Plant domestication, a unique opportunity to identify the genetic basis of adaptation

Jeffrey Ross-Ibarra, Peter L. Morrell, Brandon S. Gaut

Research output: Contribution to journalArticlepeer-review

229 Scopus citations


Despite the fundamental role of plant domestication in human history and the critical importance of a relatively small number of crop plants to modern societies, we still know little about adaptation under domestication. Here we focus on efforts to identify the genes responsible for adaptation to domestication. We start from a historical perspective, arguing that Darwin's conceptualization of domestication and unconscious selection provides valuable insight into the evolutionary history of crops and also provides a framework to evaluate modern methods used to decipher the genetic mechanisms underlying phenotypic change. We then review these methods, framing the discussion in terms of the phenotype-genotype hierarchy. Top-down approaches, such as quantitative trait locus and linkage disequilibrium mapping, start with a phenotype of interest and use genetic analysis to identify candidate genes. Bottom-up approaches, alternatively, use population genetic analyses to identify potentially adaptive genes and then rely on standard bioinformatics and reverse genetic tools to connect selected genes to a phenotype. We discuss the successes, advantages, and challenges of each, but we conclude that bottom-up approaches to understanding domestication as an adaptive process hold greater promise both for the study of adaptation and as a means to identify genes that contribute to agronomically important traits.

Original languageEnglish (US)
Pages (from-to)8641-8648
Number of pages8
JournalProceedings of the National Academy of Sciences of the United States of America
Issue numberSUPPL. 1
StatePublished - May 15 2007


  • Agronomic traits
  • Association mapping
  • Phenotype
  • Quantitative trait locus
  • Selection

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