l'aide des lignées recombinantes congéniques interspécifiques." Paris, Muséum national d'histoire naturelle, 2008. http://www.theses.fr/2008MNHN0003.
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Le déterminisme génétique de la morphologie crânio-faciale et ses relations avec la pathologie sont très mal connus chez l’homme, en partie en raison des interactions fortes entre les facteurs génétiques et des facteurs d'environnement hétérogènes et non contrôlés. La souris peut constituer un très bon modèle pour l’identification de gènes jouant un rôle clé dans la morphologie crânio-faciale du fait de l'existence de lignées consanguines très différentes génétiquement et la possibilité de maîtriser les paramètres d'environnement. Les souris recombinantes congéniques interspécifiques (IRCS) sont des lignées consanguines issues de croisements entre la lignée de laboratoire C57BL/6 et la lignée SEG/Pas établie à partir d'individus appartenant à l'espèce Mus spretus. Ces deux espèces de souris ont divergé depuis plus d'un million d'années et sont très différentes sur les plans génétique et phénotypique. Chacune des 55 lignées IRCS possède environ 1,3% de son génome provenant de la lignée SEG/Pas dans un fonds génétique provenant de la lignée C57BL/6. Vingt lignées ont été phénotypées pour des caractères physiologiques (numération de formule sanguine) et morphologiques et ont été comparés à la lignée de référence C57BL/6. Des différences importantes de conformation crânio-faciale entre plusieurs de ces lignées et C57BL/6 et le rôle compensateur des allométries ont été mis en évidence. Par l'étude de morphométrie géométrique et des analyses de contour, nous avons montré que la lignée IRCS 66H présente une modification importante de la partie antérieure du crâne et notamment que l’os nasal présente une forme intermédiaire entre celles de SEG/Pas et de C57BL/6. Cette lignée possède trois fragments sur les chromosomes 1, 13 et 18 provenant de la lignée SEG/Pas et d'une taille comprise entre 12 et 25 Mb. Pour identifier lequel de ces fragments est responsable de ce phénotype, nous avons analysé un croisement F2 entre 66H et C57BL/6 et isolé chaque segment dans des lignées congéniques et bicongéniques pour en étudier les effets individuels et nous avançons l’existence de au moins trois QTL (Quantitative Trait Loci) avec de multiples relations épistatiques entre eux. Nous avons pu reconstituer l’origine des segments SEG façonnant le phénotype de la lignée 66H et des lignées bicongéniques. Il apparaît donc que, même dans cette situation génétiquement simple qui n'implique que trois petites régions du génome, l'architecture crânio-faciale est sous un contrôle génétique complexeSince the work of James Cheverud and colleagues on the morphological integration of primate and mouse skull, studies on genetic basis of modular effect of the QTL (Quantitative Trait Loci) has been emphasized the last decade. We describe a new tool based on the cross of a distant mice species Mus spretus and the laboratory mouse C57BL/6 called Interspecific Recombinant Congenic Strains (IRCS). Each strain has inherited 1. 3% of its genome from SEG/Pas under the form of few, small-sized, chromosomal segments. Global skull shape separate in a dorsal and ventral side, was analyzed on 18 strains with Procustes superimposition method. Additive effect on SEG allele on the dorsal side was found with strong modification for the strain 49A and 120C. Canonical Variate Analysis for the dorsal and ventral side of some strain reveals strong dorsal modification for 120C, 49A and 122C and ventral modification for 49A and 66H. Covariation study based on the Two-Blocks Partial Least Squares procedure shows a strong morphological integration between the two sides of the skull suggesting compensatory effect on skull shape variation. Analysis of allometry shows first a radiation in the allometric trajectories with C57BL/6 as the starting point and strong modifications for shape for most strains corresponding to a fundamental mechanism of compensatory effect of SEG segment into strains for shape variation. Covariation analysis with removing allometry thus reveals modular organisation on the genetic control of some strains, 120C and 66H for the dorsal side and 137F and 119H for the ventral side. It also reveals modular effect for allometry of the strains 120C, 137G, 103E and 157F. This study demonstrates a strong morphological integration for shape of the majority of IRCS strains with allometry as a compensatory effect. It also demonstrates a modular organisation for shape changes and allometry of a minority of IRCS strains. IRCS is a powerful and appropriate tool for studying genetic basis on shape evolution and morphological integration
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George, Andrew Winston. "A Bayesian analysis for the mapping of a quantitative trait locus given half-sib data." Thesis, Queensland University of Technology, 1998.
