Identifying genotype-by-environment interactions in the metabolism of germinating Arabidopsis seeds using Generalized Genetical Genomics

R.V.L. Joosen, D. Arends, Y. Li, L.A.J. Willems, J.J.B. Keurentjes, W. Ligterink, R.C. Jansen, H.W.M. Hilhorst

Research output: Contribution to journalArticleAcademicpeer-review

34 Citations (Scopus)

Abstract

A complex phenotype such as seed germination is the resultant of several genetic and environmental cues and requires the concerted action of many genes. The use of well-structured recombinant inbred lines in combination with omics analysis can help to disentangle the genetic basis of such quantitative traits. This so called genetical genomics approach can effectively capture both genetic (G) and epistatic interactions (G:G). However, to understand how the environment interacts with genomic encoded information (G:E) a better understanding of the perception and processing of environmental signals is needed. In a classical genetical genomics setup this requires replication of the whole experiment in different environmental conditions. A novel generalized setup overcomes this limitation and includes environmental perturbation within a single experimental design. We developed a dedicated QTL mapping procedure to implement this approach and used existing phenotypical data to demonstrate its power. Additionally, we studied the genetic regulation of primary metabolism in dry and imbibed Arabidopsis seeds. Many changes were observed in the metabolome which are both under environmental and genetic control and their interactions. This concept offers unique reduction of experimental load with minimal compromise of statistical power and is of great potential in the field of systems genetics which requires a broad understanding of both plasticity and dynamic regulation.
Original languageEnglish
Pages (from-to)553-566
JournalPlant Physiology
Volume162
Issue number2
DOIs
Publication statusPublished - 2013

Keywords

  • quantitative trait loci
  • chromatography-mass spectrometry
  • heterogeneous inbred family
  • natural allelic variation
  • controlling root-growth
  • plant development
  • line population
  • complex traits
  • potato-tuber
  • thaliana

Fingerprint Dive into the research topics of 'Identifying genotype-by-environment interactions in the metabolism of germinating Arabidopsis seeds using Generalized Genetical Genomics'. Together they form a unique fingerprint.

  • Cite this