EVOLUTIONARY ECOLOGY OF PLANT DEFENCES
Ecological genetics and genomics of plant defences: evidence and approaches
Article first published online: 28 SEP 2010
© 2010 The Authors. Functional Ecology © 2010 British Ecological Society
Special Issue: EVOLUTIONARY ECOLOGY OF PLANT DEFENCES AGAINST HERBIVORES
Volume 25, Issue 2, pages 312–324, April 2011
How to Cite
Anderson, J. T. and Mitchell-Olds, T. (2011), Ecological genetics and genomics of plant defences: evidence and approaches. Functional Ecology, 25: 312–324. doi: 10.1111/j.1365-2435.2010.01785.x
- Issue published online: 16 MAR 2011
- Article first published online: 28 SEP 2010
- Received 1 June 2010; accepted 25 August 2010 Handling Editor: Marc Johnson
- candidate gene;
- genome wide association studies;
- plant defence;
- population genomics;
- quantitative trait loci
1. Herbivores exert significant selection on plants, and plants have evolved a variety of constitutive and inducible defences to resist and tolerate herbivory. Assessing the genetic mechanisms that influence defences against herbivores will deepen our understanding of the evolution of essential phenotypic traits.
2. Ecogenomics is a powerful interdisciplinary approach that can address fundamental questions about the ecology and evolutionary biology of species, such as: which evolutionary forces maintain variation within a population? and What is the genetic architecture of adaptation? This field seeks to identify gene regions that influence ecologically important traits, assess the fitness consequences under natural conditions of alleles at key quantitative trait loci (QTLs), and test how the abiotic and biotic environment affects gene expression.
3. Here, we review ecogenomics techniques and emphasize how this framework can address long-standing and emerging questions relating to anti-herbivore defences in plants. For example, ecogenomics tools can be used to investigate: inducible vs. constitutive defences; tradeoffs between resistance and tolerance; adaptation to the local herbivore community; selection on alleles that confer resistance and tolerance in natural populations; and whether different genes are activated in response to specialist vs. generalist herbivores and to different types of damage.
4. Ecogenomic studies can be conducted with model species, such as Arabidopsis, or their relatives, in which case myriad molecular tools are already available. Burgeoning sequence data will also facilitate ecogenomic studies of non-model species. Throughout this paper, we highlight approaches that are particularly suitable for ecological studies of non-model organisms, discuss the benefits and disadvantages of specific techniques and review bioinformatic tools for analysing data.
5. We focus on established and promising techniques, such as QTL mapping with pedigreed populations, genome wide association studies, transcription profiling strategies, population genomics and transgenic methodologies. Many of these techniques are complementary and can be used jointly to investigate the genetic architecture of defence traits and selection on alleles in nature.