Center for Genomics and Systems Biology, Department of Biology, 12 Waverly Place, New York University, New York 10003, USA.
- Rachel S. Meyer &
- Michael D. Purugganan
Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, Abu Dhabi, United Arab Emirates.
- Michael D. Purugganan
Competing interests statement
The authors declare no competing interests.
Rachel S. Meyer
Rachel S. Meyer is a US National Science Foundation Plant Genome postdoctoral fellow at New York University, USA. She obtained her doctorate at City University of New York and the New York Botanical Garden. She studies domestication- and diversification-related crop adaptations through genomic analysis, phytochemistry and ethnobotany.
Michael D. Purugganan
Michael D. Purugganan is the Dorothy Schiff Professor of Genomics and Dean for Science at New York University, USA. His laboratory studies the genomics of plant evolution with a strong focus on domesticated species. Much of his work is on the nature of selection and the genetic architecture of plant adaptations.
- Quantitative trait locus
(QTL). A genomic region with a gene (or multiple linked genes) that contains mutations which result in phenotypic variation in populations.
- Genome-wide association studies
(GWASs). Studies that use linkage disequilibrium between dense, usually single-nucleotide polymorphism, markers across the genome to identify significant associations between genes (or genomic regions) and trait phenotypes.
- Conscious selection
The intentional choice, made by humans, of preferred phenotypes in cultivated plants for use and propagation.
- Unconscious selection
Natural selection in crop species as a result of human cultivation practices and of growth in agro-ecological environments.
- Green Revolution
A series of research, breeding and technology transfer programmes in the mid-twentieth century that resulted in marked increases in agricultural productivity in developing countries.
Introduction of a wild-type allele into a mutant individual, through either genetic crosses or transgenic methods, to confirm that a particular gene causes a specific phenotype.
- Causative mutations
Mutations that lead to altered gene functions, which result in specific phenotypes.
Increase in the frequency of an allelic variant until it is found in all individuals in a population.
- Selective sweeps
Rapid increases in population frequencies of positively selected mutations and linked neutral mutations, which result in significant reductions in nucleotide diversity in localized regions of the genome that flank the selected mutations.
Recurrent crossing that leads to the sharing of alleles between gene pools (which can be unidirectional), such as between domesticated and wild populations.
- Genetic bottlenecks
Marked decreases in genetic diversity that are caused by reductions in effective population sizes.
- Domestication syndrome
The selection of traits that distinguish domesticated species from their wild progenitors; similar traits were often observed to occur in different crops, which led people to view them as a 'syndrome'.
- Nonsense mutations
Point mutations that transform amino acid-encoding codons into premature stop codons, which result in the generation of truncated proteins.
- cis-regulatory mutations
Mutations in linked, usually non-coding portions, of genes that alter levels and/or patterns of transcription of the linked gene.
- Missense mutations
Point mutations that change the identities of encoded amino acids, which result in changes in protein sequences.
- Nucleotide diversity
The number of single-nucleotide polymorphism in a genomic region, usually estimated as the mean level of pairwise nucleotide divergence in a sample or a population.
- Parallel evolution
Independent evolution of the same trait in different species.