Wild Carrot Differentiation in Europe and Selection at DcAOX1 Gene?

• Published in: PloS one 2016-10, Vol.11 (10), p.e0164872-e0164872
• Main Authors: Nobre, Tânia, Oliveira, Manuela, Arnholdt-Schmitt, Birgit
• Format: Article
• Language: English
• Subjects: Adaptation; Aldehyde Oxidase - metabolism; Alternative oxidase; Amino acid sequence; Arabidopsis; Biodiversity; Biology and Life Sciences; Breeding; Carrots; Cell Differentiation; Climatic conditions; Computer and Information Sciences; Crops; Curie, Marie (1867-1934); Daucus; Daucus carota; Daucus carota - cytology; Daucus carota - genetics; Differentiation; Domestication; Environmental gradient; Europe; Gene sequencing; Genes; Genetic aspects; Genetic diversity; Genetic resources; Genomes; Hot spots; Integrated software; Lactuca serriola; Likelihood ratio; Metabolism; Metabolites; Oxidases; Phylogeny; Picea abies; Population differentiation; Population genetics; Populations; Positive selection; Research and Analysis Methods; Ribosomal DNA; Signal transduction; Stress response
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0164872

By definition, the domestication process leads to an overall reduction of crop genetic diversity. This lead to the current search of genomic regions in wild crop relatives (CWR), an important task for modern carrot breeding. Nowadays massive sequencing possibilities can allow for discovery of novel genetic resources in wild populations, but this quest could be aided by the use of a surrogate gene (to first identify and prioritize novel wild populations for increased sequencing effort). Alternative oxidase (AOX) gene family seems to be linked to all kinds of abiotic and biotic stress reactions in various organisms and thus have the potential to be used in the identification of CWR hotspots of environment-adapted diversity. High variability of DcAOX1 was found in populations of wild carrot sampled across a West-European environmental gradient. Even though no direct relation was found with the analyzed climatic conditions or with physical distance, population differentiation exists and results mainly from the polymorphisms associated with DcAOX1 exon 1 and intron 1. The relatively high number of amino acid changes and the identification of several unusually variable positions (through a likelihood ratio test), suggests that DcAOX1 gene might be under positive selection. However, if positive selection is considered, it only acts on some specific populations (i.e. is in the form of adaptive differences in different population locations) given the observed high genetic diversity. We were able to identify two populations with higher levels of differentiation which are promising as hot spots of specific functional diversity.