BackgroundUnderstanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses.ResultsThe root transcriptomes of widely differing cultivated and wild carrots were sequenced. A method accounting for sequencing errors was introduced to optimize SNP (single nucleotide polymorphism) discovery. 11,369 SNPs were identified. Of these, 622 (out of 1000 tested SNPs) were validated and used to genotype a large set of cultivated carrot, wild carrot and other wild Daucus carota subspecies, primarily of European origin. Phylogenetic analysis indicated that eastern carrot may originate from Western Asia and western carrot may be selected from eastern carrot. Different wild D. carota subspecies may have contributed to the domestication of cultivated carrot. Genetic diversity was significantly reduced in western cultivars, probably through bottlenecks and selection. However, a high proportion of genetic diversity (more than 85% of the genetic diversity in wild populations) is currently retained in western cultivars. Model simulation indicated high and asymmetric gene flow from wild to cultivated carrots, spontaneously and/or by introgression breeding. Nevertheless, high genetic differentiation exists between cultivated and wild carrots (Fst = 0.295) showing the strong effects of selection. Expression patterns differed radically for some genes between cultivated and wild carrot roots which may be related to changes in root traits. The up-regulation of water-channel-protein gene expression in cultivars might be involved in changing water content and transport in roots. The activated expression of carotenoid-binding-protein genes in cultivars could be related to the high carotenoid accumulation in roots. The silencing of allergen-protein-like genes in cultivated carrot roots suggested strong human selection to reduce allergy. These results suggest that regulatory changes of gene expressions may have played a predominant role in domestication.ConclusionsWestern carrots may originate from eastern carrots. The reduction in genetic diversity in western cultivars due to domestication bottleneck/selection may have been offset by introgression from wild carrot. Differential gene expression patterns between cultivated and wild carrot roots may be a signature of strong selection for favorable cultivation traits.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-895) contains supplementary material, which is available to authorized users.
Mastocarpus stellatus is a common intertidal red alga in the north Atlantic. Previous work showed that the species was divided into at least two breeding groups in the northeastern Atlantic, a northern one (absent in Spain and Portugal) and a southern one, which were almost completely inter-sterile. It also showed that, in laboratory culture, at least two types of life history were evident in this species (a sexual one and a 'direct' one). The distribution of these life histories appeared to have a north-south distribution. We have used molecular markers to confirm these results and expand the sampling in certain populations. Organellar markers showed that the breeding groups have different plastid and mitochondria haplotypes and appear to be distributed along a north-south gradient. Populations in southern England and northern France (Brittany) have mixed northern and southern breeding groups, except for the Rade du Brest, as was shown previously from culture studies. Results also show that most asexual plants have a plastid haplotype corresponding to the northern breeding group and a mitochondrial haplotype corresponding to the southern breeding group, a possible case of differential organellar inheritance and hybrid formation of an asexual life history. These results using molecular markers support previous conclusions and again emphasize the high levels of genetic variation in marine algae in Brittany.
Invasion of pests may result in local adaptation and the development of biotypes specialized in different hosts. In this study, we investigated western flower thrips, Frankliniella occidentalis (Pergande), an invasive pest in Europe. Thrips from different commercial glasshouse crops within the Dutch Westland and a lab culture kept on chrysanthemum were compared. Genetic barcoding was applied for the identification of potential western flower thrips cryptic species in the Netherlands revealing that all western flower thrips populations studied belonged to the "glasshouse" strain reported in California as the only existing species in the Netherlands. Feeding and reproduction parameters in leaf disc and whole plant bioassays were scored. We detected significant differences in thrips feeding among host plants and thrips origin. Host plants differed in average thrips damage while thrips from different origins caused similar amounts of damage across host plants. In contrast, reproductive success of thrips on all plant species depended strongly on thrips origin. The thrips lab culture maintained on chrysanthemum obtained the highest levels of reproduction on chrysanthemum. Differences among the other thrips populations were relatively small. Amplified fragment length polymorphisms analyses were used to study genetic differences between western flower thrips populations and confirmed that the lab culture population was also genetically the most different of all studied populations. The results of the amplified fragment length polymorphisms analyses together with the better reproductive performance of thrips on the host plant on which they were maintained demonstrate the evolution of a lab biotype specialized in a particular host. This finding has potential relevance for future crop control and breeding programs.
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