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Дисертації з теми "Locus à caractère quantitatif – Évaluation – Tests"
Gerber, Sophie. "Variabilité des protéines de l'endosperme du pin maritime révélée par électrophorèse bidimensionnelle : interprétations génétiques, cartographie et relation avec des caractères quantitatifs." Institut national agronomique Paris-Grignon (1971-2006), 1992. http://www.theses.fr/1992INAP0126.
Повний текст джерелаThe present work is intended as a step toward a description of the maritime pine genome (Pinus pinaster Ait. ). It initiates a study of quantitative traits variation using this description, The growth performances of the trees composing the breeding population of maritime pine are known thanks to general combining abilities measured in progeny tests. Eighteen trees representing the range of performances were sampled in this population. The variability of the proteins contained in the haploid endosperms (or megagametophytes) of these pines was studied by two-dimensional electrophoresis, An average of 12 endosperms per tree were analysed and compared. After a systematic analysis of the variation observed, 84 loci were described, responsible for position or amount modifications or presence/absence of proteins, Human genetics techniques were used to build a map. Seventeen linkage groups were detected, which included 65 loci and covered 530 centimorgans, The methods used to estimate and to test for linkage between loci are discussed. The linkage data allowed us to estimate the genome length of maritime pine, It was found to be around 2000 centimorgans, Pines contain one of the greatest quantity of DNA per cell. Some considerations about the relationship between physical and genetic maps in angiosperms and gymnosperms are thus proposed. The relationship between the weight of megagametophytes and the alleles expressed in these haploid organs was studied for every locus. The effect of three loci was detected. The diploid genotype of 18 pines for the 84 loci was compared to their growth performances thanks to different statistical techniques, The results suggest that protein amount variation could be related to quantitative traits, the usefulness and limits of quantitative trait loci (QTL), particularly for forest tree breeding, are discussed
Michenet, Alexis. "Détection de QTL et sélection génomique des qualités maternelles des vaches allaitantes." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLA008.
Повний текст джерелаReproduction, calving and milking performance of beef cows are included in maternal performance which are of major economic importance for beef cattle breeding. Beef cattle selection schemes use the progeny station tool to measure these phenotypes for the selection of the best insemination bulls. This coupled with the rapid ease of access to beef cattle genomic information, creates new opportunities for a more efficient selection of maternal performance. In this study, near 2 000 females with individual maternal performance were genotyped with low density chip (7 660 SNP) in two beef breeds, Blonde d'Aquitaine and Limousine. The genotypes were imputed in high density (more than 700 000 SNP). QTL detection was performed within breed with a Bayesian approach to test the association of the imputed genotypes and the performance. Among the QTL regions identified, a total of 41 candidate genes were proposed for sexual precocity (6), calving (11), milk performance (21) and maternal behavior (3). Several genomic selection methods were compared for maternal performance traits in Blonde d'Aquitaine breed. Minor differences of accuracy were found between single-trait evaluation methods. The "Single Step Genomic BLUP" multi-trait combining records from station and farm gave the more accurate genetic values for sorting bulls. Several genomic values accuracy improvements were proposed. The conditions of use of these indexes and the evolution of the selection scheme of maternal traits and the related tools are discussed
Seye, Adama Innocent. "Prédiction assistée par marqueurs de la performance hybride dans un schéma de sélection réciproque : simulations et évaluation expérimentale pour le maïs ensilage." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS078.
Повний текст джерелаMaize (Zea mays L.) is the most cultivated crop in the world. To exploit the strong heterosis for traits related to biomass, the genetic diversity of maize is structured into heterotic groups and cultivated varieties are mainly F1 hybrids obtained by crossing lines from complementary groups. The hybrid value can be decomposed as the sum of the General Combining Ability (GCA) of each parental line and the Specific Combining Ability (ASC) of the cross. In northern Europe, maize is often used as silage for animal feed and the breeding objective is to improve productivity while ensuring a good energetic value and digestibility of the silage. The objectives of this thesis were: (i) to estimate the importance of GCA and SCA in hybrid genetic variance for silage quality traits, (ii) to identify loci (QTL) involved in these traits and to study their colocalization with QTL for productivity traits, (iii) to evaluate the interest of genomic selection for the prediction of hybrid performances and (iv) to compare the prediction accuracies of two calibration designs either based on a factorial or on the conventional use of testers from the complementary group. As part of the SAM-MCR project, 6 biparental connected families were created in the "flint" and "dent" groups from 4 founder lines. In a first phase, 822 flint and 802 dent lines were genotyped for 20k SNPs and crossed according to an incomplete factorial to produce 951 hybrids which were phenotyped for quality traits and for productivity traits (studied by H. Giraud during her phD). Quality trait analysis showed a predominance of GCA over SCA and a negative correlation between digestibility traits and silage yield. Several multi-allelic QTLs were detected, most of them being specific to one group. Several colocalizations were found with yield QTL. Using cross-validation, we observed that the predictive ability of models based on detected QTLs was lower than that obtained by genomic predictions. Considering the SCA did not improve model predictive abilities for most of the traits. In a second phase, 90 lines were chosen per group: 30 were selected based on their genomic predictions for productivity and the energetic value and 60 were randomly sampled from the 6 families. These lines were crossed according to an incomplete factorial to produce 360 new hybrids: 120 from selected lines and 240 from randomly chosen lines. The 90 lines of each group were also crossed to two lines of the complementary group (testers). Hybrids from the selected lines were more productive but had a lower silage quality. We confirmed the good accuracy of the genomic predictions obtained in the initial factorial on the new hybrids evaluated in other environments and after selection. We also observed good correlations between GCA estimated in the factorial and in the testcross design. Different factorial and testcross designs were simulated by varying the proportion of dominance/SCA, the number of hybrids and the contribution of each line to the calibration set. Considering the same number of hybrids in the calibration set, the factorial was more efficient in terms of predictive ability and cumulative genetic gain (up to + 50%) than the testcross design for traits showing SCA and was similar for purely additive traits. The results of this thesis open new perspectives to revisit hybrid breeding schemes by replacing the evaluation of candidate lines, classically made on testcross, by the direct evaluation of hybrids resulting from an incomplete factorial. The implementation of such designs will require reorganizing the logistics of selection programs
Song, Jialin. "Architecture génétique des traits de croissance et de ramification du chêne." Thesis, Paris, AgroParisTech, 2017. http://www.theses.fr/2017AGPT0010.
