Projects and grants

How hybridisation and allopolyploidisation affect the diversity in three Brassicaceae tribes

Goal: The project deals with the role of hybridization and allopolyploidy in generation of plant diversity on the examples from the three Brassicaceae tribes. We will address genomic, phenotypic and ecological consequences of within- and across-ploidy crossing and assess its relevance for plants growing in their native environment. Multiple methodical approaches, namely genomic techniques (RADseq, Hyb-Seq, enabling targeted sequencing, microsatellite markers), genomic in situ hybridization (GISH, FISH and chromosome painting – CCP), DNA content (genome size) measurements, multivariate morphometrics, artificial hybridization, ecological and climatic niche modelling will be used. Important advantage is the detailed knowledge of the plant systems by the team, including their evolutionary history, experience with proposed methods in the studied genera and already available plant material for DNA analyses. Close relationships of the studied taxa with Arabidopsis thaliana makes the use and interpretation of genomic techniques easier and grants the wide publicity of acquired results.

Principal investigator: Prof. RNDr. Karol Marhold, DrSc.

Grantor: Czech Science Foundation 

Duration: 2019-01 to 2022-06

Grant number: P506/19-06632S

Pathways and consequences of polyploidy and chromosomal variation in plant evolution – three cases from the model family Brassicaceae

Goal: The project deals with triggers and consequences of polyploidisation (whole genome duplication) on the example of three polyploid complexes of Brassicaceae. Analysis of the influence of cryptic variation of diploid and independently arisen polyploid lineages, together with ecological and morphological consequences of polyploidisation, and influence of selection on genomes of di- and polyploid lineages is carried out. For the Cardamine pratensis complex, evolutionary potential of dysploidy is also estimated. Advanced genomic techniques (RADseq, target enrichment, genome resequencing), comparative chromosome painting (CCP), ecological experiments and bioclimatic modelling are used. Key advantage is the detailed knowledge of all three plant systems by the team, including details on evolutionary history, experience with proposed methods in the studied systems and already available material for DNA analyses.

Principal investigator: Prof. RNDr. Karol Marhold, DrSc.

Grantor: Czech Science Foundation 

Duration: 2016-01 to 2018-12

Grant number: P506/16-10809S

Evolutionary patterns in polyploid complexes: congruent or discordant histories in three examples from the Brassicaceae family

Goal: The aim of the project is the comparison of evolutionary patterns and processes in three polyploid complexes coming from three different tribes of the Brassicaceae family, namely from the genera Arabidopsis, Alyssum and Cardamine. We will search for the congruent patterns and differences in the origin of polyploid taxa from ancestral diploids, for the breeding strategies, hybridization patterns, distribution areas, as well as for the invasive potential of some taxa. Methodical approaches will include a combination of different molecular markers (AFLPs, microsatellites, cpDNA and nrDNA sequences, including single copy genes). Studies will include thorough check of variation in ploidy levels using flow cytometry as well as revealing morphological patterns based on the multivariate morphometric approach. We will leverage especially the wide spectrum of molecular approaches available for the closely related model species Arabidopsis thaliana. The project aims to overcome the gap between the studies of model species in the laboratories and wild populations in nature.

Principal investigator: Prof. RNDr. Karol Marhold, DrSc.

Grantor: Czech Science Foundation 

Duration: 2012-01 to 2015-12

Grant number: P506/12/0668

Student grants

Parallel ecological speciation in polyploid plant complex

Goal: By combining evolutionary history knowledge with new genomic methods we can study the mechanism of key evolutionary processes such as speciation in unprecedented detail. Ecological adaptation has gained much scientific interest within the last years, but it has been studied mostly in animals while plants studies remain scarce. Reproductive isolation can be raised among populations as a consequence of divergent natural selection acting in populations occupying different niches. Polyploidy or whole-genome duplication is another mechanism of speciation possibly leading to shifts in the ecological tolerances of new cytotypes, which can improve the chances of new cytotypes to colonize new habitats. Despite major role of the genome-environment interaction in both processes, the joint effect of whole genome duplication and ecological divergence in speciation had not been addressed so far. In this project I plan to fill in this gap by study of ecological speciation along an elevational gradient in the Cardamine amara diploid-polyploid complex. This group includes multiple geographically separated alpine diploid subspecies, which show traits of parallel ecological speciation, as well as a tetraploid subspecies occurring in alpine habitats. Such case of likely parallel independent colonization of several mountain ranges by individuals differing in ploidy provides a great opportunity to study the interplay of polyploidization and parallel ecological speciation.

Principal investigator: Mgr. Paolo Bartolič

Grantor: Charles University Grant Agency

Duration: 2020-01 to 2022-12

Grant number: 383621

Genetic structure, evolutionary history and speciation limits of overlooked plant species Arabidopsis arenosa agg. tested by next generation sequencing

Goal: This project is focused on evolutionary history and speciation of poorly known di-tetraploid complex Arabidopsis arenosa. Thanks to close relative – Arabidopsis thaliana – this species complex represents an ideal group of taxa for molecular evolutionary analysis. Plants are biennial to perennial, morphologically variable, inhabiting broad range of habitats, with a limited knowledge about their breeding system. To reveal phylogenetic relationships of populations and lineages we choose next-generation sequencing method – RADseq (researcher obtained required know-how within a research stay in Japan last year). This method is ideal to study within-species variability and phylogeography, as it provides considerable amount of whole-genome information in SNP (single nucleotid polymorphism), which are usable even in evolutionary young groups, moreover at relatively low-cost. Information about breeding systems will be obtained by pollination experiments on plants grown from collected seeds. This dataset will be tested for the level of autogamy and, in the second year of the project, for allogamy between evolutionary distant lineages revealed by RADseq. Combination of these methods will provide us possibility to uncover loci connected with reproductive barriers and will point us to new speciation studies.

Principal investigator: Mgr. Gabriela Šrámková

Grantor: Charles University Grant Agency

Duration: 2015-01 to 2017-12

Grant number: 391315