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Komm, Karina [Verfasser]. "Fine mapping of quantitative trait loci (QTL) for osteochondrosis in Hanoverian warmblood horses on equine chromosomes (ECA) 2 and 4 / Karina Komm." Hannover : Bibliothek der Tierärztlichen Hochschule Hannover, 2010. http://d-nb.info/1004171595/34.
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Freewalt, Keith. "Creation of a High Density Soybean Linkage Map, QTL Mapping and the Effects of Marker Number, Population Size and Significance Threshold on Characterization of Quantitative Trait Loci." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1402656287.
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Nadesalingam, Jeyakumary. "Mapping and detection of quantitative trait loci (QTL) for milk production traits based on linkage analysis using microsatellite markers in Canadian Holstein cattle." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0019/NQ47403.pdf.
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Gangadharan, Sheeba Navakode [Verfasser], W. E. [Akademischer Betreuer] Weber, Andreas [Akademischer Betreuer] Börner, and W. [Akademischer Betreuer] Friedt. "Molecular mapping of quantitative trait loci (QTL) controlling aluminium tolerance in wheat and barley / Sheeba Navakode Gangadharan. Betreuer: W. E. Weber ; Andreas Börner ; W. Friedt." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2008. http://d-nb.info/1024859517/34.
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Haffke, Stefan Verfasser], and Thomas [Akademischer Betreuer] [Miedaner. "Quantitative-trait loci (QTL) mapping of important agronomical traits of the grain and biomass production in winter rye (Secale cereale L.) / Stefan Haffke. Betreuer: Thomas Miedaner." Hohenheim : Kommunikations-, Informations- und Medienzentrum der Universität Hohenheim, 2015. http://d-nb.info/1077818785/34.
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Tran, Thanh-Son. "Etudes génomiques chez la poule : applications à la résistance au portage de salmonelles et la digestibilité." Thesis, Tours, 2013. http://www.theses.fr/2013TOUR4013/document.
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Les protocoles de détection de QTL varient selon le modèle étudié, car ils dépendent de nombreux paramètres. Cette thèse s’est intéressée à la façon d’adapter ces protocoles à travers deux exemples de recherches de QTL chez la Poule, en utilisant deux méthodes statistiques différentes : maximum de vraisemblance (MV) et régression linéaire (RL), qui ont été comparées. Dans un premier temps, des QTLs de résistance au portage de salmonelles ont été identifiés, d’effets faibles et dont les positions varient selon la méthode utilisée. Dans un deuxième temps, des QTLs de caractères de digestibilité et d’anatomie du tube digestif ont été identifiés, avec des résultats semblables avec les deux méthodes. De nombreux QTLs d’effets faibles à modérés ont été identifiés. Les résultats de cette thèse montrent que la comparaison des deux méthodes est toujours utile et car dans certaines conditions les résultats obtenus diffèrent entre les deux méthodesThe QTL detection protocols vary depending on the model studied, because they depend on many parameters. This thesis has focused on how to adapt these protocols through two examples of QTL detection in Chicken, using two different statistical methods: maximum likelihood (ML) and linear regression (LR), which results were compared on two examples. Initially, QTLs controlling resistance to Salmonella carrier-state have been identified, of small effects and whose positions vary according to the method. In a second step, QTLs controlling digestibility and anatomy of the gastro-intestinal tract were identified with similar results for both methods. Many QTLs of small to moderate effects were identified. The results of this thesis show that the comparison of the two methods is always helpful as under certain conditions the results may vary with the method
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Martins, Francielle Alline. "Genotipagem de endosperma como estratégia auxiliar no mapeamento e detecção de QTLs em populações exogâmicas." Universidade Federal de Viçosa, 2006. http://locus.ufv.br/handle/123456789/4741.
