New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation

2020 ◽  
Vol 54 (1) ◽  
pp. 287-307
Author(s):  
Sebastian Soyk ◽  
Matthias Benoit ◽  
Zachary B. Lippman
Keyword(s):  
Genetic Variation ◽  
Quantitative Trait ◽  
Gene Dosage ◽  
Gene Mutations ◽  
Cumulative Effect ◽  
Developmental Pathways ◽  
Trait Variation ◽  
Individual Gene ◽  
New Horizons ◽  
New Strategies

Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.

scholarly journals A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

2019 ◽  
Vol 116 (27) ◽  
pp. 13690-13699 ◽  
Author(s):  
Héloïse Bastiaanse ◽  
Matthew Zinkgraf ◽  
Courtney Canning ◽  
Helen Tsai ◽  
Meric Lieberman ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Gene Dosage ◽  
Trait Variation ◽  
F1 Hybrid ◽  
Genome Wide ◽  
Negative Effect ◽  
Study Population ◽  
Gene Dosage Variation ◽  
Hybrid Lines ◽  
The Impact

Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.

Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 367-382 ◽  
Author(s):  
H D Bradshaw ◽  
Kevin G Otto ◽  
Barbara E Frewen ◽  
John K McKay ◽  
Douglas W Schemske
Keyword(s):  
Quantitative Trait Loci ◽  
Reproductive Isolation ◽  
Quantitative Trait ◽  
Floral Morphology ◽  
Cumulative Effect ◽  
Sympatric Species ◽  
Accurate Estimate ◽  
Phenotypic Variance ◽  
Trait Loci ◽  
Morphological Differences

Abstract Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining ≥25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.

scholarly journals Collaborative Cross Founder Expression Analysis (CCFEA)

2021 ◽  
Author(s):  
Richard R Green ◽  
Renee C Ireton ◽  
Martin Ferris ◽  
Kathleen Muenzen ◽  
David R Crosslin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Gene Expression Data ◽  
Viral Infections ◽  
Collaborative Cross ◽  
Visualization Tool ◽  
Expression Data ◽  
Individual Gene ◽  
Rnaseq Data

To understand the role of genetic variation in SARS and Influenza infections we developed CCFEA, a shiny visualization tool using public RNAseq data from the collaborative cross (CC) founder strains (A/J, C57BL/6J, 129s1/SvImJ, NOD/ShILtJ, NZO/HILtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Individual gene expression data is displayed across founders, viral infections and days post infection.

scholarly journals High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

2016 ◽  
Author(s):  
Marta R. Hidalgo ◽  
Cankut Cubuk ◽  
Alicia Amadoz ◽  
Francisco Salavert ◽  
José Carbonell-Caballero ◽  
...  
Keyword(s):  
High Throughput ◽  
Gene Mutations ◽  
Diagnostic Value ◽  
Therapeutic Interventions ◽  
Biological Knowledge ◽  
Individual Gene ◽  
Main Challenge ◽  
Activity Measurements ◽  
Cancer Types ◽  
Or Gene

AbstractUnderstanding the aspects of the cell functionality that account for disease or drug action mechanisms is a main challenge for precision medicine. Here we propose a new method that models cell signaling using biological knowledge on signal transduction. The method recodes individual gene expression values (and/or gene mutations) into accurate measurements of changes in the activity of signaling circuits, which ultimately constitute high-throughput estimations of cell functionalities caused by gene activity within the pathway. Moreover, such estimations can be obtained either at cohort-level, in case/control comparisons, or personalized for individual patients. The accuracy of the method is demonstrated in an extensive analysis involving 5640 patients from 12 different cancer types. Circuit activity measurements not only have a high diagnostic value but also can be related to relevant disease outcomes such as survival, and can be used to assess therapeutic interventions.

scholarly journals Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

2018 ◽  
Author(s):  
Jacob W. Malcom ◽  
Thomas E. Juenger ◽  
Mathew A. Leibold
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Life History ◽  
Molecular Basis ◽  
Life History Traits ◽  
Evolutionary Dynamics ◽  
Daphnia Pulex ◽  
Life History Trait ◽  
Life History Variation ◽  
Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

scholarly journals Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits

2018 ◽  
Author(s):  
Eilis Hannon ◽  
Tyler J Gorrie-Stone ◽  
Melissa C Smart ◽  
Joe Burrage ◽  
Amanda Hughes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Common Genetic Variation ◽  
Online Data ◽  
The Relationship ◽  
Methylation Quantitative Trait Loci

ABSTRACTCharacterizing the complex relationship between genetic, epigenetic and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. In this study, we describe the most comprehensive analysis of common genetic variation on DNA methylation (DNAm) to date, using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (P < 6.52x10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified using previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits, using Summary data–based Mendelian Randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression, identifying 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database (http://www.epigenomicslab.com/online-data-resources/) as a resource to the research community.

Quantitative trait loci define genes and pathways underlying genetic variation in longevity

2006 ◽  
Vol 41 (10) ◽  
pp. 1046-1054 ◽  
Author(s):  
Robert J. Shmookler Reis ◽  
Ping Kang ◽  
Srinivas Ayyadevara
Keyword(s):  
Genetic Variation ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Trait Loci
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