Author response: Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

Senescence, i.e., functional decline with age, is a major determinant of health span in a rapidly aging population, but the genetic basis of interindividual variation in senescence remains largely unknown. Visual decline and age-related eye disorders are common manifestations of senescence, but disentangling age-dependent visual decline in human populations is challenging due to inability to control genetic background and variation in histories of environmental exposures. We assessed the genetic basis of natural variation in visual senescence by measuring age-dependent decline in phototaxis using Drosophila melanogaster as a genetic model system. We quantified phototaxis at 1, 2, and 4 wk of age in the sequenced, inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) and found an average decline in phototaxis with age. We observed significant genetic variation for phototaxis at each age and significant genetic variation in senescence of phototaxis that is only partly correlated with phototaxis. Genome-wide association analyses in the DGRP and a DGRP-derived outbred, advanced intercross population identified candidate genes and genetic networks associated with eye and nervous system development and function, including seven genes with human orthologs previously associated with eye diseases. Ninety percent of candidate genes were functionally validated with targeted RNAi-mediated suppression of gene expression. Absence of candidate genes previously implicated with longevity indicates physiological systems may undergo senescence independent of organismal life span. Furthermore, we show that genes that shape early developmental processes also contribute to senescence, demonstrating that senescence is part of a genetic continuum that acts throughout the life span.

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Author response: Natural variation in stochastic photoreceptor specification and color preference in Drosophila

10.7554/elife.29593.017 ◽

2017 ◽

Author(s):

Caitlin Anderson ◽

India Reiss ◽

Cyrus Zhou ◽

Annie Cho ◽

Haziq Siddiqi ◽

...

Keyword(s):

Natural Variation ◽

Color Preference ◽

Author Response

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Genetic dissection of courtship song variation using the Drosophila Synthetic Population Resource

10.1101/006643 ◽

2014 ◽

Author(s):

Alison Pischedda ◽

Veronica A Cochrane ◽

Wesley G Cochrane ◽

Thomas L. Turner

Keyword(s):

Genetic Variation ◽

Natural Variation ◽

Natural Populations ◽

Courtship Song ◽

Grand Challenge ◽

Genetic Dissection ◽

Trait Variation ◽

Song Variation ◽

Synthetic Population ◽

Causal Allele

Connecting genetic variation to trait variation is a grand challenge in biology. Natural populations contain a vast reservoir of fascinating and potentially useful variation, but it is unclear if the causal alleles will generally have large enough effects for us to detect. Without knowing the effect sizes or allele frequency of typical variants, it is also unclear what methods will be most successful. Here, we use a multi-parent advanced intercross population (the Drosophila Synthetic Population Resource) to map natural variation in Drosophila courtship song traits. Most additive genetic variation in this population can be explained by a modest number of highly resolved QTL. Mapped QTL are universally multiallelic, suggesting that individual genes are "hotspots" of natural variation due to a small target size for major mutations and/or filtering of variation by positive or negative selection. Using quantitative complementation in randomized genetic backgrounds, we provide evidence that one causal allele is harbored in the gene Fhos, making this one of the few genes associated with behavioral variation in any taxon.

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Accelerating structure-function mapping using the ViVa webtool to mine natural variation

10.1101/488395 ◽

2018 ◽

Author(s):

Morgan O Hamm ◽

Britney L Moss ◽

Alexander R Leydon ◽

Hardik P Gala ◽

Amy Lanctot ◽

...

Keyword(s):

Genetic Variation ◽

Gene Network ◽

Natural Variation ◽

Genetic Resource ◽

Gene Families ◽

Auxin Signaling ◽

Human Genetic Variation ◽

Auxin Signaling Pathway ◽

Accelerating Structure ◽

Or Gene

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).

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Author response: Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

10.7554/elife.44080.041 ◽

2019 ◽

Author(s):

Satish K Nandakumar ◽

Sean K McFarland ◽

Laura M Mateyka ◽

Caleb A Lareau ◽

Jacob C Ulirsch ◽

...

Keyword(s):

Genetic Variation ◽

Author Response ◽

Human Genetic Variation ◽

Response Gene

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Partitioning plant genetic and environmental drivers of above and belowground community assembly

10.1101/173500 ◽

2017 ◽

Author(s):

Matthew Barbour ◽

Sonya Erlandson ◽

Kabir Peay ◽

Brendan Locke ◽

Erik S. Jules ◽

...