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In the genetic mapping in outbred populations not always it is possible to determine the linkage phase of the alleles. Thus, heterozygous individuals are discarded from these analyses due to the lack of information, once it is not possible, through their genotype, to distinguish the origin of their parental alleles. In this way, the main objective of this work was to propose the endosperm genotyping as a strategy to identify the allelic origin of those heterozygotes individuals. Initially, fragments from the endosperm representing 10, 25 and 50% of the corn seeds weight were extracted and the seeds were submitted to the germination test. The results suggest that the elimination of up to 50% of the endosperm did not affected the seed germination. The methodology of semiquantitative PCR was optimized to differentiate doses of the alleles in the mixtures of DNA derived from leaves of two maize inbred lines (L3 and L1113- 01). It was represented different allelic proportions observed in the endosperm of their reciprocal crosses, based on the maximum amount of endosperm that could be used for DNA extraction. SSR markers were generated by semiquantitative PCR technique and the amplified fragments were evaluated in both agarose gels treated with ethidium bromide and poliacrylamide gels using fluorescently labeled primers. Gel resolution using agarose did not allow the differentiation of the mixtures of parental DNAs. However, through the regression analysis and comparison of the band intensity corresponding to the same allele in the different mixtures, the initial concentration of each one of the alleles could be inferred. The requirement of an allelic pattern limited the use of this technique to QTL analysis in populations where at least one of the genitors is known. Although the resolution of poliacrylamide gels using fluorescent markers was more efficient in the endosperm genotyping, once it was allowed to differentiate the maternal origin of reciprocal hybrids seed´s. So, the strategy of endosperm genotyping using fluorescent SSR primer amplified by semiquantitative PCR allowed the determination of allelic origin in the heterozygous offspring derived from outbred populations, including these individuals in the QTL detection, and consequently, increasing the precision of this analysis.
No mapeamento genético e detecção de QTLs em populações exogâmicas nem sempre é possível a determinação da fase de ligação dos alelos. Assim, indivíduos heterozigotos são descartados dessas análises por serem não informativos, uma vez que não é possível, por meio do seu genótipo, distinguir a origem de seus alelos em relação aos dois genitores. Dessa forma, o objetivo principal deste trabalho foi propor a genotipagem do endosperma para identificar a origem alélica dos indivíduos heterozigotos. Inicialmente, fragmentos do endosperma representando 10, 25 e 50% do peso das sementes de milho foram retirados, sendo as sementes submetidas ao teste de germinação. Observou-se que a remoção de até 50% do endosperma não afetou a taxa de germinação das sementes. A metodologia de PCR semiquantitativo foi otimizada para diferenciar doses dos alelos nas misturas de DNA foliar de duas linhagens de milho (L3 e L1113-01), representando as diferentes proporções alélicas observadas no tecido endospermático dos seus cruzamentos recíprocos, tendo como base a quantidade máxima de endosperma que podia ser utilizada na extração do DNA. Marcadores SSR foram gerados pela técnica de PCR semiquantitativo, e os fragmentos amplificados foram avaliados tanto em gel de agarose tratado com brometo de etídio quanto em gel de poliacrilamida, usando-se primers fluorescentes. A resolução do gel de agarose não possibilitou a diferenciação das misturas dos DNAs parentais. No entanto, por meio da análise de regressão e da comparação da intensidade da banda correspondente a um mesmo alelo nas diferentes misturas, pôde-se inferir a concentração inicial de cada um dos alelos. A necessidade de um padrão de alelos limitou o uso dessa técnica nas análises de QTLs em populações nas quais pelo menos um dos genitores é conhecido. Já a resolução do gel de poliacrilamida utilizando marcadores fluorescentes foi mais eficiente na genotipagem de endospermas, uma vez que possibilitou a diferenciação da origem materna das sementes dos híbridos recíprocos. Assim, a estratégia de genotipagem do endosperma utilizando primers SSR fluorescentes amplificados pela técnica de PCR semiquantitativo possibilitou a determinação da origem dos alelos dos descendentes heterozigotos derivados de populações exogâmicas, permitindo a inclusão destes na detecção de QTLs e, conseqüentemente, aumentando a precisão das análises.
