Heike Schmuths

Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics

Despite Arabidopsis thalianas pre‐eminence as a model organism, major questions remain regarding the geographic structure of its genetic variation due to the geographically incomplete sample set available for previous studies. Many of these questions are addressed here with an analysis of genome‐wide variation at 10 loci in 475 individuals from 167 globally distributed populations, including many from critical but previously un‐sampled regions. Rooted haplotype networks at three loci suggest that A. thaliana arose in the Caucasus region. Identification of large‐scale metapopulations indicates clear east–west genetic structure, both within proposed Pleistocene refugia and post‐Pleistocene colonized regions. The refugia themselves are genetically differentiated from one another and display elevated levels of within‐population genetic diversity relative to recolonized areas. The timing of an inferred demographic expansion coincides with the Eemian interglacial (approximately 120 000 years ago). Taken together, these patterns are strongly suggestive of Pleistocene range dynamics. Spatial autocorrelation analyses indicate that isolation by distance is pervasive at all hierarchical levels, but that it is reduced in portions of Europe.

The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis

The N-end rule pathway targets protein degradation through the identity of the amino-terminal residue of specific protein substrates. Two components of this pathway in Arabidopsis thaliana, PROTEOLYSIS6 (PRT6) and arginyl-tRNA:protein arginyltransferase (ATE), were shown to regulate seed after-ripening, seedling sugar sensitivity, seedling lipid breakdown, and abscisic acid (ABA) sensitivity of germination. Sensitivity of prt6 mutant seeds to ABA inhibition of endosperm rupture reduced with after-ripening time, suggesting that seeds display a previously undescribed window of sensitivity to ABA. Reduced root growth of prt6 alleles and the ate1 ate2 double mutant was rescued by exogenous sucrose, and the breakdown of lipid bodies and seed-derived triacylglycerol was impaired in mutant seedlings, implicating the N-end rule pathway in control of seed oil mobilization. Epistasis analysis indicated that PRT6 control of germination and establishment, as exemplified by ABA and sugar sensitivity, as well as storage oil mobilization, occurs at least in part via transcription factors ABI3 and ABI5. The N-end rule pathway of protein turnover is therefore postulated to inactivate as-yet unidentified key component(s) of ABA signaling to influence the seed-to-seedling transition.

Gene Expression Profiling Reveals Defined Functions of the ATP-Binding Cassette Transporter COMATOSE Late in Phase II of Germination

Phase II of germination represents a key developmental stage of plant growth during which imbibed seeds either enter stage III of germination, completing the germination process via radicle protrusion, or remain dormant. In this study, we analyzed the influence of the peroxisomal ATP-binding cassette transporter COMATOSE (CTS) on the postimbibition seed transcriptome of Arabidopsis (Arabidopsis thaliana) and also investigated interactions between gibberellin (GA) and CTS function. A novel method for analysis of transcriptome datasets allowed visualization of developmental signatures of seeds, showing that cts-1 retains the capacity to after ripen, indicating a germination block late in phase II. Expression of the key GA biosynthetic genes GA3ox1 and 2 was greatly reduced in cts seeds and genetic analysis suggested that CTS was epistatic to RGL2, a germination-repressing DELLA protein that is degraded by GA. Comparative analysis of seed transcriptome datasets indicated that specific cohorts of genes were influenced by GA and CTS. CTS function was required for expression of the flavonoid biosynthetic pathway. Confocal imaging demonstrated the exclusive accumulation of flavonoids in the epidermis of wild-type seeds. In contrast, flavonoids were absent from cts and kat2-1 mutant seeds, but accumulated following the application of sucrose, indicating an essential role for β-oxidation in inducing flavonoid biosynthetic genes. These results demonstrate that CTS functions very late in phase II of germination and that its function is required for the expression of specific gene sets related to an important biochemical pathway associated with seedling establishment and survival.

Analysis of molecular data of Arabidopsis thaliana (L.) Heynh. (Brassicaceae) with Geographical Information Systems (GIS)

A Geographical Information System (GIS) is used to analyse allelic information of 13 sequenced loci of natural populations of Arabidopsis thaliana and to identify geographical structures. GIS provides tools for visualization and analysis of geographical population structures using molecular data. The geographical distribution of the number of variable positions in the alignments, the distribution of recombinant sequence blocks, and the distribution of a newly defined measure, the differentiation index, are studied. The differentiation index is introduced to measure the sequence divergence among individual plants sampled from various geographical localities. The numbers of variable positions and the differentiation index are also used for a metadata analysis covering about 26 kb of the genome. This analysis reveals, for the first time, differences in DNA sequence structures of geographically different populations of A. thaliana. The broadly defined west Mediterranean region consists of accessions with the highest numbers of polymorphic positions followed by the west European region. The GIS technology Kriging is used to define Arabidopsis specific diversity zones in Europe. The highest genetic variability is observed along the Atlantic coast from the western Iberian Peninsula to southern Great Britain, while lowest variability is found in central Europe.

Comparative Analysis of Growth, Genome Size, Chromosome Numbers and Phylogeny of Arabidopsis thaliana and Three Cooccurring Species of the Brassicaceae from Uzbekistan

Contrary to literature data Arabidopsis thaliana was rarely observed in Middle Asia during a collection trip in 2001. Instead, three other Brassicaceae species were frequently found at places where A. thaliana was expected. To reveal reasons for this frequency pattern, we studied chromosome numbers, genome sizes, phylogenetic relationships, developmental rates, and reproductive success of A. thaliana, Olimarabidopsis pumila, Arabis montbretiana, and Arabis auriculata from Uzbekistan in two temperature treatments. There are little but partially significant differences between phenotypes. All studied species have very small genomes. The 1Cx-values of different genotypes within the sampled species are correlated with altitude. Developmental rates are also correlated with 1Cx-values. In our growth experiments, Arabidopsis had high seed sterility at higher temperature, which might be one reason for the rarity of A. thaliana in Middle Asia.