Search results for "Quantitative Trait"
showing 10 items of 127 documents
Selective phenotyping, entropy reduction, and the mastermind game.
2011
Abstract Background With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. Results Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of p…
Genome-wide scan for selection signatures reveals novel insights into the adaptive capacity in local North African cattle
2020
International audience; Natural-driven selection is supposed to have left detectable signatures on the genome of North African cattle which are often characterized by the fixation of genetic variants associated with traits under selection pressure and/or an outstanding genetic differentiation with other populations at particular loci. Here, we investigate the population genetic structure and we provide a first outline of potential selection signatures in North African cattle using single nucleotide polymorphism genotyping data. After comparing our data to African, European and indicine cattle populations, we identified 36 genomic regions using three extended haplotype homozygosity statistic…
Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies.
2015
Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have undergone an adaptive radiation for wing-pattern mimicry and are influenced by distinct selection regimes. Using crosses between natural wing-pat…
A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk
2010
Combined analyses of gene networks and DNA sequence variation can provide new insights into the aetiology of common diseases that may not be apparent from genome-wide association studies alone. Recent advances in rat genomics are facilitating systems-genetics approaches. Here we report the use of integrated genome-wide approaches across seven rat tissues to identify gene networks and the loci underlying their regulation. We defined an interferon regulatory factor 7 (IRF7)-driven inflammatory network (IDIN) enriched for viral response genes, which represents a molecular biomarker for macrophages and which was regulated in multiple tissues by a locus on rat chromosome 15q25. We show that Epst…
European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci
2022
A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent seco…
Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma
2014
Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma subtype and is clinically aggressive. To identify genetic susceptibility loci for DLBCL, we conducted a meta-analysis of 3 new genome-wide association studies (GWAS) and 1 previous scan, totaling 3,857 cases and 7,666 controls of European ancestry, with additional genotyping of 9 promising SNPs in 1,359 cases and 4,557 controls. In our multi-stage analysis, five independent SNPs in four loci achieved genome-wide significance marked by rs116446171 at 6p25.3 (EXOC2; P = 2.33 × 10 '21), rs2523607 at 6p21.33 (HLA-B; P = 2.40 × 10 '10), rs79480871 at 2p23.3 (NCOA1; P = 4.23 × 10 '8) and two independent SNPs, rs13255292 and rs47336…
Immune-mediated change in the expression of a sexual trait predicts offspring survival in the wild.
2011
9 pages; International audience; BACKGROUND: The "good genes" theory of sexual selection postulates that females choose mates that will improve their offspring's fitness through the inheritance of paternal genes. In spite of the attention that this hypothesis has given rise to, the empirical evidence remains sparse, mostly because of the difficulties of controlling for the many environmental factors that may covary with both the paternal phenotype and offspring fitness. Here, we tested the hypothesis that offspring sired by males of a preferred phenotype should have better survival in an endangered bird, the houbara bustard (Chlamydotis undulata undulata). METHODOLOGY/PRINCIPAL FINDINGS: We…
GENETIC BASIS OF THE TRADE-OFF BETWEEN OFFSPRING NUMBER AND QUALITY IN THE BANK VOLE
2004
One of the main tenets of modern life-history theory is the negative relationship (trade-off) between the number and quality of offspring produced. Theory predicts a negative genetic correlation between these traits since both are closely related to fitness of individuals. However, the genetic basis of the trade-off has only been tested to a limited extent in natural populations. We examined whether size and quality of offspring are negatively related to litter size in the bank vole Clethrionomys glareolus. First, we found a significant negative phenotypic correlation between the number and size of offspring at birth in both laboratory and field populations of the bank vole. Second, a large…
Coevolution of parental investment and sexually selected traits drives sex-role divergence
2016
Sex-role evolution theory attempts to explain the origin and direction of male–female differences. A fundamental question is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in subsequent parental care. Here we construct models to confirm predictions that individuals benefit less from caring when they face stronger sexual selection and/or lower certainty of parentage. However, we overturn the widely cited claim that a negative feedback between the operational sex ratio and the opportunity cost of care selects for egalitarian sex roles. We further argue that our model does not predict any effect of the adult sex ratio (ASR) that is …
Environmental stress affects the expression of a carotenoid-based sexual trait in male zebra finches.
2007
SUMMARY Abiotic factors including thermal stress are suggested to exert constrains on sexual ornaments through trade-offs between sexual displays and physiological functions related to self-maintenance. Given the health properties of carotenoid pigments, carotenoid-based ornaments offer a relevant context in which to investigate the effect of environmental stress, such as ambient temperature, on the production and maintenance of secondary sexual traits and, also, to explore the proximate mechanisms shaping their expression. In this study, we exposed male zebra finches (Taeniopygia guttata) to environmental stress by exposing them to two temperature regimes (6 and 26°C) over a 4 week period.…