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Vontimitta, Vijay. "Genetic Mapping of Genes Controlling Two Leaf Surface Chemistry Traits and Identification of Quantitative Trait Loci (QTL) Associated with Resistance to Phytophthora nicotianae in Tobacco (Nicotiana tabacum L.)." NCSU, 2010. http://www.lib.ncsu.edu/theses/available/etd-12102009-174020/.
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The ultimate objective of a tobacco breeder is to use genetics to improve traits contributing to improved crop production efficiency and that affect product quality. Two leaf surface chemistries, cis-abienol and β-methylvaleric acid-containing sucrose esters (BMVSEs), are known to be associated with organoleptic properties of tobacco products and may contribute to resistance against insect pests and fungal pathogens. The black shank disease, caused by Phytophthora nicotianae, causes severe crop losses annually in many tobacco growing regions of the world. Multiple races of this pathogen make it difficult to develop tobacco cultivars with high levels of resistance to all races. In the current study, an investigation was carried out to gain insight into the genetics controlling two leaf surface chemistry traits and black shank resistance using the assistance of microsatellite markers. A cigar tobacco line, âBeinhart 1000,â was chosen as a source of the ability to accumulate the two leaf surface chemistries and as a source of high levels of resistance against multiple races of the black shank pathogen. A doubled haploid population of 118 lines was developed from a cross between Beinhart 1000 and the flue cured cultivar, Hicks, which lacks the ability to produce the two leaf surface chemistries and is highly susceptible to the black shank disease. Field evaluations in disease nurseries were conducted using replicated trials in three environments. A genetic linkage map with 24 linkage groups was constructed by genotyping the mapping population with 190 microsatellite markers. Both genes controlling leaf surface chemistry traits were positioned on linkage group 4 and were separated by a genetic distance of 8.5 centimorgans (cM). Multiple interval mapping (MIM) analysis identified a total of six quantitative trait loci (QTL) (on linkage groups 2, 4, 8, 9, 11, and 14) associated with black shank disease resistance in Beinhart 1000. Two QTLs on linkage groups 4 and 8 were identified as having major effects and explained 20.5% and 23.5% of the phenotypic variation for end percent survival, respectively. The QTL on linkage group 4 was found to be strongly linked with the gene, Abl, controlling cis-abienol accumulation. Growth chamber evaluations of the mapping population with specific races (Race 0 and Race 1) revealed that the two major QTLs on linkage groups 4 and 8 were significantly associated with resistance to both races. The QTL on linkage group 8 was observed to have consistent large effects in both field and growth chamber evaluations. An attempt was also made to draw genetic comparisons between Beinhart 1000 and the currently most widely exploited source of black shank disease resistance, âFlorida 301â. A mapping population of 125 recombinant inbred lines (RILs) developed from the cross between Florida 301 and Hicks was used for this study. Microsatellite markers representing the six genomic regions identified to be associated with resistance in Beinhart 1000 were tested for their association with resistance in Florida 301. Markers on linkage group 8 and 2 were identified to be associated with resistance in Florida 301. Markers on linkage group 4 and other regions of interest were not significantly associated with resistance in Florida 301. Results may be useful for transferring the two leaf surface chemistry traits and black shank resistance into new cultivars using marker assisted breeding.
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Poudel, Bikash. "Understanding Host Resistance and Pathogen Biology in the Wheat-Fusarium graminearum Pathosystem." Diss., North Dakota State University, 2020. https://hdl.handle.net/10365/31811.
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Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.
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Montoya, Jaramillo Carmenza. "Etude du déterminisme génétique de la composition en acides gras de l’huile de palme du genre Elaeis (E. guineensis et E. oleifera) par cartographie génétique et analyse différentielle de gènes candidats." Thesis, Montpellier 2, 2013. http://www.theses.fr/2013MON20007.