Keyword(s):

Genetic Variation ◽

Phenotypic Plasticity ◽

Host Plant ◽

Environmental Effects ◽

Natural Variation ◽

Plant Traits ◽

Genetic Effects ◽

Environmental Drivers ◽

Leaf Quality ◽

Wind Exposure

Host-plant genetic variation affects the diversity and composition of associated above and belowground communities. Most evidence supporting this view is derived from studies within a single common garden, thereby constraining the range of biotic and abiotic environmental conditions that might directly or indirectly (via phenotypic plasticity) affect communities. If natural variability in the environment renders host-plant genetic effects on associated communities unimportant, then studying the community-level consequences of genetic variation may not be warranted. We addressed this knowledge gap by planting a series of common gardens consisting of 10 different clones (genotypes) of the willow Salix hookeriana in a coastal dune ecosystem and manipulated natural variation in ant-aphid interactions (biotic) and wind exposure (abiotic) in two separate experiments. We then quantified the responses of associated species assemblages both above (foliar arthropods) and belowground (rhizosphere fungi and bacteria). In addition, we quantified plant phenotypic responses (plant growth, leaf quality, and root quality) to tease apart the effects of genetic variation, phenotypic plasticity, and direct environmental effects on associated communities. In the ant-aphid experiment, we found that willow genotype explained more variation in foliar arthropod communities than aphid additions and proximity to aphid-tending ant mounds. However, aphid additions modified willow genetic effects on arthropod community composition by attracting other aphid species to certain willow genotypes. In the wind experiment, wind exposure explained more variation than willow genotype in structuring communities of foliar arthropods and rhizosphere bacteria. Still, willow genotype had strong effect sizes on several community properties of arthropods and fungi, indicating that host-plant genetic variation remains important. Across both experiments, genetic variation in plant traits was more important than phenotypic plasticity in structuring associated communities. The relative importance of genetic variation vs. direct environmental effects though depended on the type of environmental gradient (G > E-aphid, but E-wind > G). Taken together, our results suggest that host-plant genetic variation is an important driver of above and belowground biodiversity, despite natural variation in the biotic and abiotic environment.

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Heritability of Directional Asymmetry in Drosophila melanogaster

International Journal of Evolutionary Biology ◽

10.4061/2009/759159 ◽

2009 ◽

Vol 2009 ◽

pp. 1-7 ◽

Cited By ~ 12

Author(s):

Ashley J. R. Carter ◽

Elizabeth Osborne ◽

David Houle

Keyword(s):

Drosophila Melanogaster ◽

Genetic Variation ◽

Artificial Selection ◽

Natural Variation ◽

The Other ◽

Directional Asymmetry ◽

Consistent Difference ◽

Selection Experiment ◽

Response To Selection ◽

Powerful Technique

Directional asymmetry (DA), the consistent difference between a pair of morphological structures in which the same side is always larger than the other, presents an evolutionary mystery. Although many paired traits show DA, genetic variation for DA has not been unambiguously demonstrated. Artificial selection is a powerful technique for uncovering selectable genetic variation; we review and critique the limited number of previous studies that have been performed to select on DA and present the results of a novel artificial selection experiment on the DA of posterior crossvein location in Drosophila wings. Fifteen generations of selection in two genetically distinct lines were performed and none of the lines showed a significant response to selection. Our results therefore support and reconfirm previous findings; despite apparent natural variation and evolution of DA in nature, DA remains a paradoxical trait that does not respond to artificial selection.

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Genetic basis and natural variation of α-amylase isozymes in barley

Genetics Research ◽

10.1017/s0016672300019182 ◽

1982 ◽

Vol 40 (3) ◽

pp. 315-324 ◽

Cited By ~ 69

Author(s):

A. H. D. Brown ◽

J. V. Jacobsen

Keyword(s):

Genetic Variation ◽

Natural Variation ◽

Genetic Basis ◽

Seed Storage Protein ◽

Amylase Activity ◽

Seed Storage ◽

Hordeum Spontaneum ◽

Wild Progenitor ◽

Isoelectric Points ◽

Allozyme Loci

SUMMARYTwo physiologically and biochemically distinct groups of α-amylase (E.C.3.2.1.1) isozymes are synthesized when isolated aleurone layers of barley are incubated with gibberellic acid (GA3). Isoelectric focusing of the α-amylases showed that the isoelectric points of the isozymes of one group were near pH 5, whereas those of the second group were close to pH 6. Using wheat–barley addition lines, the genes for these groups were located in barley chromosomes 1 and 6 respectively. Joint segregation in the F2 generation of appropriate crosses indicated that the isozymes within each group were inherited collectively, and were attributed to codominant alleles segregating at two presumably complex loci, α-Amy 2 and α-Amy 1.The extent of genetic variation at these two loci was examined in 40 lines of Hordeum spontaneum (the wild progenitor of barley), and in a complex gene pool representative of H. vulgare (composite cross XXI). Variation at the α-Amy 1 locus was much more extensive than that at the α-Amy 2 locus. The genetic variation at both α-amylase loci exceeded that at the majority of other allozyme loci. However the α-amylase loci were less variable than the two loci coding for the seed storage protein, hordein. The wild species was found to contain much genetic diversity, which might be useful in modifying α-amylase activity by breeding. Parallels between the genetics and variation of α-amylase in barley and wheat were noted.

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