Showing papers by "Alex Widmer published in 2014"

Genomics and the origin of species

Abstract: Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.

Genome-wide Comparative Analysis of the GRAS Gene Family in Populus, Arabidopsis and Rice

Abstract: GRAS genes belong to a gene family of transcription regulators that function in the regulation of plant growth and development. Our knowledge about the expansion and diversification of this gene family in flowering plants is presently limited to the herbaceous species Arabidopsis and rice. Numerous aspects, including the phylogenetic history, expansion, functional divergence and adaptive evolution await further study, especially in woody tree species. Based on the latest genome assemblies, we found 106, 34 and 60 putative GRAS genes in Populus, Arabidopsis and rice, respectively. Phylogenetic analysis revealed that GRAS proteins could be divided into at least 13 subfamilies. Tandem and segmental duplications are the most common expansion mechanisms of this gene family, and their frequent joint action may explain the rapid expansion in Populus. Site-specific shifts in evolutionary rates might be the main force driving subfamily-specific functional diversification. Adaptive evolution analysis revealed that GRAS genes have evolved mainly under purifying selection after duplication, suggesting that strong functional constraints have a bearing on the evolution of GRAS genes. Both expressed sequence tags (EST) and microarray data revealed that GRAS genes in Populus have broad expression patterns across a variety of organs/tissues. Expression divergence analyses between paralogous pairs of GRAS genes suggested that the retention of GRAS genes after duplication could be mainly attributed to substantial functional novelty such as neo-functionalization or sub-functionalization. Our study highlights the expansion and diversification of the GRAS gene family in Populus and provides the first comprehensive analysis of this gene family in the Populus genome.

Gene Regulatory Variation Mediates Flowering Responses to Vernalization along an Altitudinal Gradient in Arabidopsis

Abstract: Steep environmental gradients provide ideal settings for studies of potentially adaptive phenotypic and genetic variation in plants. The accurate timing of flowering is crucial for reproductive success and is regulated by several pathways, including the vernalization pathway. Among the numerous genes known to enable flowering in response to vernalization, the most prominent is FLOWERING LOCUS C (FLC). FLC and other genes of the vernalization pathway vary extensively among natural populations and are thus candidates for the adaptation of flowering time to environmental gradients such as altitude. We used 15 natural Arabidopsis (Arabidopsis thaliana) genotypes originating from an altitudinal gradient (800–2,700 m above sea level) in the Swiss Alps to test whether flowering time correlated with altitude under different vernalization scenarios. Additionally, we measured the expression of 12 genes of the vernalization pathway and its downstream targets. Flowering time correlated with altitude in a nonlinear manner for vernalized plants. Flowering time could be explained by the expression and regulation of the vernalization pathway, most notably by AGAMOUS LIKE19 (AGL19), FLOWERING LOCUS T (FT), and FLC. The expression of AGL19, FT, and VERNALIZATION INSENSITIVE3 was associated with altitude, and the regulation of MADS AFFECTING FLOWERING2 (MAF2) and MAF3 differed between low- and high-altitude genotypes. In conclusion, we found clinal variation across an altitudinal gradient both in flowering time and the expression and regulation of genes in the flowering time control network, often independent of FLC, suggesting that the timing of flowering may contribute to altitudinal adaptation.

Identification of Internal Reference Genes for Gene Expression Normalization between the Two Sexes in Dioecious White Campion

Abstract: Quantitative real time (qRT)-PCR is a precise and efficient method for studying gene expression changes between two states of interest, and is frequently used for validating interesting gene expression patterns in candidate genes initially identified in genome-wide expression analyses, such as RNA-seq experiments. For an adequate normalisation of qRT-PCR data, it is essential to have reference genes available whose expression intensities are constant among the different states of interest. In this study we present and validate a catalogue of traditional and newly identified reference genes that were selected from RNA-seq data from multiple individuals from the dioecious plant Silene latifolia with the aim of studying gene expression differences between the two sexes in both reproductive and vegetative tissues. The catalogue contains more than 15 reference genes with both stable expression intensities and a range of expression intensities in flower buds and leaf tissues. These reference genes were used to normalize expression differences between reproductive and vegetative tissues in eight candidate genes with sex-biased expression. Our results suggest a trend towards a reduced sex-bias in sex-linked gene expression in vegetative tissues. In this study, we report on the systematic identification and validation of internal reference genes for adequate normalization of qRT-PCR-based analyses of gene expression differences between the two sexes in S. latifolia. We also show how RNA-seq data can be used efficiently to identify suitable reference genes in a wide diversity of species.

Inheritance and reproductive consequences of floral anthocyanin deficiency in Silene dioica (Caryophyllaceae)

Abstract: UNLABELLED • PREMISE OF THE STUDY Flower color is one of the most important traits for pollinator attraction. However, natural plant populations often harbor rare flower color variants resulting from mutations in biochemical pathways for floral pigment production. It is unclear how such mutations can persist because they can affect not only pollinator visitation but also plant fertility and performance.• METHODS We collected rare white-flowered (anthocyanin-deficient) and common pink-flowered morphs of Silene dioica from natural populations in Switzerland. First- and second-generation hybrids between pink and white morphs, as well as backcrosses toward white morphs were produced, and the proportion of white-flowered offspring was determined. We compared seed siring ability and seed production between morphs using hand pollination experiments. Moreover, we scored the transfer of pollen analogues (fluorescent dyes) in a 50:50 array of the two morphs.• KEY RESULTS The proportions of white-flowered plants in the offspring of our crosses were consistent with more than one recessive mutation as the cause of floral anthocyanin deficiency and further suggested a role of maternal effects for flower color. Seed siring ability and seed set did not differ significantly between pink and white morphs. Pollen transfer occurred preferentially within morphs.• CONCLUSIONS Overall, our results imply that the white morph of S. dioica likely is caused by recessive mutations that do not impair reproduction. However, as this flower color polymorphism led to assortative mating in our experiment, it may represent standing genetic variation with the potential to contribute to evolutionary divergence.

The Governance of Climate Change Adaption in Switzerland: Issues, Actors, and Processes at the National and Cantonal Level and in Land-use relevant Policies

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