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Les allèles en ségrégation des deux génomes Elaeis ont été tracés dans un pseudo backcross interspécifique Elaeis (E. oleifera x E. guineensis) x E. guineensis. Dix-neuf QTL de proportion d'acides gras de l'huile de palme par rapport à 16 QTL des mêmes caractères d'un croisement intraspécifique E. guineensis ont mis en évidence des QTL communs ou spécifiques aux deux espèces. Aucune corrélation n'existe entre proportions d'acides gras et le rendement en huile de palme. Le déterminisme génétique et les principaux gènes associés aux acides gras du mésocarpe ont été étudiés, à l'aide de banques d'ADNc pleine longueur et des extraits d'ARNm de mésocarpe de fruits en développement des espèces Elaeis chacune représentée par quatre fonds génétiques. L'expression de 113 gènes Elaeis clés ou de facteurs putatifs de régulation des voies de synthèse de novo des acides gras et des triacylglycérols fut caractérisée au niveau de l'espèce par analyse in silico de profils de transcription et par analyse Real Time RT-qPCR. Les gènes ont été cartographiés sur le pseudo backcross avec 180 marqueurs SNP intra-géniques. Quarante-huit gènes étaient exprimés différemment entre espèces dont 94% plus exprimés chez E. guineensis. Le facteur de transcription EgAP2-2 (WRI1-like) influence le début de la synthèsede novo des acide gras par action principale sur les gènes MAT et KAS III, parait indépendant de l'expression d'autres gènes et non différentiel entre espèces. Les variations en C16:0 et C18:0 entre espèces s'expliquent par niveau d'expression allélique et l'activité enzymatique relative des isoformes présentes dans le génome de FATB (2), KAS II (1) et SAD (3)An Elaeis interspecific pseudo-backcross of first generation (E. oleifera x E. guineensis) x E. guineensis allowed tracing segregating alleles from both Elaeis genomes. Nineteen quantitative trait loci (QTLs) associated to palm oil fatty acid proportions compared to 16 QTLs of same traits in an intra-specific oil palm cross evidenced common or specific QTLs in E. guineensis and E. oleifera. No correlation was found in oil palm between mesocarp fatty acid proportions and yieldtraits. The genetic determinism of main fatty acid proportions was confirmed. Genes related to palm oil fatty acids were investigated using full-length cDNA libraries and mRNA extracts from the mesocarp of developing fruits in each Elaeis species represented by four genetic pools. Expression of 113 key Elaeis genes or putative regulation factors of de novo fatty acid and triacylglycerol pathways were characterized at species level by in silico transcript profiling and Real Time RT-qPCR analysis. Genes were mapped on the pseudo-backcross using 180 intra-gene SNP markers. Forty-eight genes were differentially expressed between Elaeis species, with 94% over expressed in E. guineensis. The EgAP2-2 (WRI1-like) transcription factor might influence the start of the de novo fatty acid pathway by main action only on the MAT and KAS III genes, as independent in expression from other genes and not differential between species. Between species variations in C16:0 and C18:0 can be deciphered by relative expression levels and enzyme activities of the isoforms in the genome of FATB (2), KAS II (1) and SAD (3). An oil palm producing more oleic acid in proportion than pure E. oleifera is feasible
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Gutiérrez, Humberto Ignácio. "Mapeamento de QTLs para resistência a grãos ardidos causados por diplodia (Stenocarpella Sp.) em milho (Zea Mays L.)." Universidade Federal de Uberlândia, 2008. https://repositorio.ufu.br/handle/123456789/15787.
