Search results for "Gwas"
showing 10 items of 50 documents
Genome-wide association study for milk production traits in Valle del Belice sheep
2017
Over the last years, high-throughput technologies have provided the opportunity to explore the genomes of livestock species to identify regions influencing traits of economic interest. Genome wide association studies (GWAS) have been widely used to disentangle the genetic variation in complex phenotypes, such as milk production traits in sheep. The study presented here investigated the possible association of genome-wide SNPs and breeding values for milk production traits in the Valle del Belice sheep. The studied population consisted of a total of 481 ewes belonging to 9 half-sib families with available records for milk yield (MY), protein and fat percentage (P% and F%, respectively). All …
How Important Are Genes to Achieve Longevity?
2022
Several studies on the genetics of longevity have been reviewed in this paper. The results show that, despite efforts and new technologies, only two genes, APOE and FOXO3A, involved in the protection of cardiovascular diseases, have been shown to be associated with longevity in nearly all studies. This happens because the genetic determinants of longevity are dynamic and depend on the environmental history of a given population. In fact, population-specific genes are thought to play a greater role in the attainment of longevity than those shared between different populations. Hence, it is not surprising that GWAS replicated associations of common variants with longevity have been few, if an…
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
2015
This is a post-peer-review, pre-copyedit version of an article published in Journal of Computational Science. The final authenticated version is available online at: https://doi.org/10.1016/j.jocs.2015.04.001 [Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting epistasis, i.e. interactions among k markers (k ≥ 2), is an important but time consuming operation since statistical computations have to be performed for each k-tuple of measured markers. Efficient exhaustive methods have been proposed for k = 2, but exhaustive thi…
Genetic determinism of the plasticity of legume seed protein in different environments : role of sulfur metabolism
2021
The renewed interest in plant proteins has stimulated research aimed at developing markers to aid in the selection of legume varieties better adapted to nutritional needs. Among the traits to be improved and stabilized is the amino acid balance of seeds, the essential amino acids methionine and tryptophan being particularly under-represented in legume seeds. This thesis focuses on seed protein composition, which is a major determinant of the seed amino acid balance. The objective was to explore the genetic and environmental variability in this trait and to identify genes potentially involved in its plasticity when subjected to environmental stresses. In the first part of the thesis, the pro…
Plant genotype: a lever in the interactions between plant and its associated rhizosphere microbiome
2018
International audience; In the context of highly pressured agricultural production using low levels of inputs, cropping strategies could take advantage of existing plant-microbiome interactions that can improve both plant growth and health. We believe that plant genetics can provide some clues to better understand the mechanisms underlying microbiome recruitment by the plant.The aims of this work were (i) to assess plant genotype effect on the rhizosphere bacterial communities in relation to the plant nutritional strategies for a core collection of 155 genotypes of Medicago truncatula and (ii) to highlight the genetic determinisms potentially associated in these interactions. To achieve the…
Déterminisme génétique de la composition protéique des graines de légumineuses et de sa plasticité vis-à-vis de l’environnement
2018
Les légumineuses sont capables de produire des graines riches en protéines sans apport d’engrais azoté grâce à la symbiose racinaire avec des bactéries du genre rhizobium. Riches en lysine, ces protéines sont utilisées pour l’alimentation des animaux d’élevage et en nutrition humaine. Afin de promouvoir la culture des légumineuses, il est nécessaire d’optimiser et de stabiliser la qualité de cette fraction protéique. L’objectif de ma thèse est de mettre en évidence les déterminismes génétiques sous-jacents à la teneur et à la composition protéique des graines de légumineuses ainsi qu’à la plasticité de ces composantes vis-à-vis de l’environnement. Afin de répondre à cet objectif, l’approche…
Identification des déterminants génétiques impliqués dans les défenses du pois contre le puceron Acyrthosiphon pisum.
2021
National audience; Le pois (Pisum sativum) constitue une culture d’importance majeure parmi les légumineuses pour ses qualités de plante protéagineuse, notamment en Europe en réduisant la part de protéines végétales importées ainsi que pour son rôle dans la rotation des cultures en fixant l’azote atmosphérique dans le sol. Cependant, ces dernières années, les rendements ont été rendus instables dus aux contraintes biotiques et abiotiques. Pour lutter contre certains ravageurs, les producteurs ont recours à de grandes quantités de pesticides qui sont coûteuses et dangereuses pour l’environnement et la santé humaine. Pour ces raisons, des alternatives sont mises en œuvre tels que le développe…
Déterminisme génétique de la plasticité de la composition protéique des graines de légumineuses vis-à-vis de l'environnement : rôle du métabolisme du…
2021
The renewed interest in plant proteins has stimulated research aimed at developing markers to aid in the selection of legume varieties better adapted to nutritional needs. Among the traits to be improved and stabilized is the amino acid balance of seeds, the essential amino acids methionine and tryptophan being particularly under-represented in legume seeds. This thesis focuses on seed protein composition, which is a major determinant of the seed amino acid balance. The objective was to explore the genetic and environmental variability in this trait and to identify genes potentially involved in its plasticity when subjected to environmental stresses. In the first part of the thesis, the pro…
FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS
2014
Abstract Genotype-by-genotype interactions (epistasis) are believed to be a significant source of unexplained genetic variation causing complex chronic diseases but have been ignored in genome-wide association studies (GWAS) due to the computational burden of analysis. In this work we show how to benefit from FPGA technology for highly parallel creation of contingency tables in a systolic chain with a subsequent statistical test. We present the implementation for the FPGA-based hardware platform RIVYERA S6-LX150 containing 128 Xilinx Spartan6-LX150 FPGAs. For performance evaluation we compare against the method iLOCi[9]. iLOCi claims to outperform other available tools in terms of accuracy.…
Disentangling directional and fluctuating asymmetry in a genome-wide association study.
2018
8 pages; International audience; Although directional and fluctuating asymmetry have been frequently assessed independently, they are indeed associated concepts both in theory and in practice. However, they can be difficult to disentangle in genome-wide association studies, where the appropriate shape statistics are not fully developed. Although the usage of Procrustes distances to overcome this problem may be tempting, this does not reliably help to identify the underlying genetic components of directional and fluctuating asymmetries. Here, similarities and differences among different approaches have revealed that the genetic component of the skull asymmetry in this population of mice is m…