Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 29, 2010
Publication Date: January 1, 2011
Citation: Gross, B.L. 2011. MADS-box out of the black box. Molecular Ecology. 20:25-26. Interpretive Summary: Problem: Although advances in genomic techniques have made it possible to detect evidence of selection at the genetic level in non-model crops and wild plants, identifying the functional gene and the trait that is the target of selection is still difficult. This prevents researchers from fully utilizing the information provided by these experiments. Accomplishment: This manuscript represents a summary and perspective on a recent advancement in the field of molecular ecology, specifically dealing with the detection of genes under artificial and natural selection in domesticated plants. In this paper, I describe how a new combination of methods makes it possible to identify genes under selection in species with limited genetic resources, and review how this is an important departure from previous studies. The manuscript will serve as a quick source of information for researchers interested in learning about new approaches to unraveling the genetics of non-model crop species.
Technical Abstract: The compelling elegance of using genome-wide scans to detect the signature of selection is difficult to resist, but is countered by the low demonstrated efficacy of pinpointing the actual genes and traits that are the targets of selection in non-model species. While the difficulty of going from a suggestive signature to a functional nucleotide polymorphism should not prevent researchers from using genome scans, it does lessen their long-term utility within and across study systems. In a new study published in this issue, Mariac et al. (2010) have gone a long way towards increasing the relevance of genome-wide scans for selection via two approaches: 1) they tailored the markers used in the scan to target a family of developmental genes that were good candidates for controlling a trait of interest, and 2) they used an independent mapping population to confirm the association of the gene with polymorphism in the trait of interest. All of this was completed in the non-model system of pearl millet (Pennisetum glaucum), and may provide a road map for other researchers hoping to pin down solid candidate genes for selected traits in natural or cultivated systems. Outside of these broad methodological innovations, the paper specifically focuses on a trait (flowering time) that varies across an environmental gradient (rainfall). This environmental gradient potentially serves as a model for environmental change over time, and allele frequencies at the gene can therefore be used to track how populations of pearl millet adapt to future climate shifts at the genetic level.