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Diplodia ear rot caused by the fungus Stenocarpella maydis (Berkeley) and Stenocarpella
macrospora (Earle) have become one of the most important limiting factors for the production
of Corn (Zea mays L.) in Brazil. The fungus can attack the stalks, leaves and the grain
causing significant reductions on yield and the overall quality of the grain, since it can produce
micotoxinas that are dangerous to livestock. Resistance to ear rot by Stenocarpella sp in corn
is quantitative and highly influenced by the environment and even that artificial inoculation
techniques are available to screen for the disease the overall cost is very expensive. The
objective of this study was the identification of quantitative trait loci (QTL s) associated with
ear rot resistance by Stenocarpella sp in one breeding population composed of 141 doublehaploid
progenies resulted from the cross among the resistant inbred MONDR1 and the
susceptible inbred MONDS1 in testcrosses with the susceptible tester MONDS5. Testcrosses
were evaluated at harvest time after artificial inoculation for ear rot at three different locations
in the central region of Brazil during the 2005/06 summer season. Thru Composite interval
mapping (CIM), a total of three QTL s (LOD>2.5) for ear rot resistance were identified at
chromosomes 2, 3 and 5, all together accounting for up 26% of total phenotypic variation for
this character. The identification of two QTL s for ear rot resistance coming from the
susceptible parent MONDS1 appear to indicate the presence of the phenomena of
transgressive segregation. Additionally we were able to identify six double-haploid progenies
with high level of resistance to ear rot by Stenocarpella (MDH15, MDH443, MDH95, MDH2,
MDH120 e MDH81), being those recommended for their incorporation into the breeding
program as new breeding sources for the Central Brazil regions.Grãos ardidos causados pelos fungos Stenocarpella maydis (Berkeley) e Stenocarpella macrospora (Earle) tem se constituído num dos maiores fatores limitantes para a produção de milho (Zea mays L.) no Brasil. Estes fungos podem causar infecções no colmo, folhas e grãos, podendo ocasionar reduções significativas na produtividade e na qualidade do grão, pela produção de micotoxinas daninhas para aves e bovinos. A resistência para podridão de grão por Stenocarpella sp apresenta herança quantitativa e pode ser altamente influenciada pelo meio ambiente, e embora existam técnicas de inoculação que facilitam a discriminação de materiais suscetíveis, isto requer de grande quantidade de recursos. O objetivo do presente trabalho foi à identificação de locos de caracteres quantitativos (QTL) associados à resistência para podridão de grãos ( grãos ardidos ) ocasionados por Stenocarpella sp numa população de 141 progênies duplo-haplóides derivadas do cruzamento entre a linhagem resistente MONDR1 e a linhagem susceptível MONDS1 em testcross com o testador susceptível MONDS5. A porcentagem de espigas infectadas por Stenocarpella sp foi registrada para cada uma das testcrosses apos da inoculação artificial em três localidades na região Central de Brasil durante a Safra agrícola 2005/06. Mediante a análise de mapeamento por intervalo composto foram identificados três QTL s com LOD>2.5 para resistência à grãos ardidos nos cromossomos 2, 3 e 5, sendo estes em conjunto, responsáveis por ate 26% de variação fenotípica para este caráter. A identificação de dois QTL s para resistência a grãos ardidos por Stenocarpella sp com origem no progenitor susceptível parece indicar a presença do fenômeno de segregação transgressiva. Adicionalmente foram identificadas seis progênies duplohaplóides com alto nível de resistência a grãos ardidos (MDH15, MDH443, MDH95, MDH2, MDH120 e MDH81), sendo estas recomendadas para sua incorporação no programa de melhoramento para a região central do Brasil.
Mestre em Genética e Bioquímica
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Nauth, Brittany J. "Soybean QTL Mapping and Candidate Gene Identification for Pythium irregulare and Phytophthora sojae Partial Resistance; and Root-Knot Nematode Induced Suppression of Gene Silencing." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1406151869.
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Teyssèdre, Simon. "Dissection génétique des caractères par analyse de liaison et d'association : aspects méthodologiques et application à la sensibilité à l'ostéochondrose chez les Trotteurs Français." Thesis, Toulouse, INPT, 2011. http://www.theses.fr/2011INPT0082/document.
