Systems genetics for evolutionary studies

Pjotr Prins, Geert Smant, Danny Arends, Megan Mulligan, Rob W. Williams, Ritsert C. Jansen

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Systems genetics combines high-throughput genomic data with genetic analysis. In this chapter, we review and discuss application of systems genetics in the context of evolutionary studies, in which high-throughput molecular technologies are being combined with quantitative trait locus (QTL) analysis in segregating populations. The recent explosion of high-throughput data—measuring thousands of RNAs, proteins, and metabolites, using deep sequencing, mass spectrometry, chromatin, methyl-DNA immunoprecipitation, etc.—allows the dissection of causes of genetic variation underlying quantitative phenotypes of all types. To deal with the sheer amount of data, powerful statistical tools are needed to analyze multidimensional relationships and to extract valuable information and new modes and mechanisms of changes both within and between species. In the context of evolutionary computational biology, a well-designed experiment and the right population can help dissect complex traits likely to be under selection using proven statistical methods for associating phenotypic variation with chromosomal locations. Recent evolutionary expression QTL (eQTL) studies focus on gene expression adaptations, mapping the gene expression landscape, and, tentatively, define networks of transcripts and proteins that are jointly modulated sets of eQTL networks. Here, we discuss the possibility of introducing an evolutionary “prior” in the form of gene families displaying evidence of positive selection, and using that prior in the context of an eQTL experiment for elucidating host-pathogen protein-protein interactions. Here we review one exemplar evolutionairy eQTL experiment and discuss experimental design, choice of platforms, analysis methods, scope, and interpretation of results. In brief we highlight how eQTL are defined; how they are used to assemble interacting and causally connected networks of RNAs, proteins, and metabolites; and how some QTLs can be efficiently converted to reasonably well-defined sequence variants.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages635-652
Number of pages18
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1910
ISSN (Print)1064-3745

Fingerprint

Quantitative Trait Loci
Proteins
RNA
Gene Expression
High-Throughput Nucleotide Sequencing
Explosions
Computational Biology
Immunoprecipitation
Population
Chromatin
Dissection
Mass Spectrometry
Research Design
Technology
Phenotype
DNA
Genes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Prins, P., Smant, G., Arends, D., Mulligan, M., Williams, R. W., & Jansen, R. C. (2019). Systems genetics for evolutionary studies. In Methods in Molecular Biology (pp. 635-652). (Methods in Molecular Biology; Vol. 1910). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9074-0_21

Systems genetics for evolutionary studies. / Prins, Pjotr; Smant, Geert; Arends, Danny; Mulligan, Megan; Williams, Rob W.; Jansen, Ritsert C.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 635-652 (Methods in Molecular Biology; Vol. 1910).

Research output: Chapter in Book/Report/Conference proceedingChapter

Prins, P, Smant, G, Arends, D, Mulligan, M, Williams, RW & Jansen, RC 2019, Systems genetics for evolutionary studies. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1910, Humana Press Inc., pp. 635-652. https://doi.org/10.1007/978-1-4939-9074-0_21
Prins P, Smant G, Arends D, Mulligan M, Williams RW, Jansen RC. Systems genetics for evolutionary studies. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 635-652. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9074-0_21
Prins, Pjotr ; Smant, Geert ; Arends, Danny ; Mulligan, Megan ; Williams, Rob W. ; Jansen, Ritsert C. / Systems genetics for evolutionary studies. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 635-652 (Methods in Molecular Biology).
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