A Quantitative Genomic Approach for Analysis of Fitness and Stress Related Traits in a Drosophila Melanogaster Model Population

Overview

Journal Int J Genomics

Publisher Wiley

Date 2016 Jun 9

PMID 27274984

Citations 4

Authors

Palle Duun Rohde

Kristian Krag

Volker Loeschcke

Johannes Overgaard

Peter Sorensen

Torsten Nygaard Kristensen

Affiliations

Soon will be listed here.

Abstract

The ability of natural populations to withstand environmental stresses relies partly on their adaptive ability. In this study, we used a subset of the Drosophila Genetic Reference Panel, a population of inbred, genome-sequenced lines derived from a natural population of Drosophila melanogaster, to investigate whether this population harbors genetic variation for a set of stress resistance and life history traits. Using a genomic approach, we found substantial genetic variation for metabolic rate, heat stress resistance, expression of a major heat shock protein, and egg-to-adult viability investigated at a benign and a higher stressful temperature. This suggests that these traits will be able to evolve. In addition, we outline an approach to conduct pathway associations based on genomic linear models, which has potential to identify adaptive genes and pathways, and therefore can be a valuable tool in conservation genomics.

Citing Articles

The Role of Genetic Variation in Shaping Phenotypic Responses to Diet in Aging .

Bak N, Mackay T, Morgante F, Nielsen K, Nielsen J, Kristensen T bioRxiv. 2025; .

PMID: 39868103 PMC: 11761520. DOI: 10.1101/2025.01.09.632132.

Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in .

Lecheta M, Awde D, OLeary T, Unfried L, Jacobs N, Whitlock M Front Genet. 2020; 11:658.

PMID: 32655626 PMC: 7324644. DOI: 10.3389/fgene.2020.00658.

Genetic variation for tolerance to high temperatures in a population of .

Rolandi C, Lighton J, de la Vega G, Schilman P, Mensch J Ecol Evol. 2018; 8(21):10374-10383.

PMID: 30464811 PMC: 6238130. DOI: 10.1002/ece3.4409.

Genetic Decoupling of Thermal Hardiness across Metamorphosis in Drosophila melanogaster.

Freda P, Alex J, Morgan T, Ragland G Integr Comp Biol. 2017; 57(5):999-1009.

PMID: 29045669 PMC: 5886339. DOI: 10.1093/icb/icx102.

Genomic Analysis of Genotype-by-Social Environment Interaction for Aggressive Behavior.

Rohde P, Gaertner B, Ward K, Sorensen P, Mackay T Genetics. 2017; 206(4):1969-1984.

PMID: 28550016 PMC: 5560801. DOI: 10.1534/genetics.117.200642.

References

Sarup P, Sorensen J, Kristensen T, Hoffmann A, Loeschcke V, Paige K . Candidate genes detected in transcriptome studies are strongly dependent on genetic background. PLoS One. 2011; 6(1):e15644. PMC: 3026803. DOI: 10.1371/journal.pone.0015644. View

Mackay T, Richards S, Stone E, Barbadilla A, Ayroles J, Zhu D . The Drosophila melanogaster Genetic Reference Panel. Nature. 2012; 482(7384):173-8. PMC: 3683990. DOI: 10.1038/nature10811. View

Stetler R, Gan Y, Zhang W, Liou A, Gao Y, Cao G . Heat shock proteins: cellular and molecular mechanisms in the central nervous system. Prog Neurobiol. 2010; 92(2):184-211. PMC: 2939168. DOI: 10.1016/j.pneurobio.2010.05.002. View

Marron M, Markow T, Kain K, Gibbs A . Effects of starvation and desiccation on energy metabolism in desert and mesic Drosophila. J Insect Physiol. 2003; 49(3):261-70. DOI: 10.1016/s0022-1910(02)00287-1. View

Patnala R, Clements J, Batra J . Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genet. 2013; 14:39. PMC: 3655892. DOI: 10.1186/1471-2156-14-39. View

Wang K, Li M, Hakonarson H . Analysing biological pathways in genome-wide association studies. Nat Rev Genet. 2010; 11(12):843-54. DOI: 10.1038/nrg2884. View

VanRaden P . Efficient methods to compute genomic predictions. J Dairy Sci. 2008; 91(11):4414-23. DOI: 10.3168/jds.2007-0980. View

Hasanuzzaman M, Nahar K, Alam M, Roychowdhury R, Fujita M . Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants. Int J Mol Sci. 2013; 14(5):9643-84. PMC: 3676804. DOI: 10.3390/ijms14059643. View

Mooney M, Nigg J, McWeeney S, Wilmot B . Functional and genomic context in pathway analysis of GWAS data. Trends Genet. 2014; 30(9):390-400. PMC: 4266582. DOI: 10.1016/j.tig.2014.07.004. View

10.

Dalman K, Himmelstrand K, Olson A, Lind M, Brandstrom-Durling M, Stenlid J . A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s. PLoS One. 2013; 8(1):e53525. PMC: 3547014. DOI: 10.1371/journal.pone.0053525. View

11.

Davey J, Hohenlohe P, Etter P, Boone J, Catchen J, Blaxter M . Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011; 12(7):499-510. DOI: 10.1038/nrg3012. View

12.

Wang K, Li M, Bucan M . Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet. 2007; 81(6):1278-83. PMC: 2276352. DOI: 10.1086/522374. View

13.

Niitepold K, Hanski I . A long life in the fast lane: positive association between peak metabolic rate and lifespan in a butterfly. J Exp Biol. 2012; 216(Pt 8):1388-97. DOI: 10.1242/jeb.080739. View

14.

Lango Allen H, Estrada K, Lettre G, Berndt S, Weedon M, Rivadeneira F . Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010; 467(7317):832-8. PMC: 2955183. DOI: 10.1038/nature09410. View

15.

Welte M, Tetrault J, Dellavalle R, Lindquist S . A new method for manipulating transgenes: engineering heat tolerance in a complex, multicellular organism. Curr Biol. 1993; 3(12):842-53. DOI: 10.1016/0960-9822(93)90218-d. View

16.

El Golli-Bennour E, Bacha H . Hsp70 expression as biomarkers of oxidative stress: mycotoxins' exploration. Toxicology. 2011; 287(1-3):1-7. DOI: 10.1016/j.tox.2011.06.002. View

17.

Durham M, Magwire M, Stone E, Leips J . Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits. Nat Commun. 2014; 5:4338. DOI: 10.1038/ncomms5338. View

18.

Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S . Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMC: 545600. DOI: 10.1186/gb-2004-5-10-r80. View

19.

Shafer A, Wolf J, Alves P, Bergstrom L, Bruford M, Brannstrom I . Genomics and the challenging translation into conservation practice. Trends Ecol Evol. 2014; 30(2):78-87. DOI: 10.1016/j.tree.2014.11.009. View

20.

Bubliy O, Kristensen T, Kellermann V, Loeschcke V . Humidity affects genetic architecture of heat resistance in Drosophila melanogaster. J Evol Biol. 2012; 25(6):1180-8. DOI: 10.1111/j.1420-9101.2012.02506.x. View