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Diverses lésions ostéochondrales peuvent affecter les articulations des jeunes chevaux et réduire leurs futures performances en course. L’objectif de cette thèse est d’identifier les régions du génome, appelées locus à caractère quantitatif (QTL), associées avec des caractères mesurant l’ostéochondrose (OC) enregistrés dans le programme GENEQUIN sur une population de Trotteurs Français. Le génotypage a été réalisé à l’aide de la puce SNP Illumina BeadChip EquineSNP50, qui est dense et permet d’exploiter le déséquilibre de liaison par des analyses d’association. Ces analyses sont sujettes à certains problèmes en présence d’une structure familiale des données. Dans la première partie de la thèse, une comparaison de la puissance et de la robustesse d’un choix restreint de méthodes d’analyses est effectuée. L’originalité de ce travail réside dans la dérivation algébrique des moments des distributions des statistiques de test comparées, donnant ainsi plus de généralité à nos résultats et permettant une meilleure compréhension des différences. Les résultats peuvent notamment servir à l’optimisation du dispositif expérimental. La deuxième partie est consacrée à la cartographie des régions QTL des caractères mesurant l’OC en différents sites articulaires dans une population de 583 Trotteurs Français. Cette étude a permis de mettre en évidence plusieurs régions QTL d’effets moyens et faibles à un niveau significatif mais pas hautement significatif. Nous montrons que l’OC est un caractère polygénique et qu’aucun QTL, ayant un effet à la fois sur l’OC du jarret et l’OC du boulet, n’est détectable dans ce protocole QTL, ce qui infirme l’hypothèse simple d’une cause génétique commune de la sensibilité à cette maladie sur les différents sites anatomiques. Suite à ces travaux, l’identification des gènes candidats et des mutations causales devrait clarifier la physiopathologie moléculaire de l’OC et ainsi permettre de développer des stratégies efficaces pour l’évaluation des risques. Pendant ce temps, les marqueurs peuvent être utilisés dans un contexte de sélection assistée par marqueurs afin d’améliorer la santé et le bien-être du chevalOsteochondral lesions are commonly observed in young horses and may be responsible for reduced performances in racing. The purpose of the PhD thesis was to identify genome regions, called quantitative trait loci (QTL), associated with various traits measuring osteochondrosis (OC) and recorded in the GENEQUIN program in a population of French Trotters horses. Genotyping was performed using the EquineSNP50 Illumina high density chip, which allows to exploit the linkage disequilibrium with genome-wide association studies. These analyses are subject to several problems in presence of family structure. We hence first proposed a comparison of power and robustness of a limited choice of models for this type of analysis. The originality of this work lies in the algebraic derivation of the distribution moments of the test statistics compared, making the outcome of this comparison more general and allowing a better understanding of differences. The results can be used to establish an experimental design. The second part was devoted to the QTL fine mapping of traits that measure OC in different joint sites. This study highlighted several significant QTL with low and medium effects but none of them were highly significant. We showed that OC is a polygenic trait and we were not able to identify QTL affecting both OC on the hock and the fetlock, rejecting the hypothesis of a single genetic determinism of susceptibility to this desease accross anatomical sites. Further studies will now focus on the identification of candidate genes and screening for mutation in an attempt to clarify the molecular physiopathology of OC and develop efficient strategies for risk assessment. Meanwhile, markers could be used in a marker-assisted selection context to improve horse health and welfare
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Bouffier, Bruno. "Genetic and ecophysiological dissection of tolerance to drought and heat stress in bread wheat : from environmental characterization to QTL detection." Thesis, Clermont-Ferrand 2, 2014. http://www.theses.fr/2014CLF22532/document.
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L’étude des rendements en blé a mis en évidence une stagnation apparue dans les années 1990, notamment en France, et principalement lié aux stress hydrique et thermique. Dans ce contexte, améliorer la tolérance du blé européen à ces stress est de première importance. Cette étude avait pour but d’étudier le déterminisme génétique de la tolérance à ces stress chez le blé. Pour ce faire, trois populations de blé tendre du CIMMYT combinant des caractères d’adaptation à ces stress ont été cultivées en conditions irriguée, sèche et stress thermique irriguée plusieurs années. Des caractères physiologiques et agronomiques ont été mesurés sur un réseau de 15 essais. Une méthodologie de caractérisation environnementale a été développée et a permis l’identification de six scenarii de stress au sein du réseau. Une covariable environnementale représentative de chacun a été extraite. L’utilisation des modèles de régression factorielles a permis la décomposition de l’interaction génotype x environnement ainsi que la mise en évidence d’une sensibilité différentielle au stress dans le germplasm. Une recherche de QTL multi-environnementale a conduit à la détection de