Common garden experiments in the genomic era: new perspectives and opportunities

Heredity (2016) 116, 249254

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Common garden experiments in the genomic era: new perspectives and opportunities

P de Villemereuil1, OE Gaggiotti1,2, M Mouterde1 and I Till-Bottraud1

The study of local adaptation is rendered difcult by many evolutionary confounding phenomena (for example, genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specically designed to deal with phenotypic plasticity, has a clear role to play in the study of local adaptation, even (if not specically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efcient, thorough and integrative study of local adaptation. Especially, evidence from genomic (for example, genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits. Heredity (2016) 116, 249254; doi:http://dx.doi.org/10.1038/hdy.2015.93

Web End =10.1038/hdy.2015.93; published online 21 October 2015

INTRODUCTIONStudying adaptation and the genetic bases of the adaptive traits is an ambitious but daunting enterprise, especially for complex traits that have a polygenic basis and are strongly inuenced by the environment. Indeed, uncovering the evidence of genetic adaptation is almost always hampered by the pervasive effects of evolutionary phenomena such as genetic drift, phenotypic plasticity, complex demographic history and complex genetic architecture. In the particular case of local adaptation, evolutionary biologists have developed efcient tools to overcome these challenges and the common garden experiment is one of them. The rationale behind this protocol is to control for the effects of phenotypic plasticity and, to a certain extent, genotype-by-environment interactions by growing individuals from different populations in a common environment, and by using the quantitative genetics toolbox (see Box...