Повний текст джерелаEpicormics may seriously impair the wood quality of oaks which are the most important hardwoods in French forestry. Successive projects have been carried out to understand the ontogenic and silviculture effects on sequential and epicormic branching. Effects of environment and genetics have been reported in the literature, but the knowledge about the genetic architecture of branching on oak and on epicormics in general is still limited. This last project quantifies this genetic architecture on growth, branching and especially epicormics traits. It takes advantage of observations from computed tomography (CT) or externally recorded, the genetic map of oak being built and a full-sib progeny installed in two experimental designs. The aim was to analyze and localize the Quantitative Trait Locus (QTLs) of the growth and branching traits on the genetic map of pedunculate oak, in order to contribute to characterize the genetic architecture of the sequential and epicormic branching on oak. A full-sibs offspring from an interspecific crossing of Quercus robur was planted at two sites in north-eastern France (CH) and south-western France (BR) with quite different environments and silvicultural intervention. In a first study, 1m-long logs from BR were scanned by CT; wood quality and branching traits were deduced on which a QTL analysis was performed. In a second study, QTL analysis was performed with traits deduced from external observation made on standing trees at the two sites. The QTL stability in two sites was evaluated. Finally, we questioned the impact of the tree growth on the branching through the QTLs detected. The QTL analysis revealed a moderate genetic control for latent bud production mainly. The interaction between the QTLs and the sites was highlighted especially concerning the development of epicormic branches. An independent genetic control was assumed for the sequential branches. Several “hot-spots” were identified on the genetic map of oak for the epicormic and growth traits. We suggest that some genetic controls of these regions are related to the axillary meristem initiation and that some genetic controls of the epicormic branching are probably involved also in the control of the tree growth. These results showed that the genetic control of epicormic branching is moderate and that the environment effect is likely involved more in the fate of these latent buds in interaction with the genetic effect. Since the oak genome was recently sequenced, a bioinformatics analysis is being performed on these regions for testing whether the candidate genes involved in plant hormones could explain the genetic mechanisms underlying these genomic regions related to the epicormic branching traits of the oak
Uddin, Md Mesbah. "Identification of causal factors for recessive lethals in dairy cattle with special focus on large chromosomal deletions." Thesis, Paris, Institut agronomique, vétérinaire et forestier de France, 2019. http://www.theses.fr/2019IAVF0018/document.
Повний текст джерелаThe overall aim of this PhD thesis is to identify causal variants for recessive lethal mutations and select a set of predictive markers that are in high linkage-disequilibrium with the causal variants for female fertility in dairy cattle. We addressed this broad aim under five articles: (i) describes a systematic approach of mapping recessive lethals in French Normande cattle using homozygous haplotype deficiency (HHD). This study shows the influence of sample size, quality of genotypes, quality of (genotype) phasing and imputation, age of haplotype (of interest), and last but not the least, multiple testing corrections, on discovery and replicability of HHD results. It also illustrates the importance of fine-mapping with pedigree and whole-genome sequence (WGS) data, (cross-species) integrative annotation to prioritize candidate mutation, and finally, large-scale genotyping of the candidate mutation, to validate or invalidate initial results. (ii) describes a high-resolution population-scale mapping of large chromosomal deletions from whole-genome sequences of 175 animals from three Nordic dairy breeds. This study employs three different approaches to validate identified deletions. Next, it describes population genetic properties and functional importance of these deletions. (iii) deals with three main issues related to imputation of structural variants, in this case, large chromosomal deletions, e.g. availability of deletion genotypes, size of haplotype reference panel, and finally, imputation itself. To address the first two issues, this study describes a Gaussian mixture model-based approach where read-depth data from the variant call format (VCF) file is used to genotype a known deletion locus, without the need for raw sequence (BAM) file. Finally, it presents a pipeline for joint imputation of WGS variants along with large chromosomal deletions. (iv) describes genome-wide association studies for female fertility in three Nordic dairy cattle breeds using imputed WGS variants including large chromosomal deletions. This study is based on the analyses of eight fertility related traits using single-marker association, conditional and joint analyses. This study illustrates that inflation in association test-statistics could be seen even after correcting for population stratification using (genomic) principal components, and relatedness among the samples using genomic relationship matrices; however, this was known for traits with strong polygenic effects, among other factors. Finally, mapping of several new quantitative trait loci (QTL), along with the previously known ones, are reported in this study. This study also highlights the importance of including (imputed) large deletions for association mapping of fertility traits. (v) describes prediction of genomic breeding values for fertility using SNP array-chip genotypes, selected QTL and large chromosomal deletion. Using genomic best linear unbiased prediction (GBLUP) method with one or several genomic-relationship matrices derived from a set of selected markers, this study reports higher prediction accuracy compared with previous report. This study also highlights the influence of selecting markers with best predictability, especially for a breed with small training population, in accuracy of genomic prediction. The results demonstrate that large deletions in general have a high predictive performance