régions génomiques contrôlant les caractères physiologiques et agronomiques ainsi que leurs interactions avec l’environnement. De la caractérisation environnementale à la détection de QTL, cette étude a abouti au développement d’un outil pour les sélectionneurs permettant l’évaluation du potentiel des génotypes face à une gamme d’environnement, mais aussi à l’identification de régions génomiques impliquées dans le contrôle de la tolérance aux stress hydrique et thermique chez le blé tendre. Ceci pourrait améliorer la tolérance à ces stress au sein du germplasm européenA stagnation of wheat yield was reported in France and other countries worldwide since the 1990’s, which incriminated mainly drought and heat stress. Improving the European wheat tolerance to them is of first importance. This study aimed to investigate the genetic determinism of the tolerance to such stresses. Three CIMMYT bread wheat populations combining complementary heat and drought adaptive habits were grown in Northern Mexico under irrigated, drought and heat-irrigated treatments from 2011 to 2013. The trial network comprised 15 trials and both physiological and agronomic traits were scored. First, an environmental characterization methodology was developed and resulted in the identification of six main environmental scenarios in the network. A representative environmental covariate was extracted from each of them. Then, a factorial regression model leaded to the dissection of the genotype-by-environment interaction and highlighted differential stress sensitivity of the germplasm. Finally, a multi-environmental QTL detection resulted in the discovery of genomic regions involved in the control of both physiological and agronomic traits and the study of their sensitivity to the environment. From the environmental characterization to the QTL detection, this study resulted in the development of a tool for breeders which may enable the evaluation of the potential of any genotypes in front of a range of environment, but also the identification of genomic regions involved in the control of the tolerance to drought and heat stress in bread wheat. This may help in improving the tolerance of the European bread wheat germplasm to drought and heat stress
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Rachid, Alchaarani Ghias. "Variabilité génétique et identification des QTLs liés à la qualité des semences chez le tournesol (Helianthus annuus L. )." Toulouse, INPT, 2004. http://www.theses.fr/2004INPT002A.
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Afin de progresser dans le domaine de la sélection assistée par marqueurs moléculaires chez le tournesol, nous avons réalisé plusieurs expérimentations sur une population de lignées recombinantes (RILs) issues du croisement entre deux génotypes 'PAC-2' et 'RHA-266'. La variabilité génétique pour la résistance partielle au mildiou (Plasmopara halstedii) et à la maladie des taches noires (Phoma macdonaldii), ainsi que pour quelques caractères d'intérêt agronomique et des paramètres de la germination et du développement des plantules ont été étudiés chez les RILs et leurs parents. L'analyse de variance montre une grande variabilité entre les RILs pour la résistance partielle pour les deux maladies et les caractères d'intérêt agronomique étudiés. Afin d'identifier les QTLs contrôlant les caractères étudiés, la carte génétique construite à partir des RILs et leurs parents mentionnés ci-dessus a été améliorée en augmentant le nombre de marqueurs AFLPs et additionnant des marqueurs SSRs. Plusieurs QTLs liés aux caractères étudiés ont été identifiés. Les effet de chaque QTL sont entre 6. 4% et 20. 2% pour la résistance partielle aux deux maladies, entre 7% et 37% pour les caractères d'intérêt agronomique et entre 6% et 33% pour les paramètres de germination et de développement des plantules. Les QTLs détectés se trouvent parfois sur le même groupe de liaison les uns proches des autres et les corrélations génétiques entre les caractères confirment également cette relation. Ces régions chromosomiques devront être cartographiées de façon plus précise si l'on souhaite les utiliser dans un programme de sélection assistée par marqueurs. Afin d'augmenter la variabilité génétique par l'irradiation et la culture in vitro, les graines d'un hybride F1 et ses deux parents 'AS613' et 'AS616' ont été irradiées par sept doses de rayons (5, 15, 25, 35, 45, 55 et 66 Grays). Trois paramètres d'organogenèse ont été étudiés pour les génotypes avec les graines irradiées et les graines non irradiées (contrôle). La variabilité génétique, l'effet d'irradiation et l'interaction entre génotype-irradiation ont été déterminés pour tous les paramètres étudiés. L'irradiation des graines de l'hybride F1 par 5 et 15 Grays de rayons gamma a un effet positif sur l'augmentation de l'aptitude à la régénération par organogenèse à partir de cotylédons chez le tournesol. Les mutants induits par les deux moyens; irradiation et variation somaclonale peuvent être dans l'amélioration de cette espèce.
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Berg, Frida. "Genetic Analysis of Fat Metabolism in Domestic Pigs and their Wild Ancestor." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7089.
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Yu, Miao. "Quantitative trait loci (QTL) mapping with longitudinal traits." 2007. http://www.lib.ncsu.edu/theses/available/etd-06142007-082353/unrestricted/etd.pdf.
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