Population structure and phylogeography of Elymus mutabilis and its genetic relationships with E. transbaicalensis (Poaceae)

Elymus mutabilis is a morphologically diverse species in the Poaceae family growing in Eurasia from northern Europe to far east Russia and southwards to central Asia. Elymus transbaicalensis occurs in similar habitats and is considered closely related to E. mutabilis and sometimes even referred to as a subspecies or synonym. Based on high similarity in morphology and habitat, molecular studies are needed to establish whether E. mutabilis and E. transbaicalensis can be considered as two distinct species. Thus, the objective of this study was to study diversity, relationships among populations and the phylogeographical structure of E. mutabilis and E. transbaicalensis using genotyping-by-sequencing (GBS). In total 68 individuals of E. mutabilis were sampled from 18 populations collected from northern Europe, central Asia and far east Russia, representing the central and two peripheral parts of the natural distribution of the species. The results reveal a clear distinction between E. mutabilis and E. transbaicalensis and no introgression. The phylogeographic structure of E. mutabilis follows the geographical distribution of the species. Populations from northern Europe, southern Siberia and far east Russia together form a clade separated from the peripheral populations in central Asia, indicating a common ancestry of the latter. Phylogenetic analyses revealed a radiation pattern among populations in northern Europe indicating a founding followed by rapid dispersal

Genomic, karyological and morphological changes of South American garlics (Ipheion) provide insights into mechanisms of speciation in the Pampean region

Speciation proceeds through mechanisms that promote reproductive isolation and shape the extent of genetic variation in natural populations, and thus its study is essential to understand the evolutionary processes leading to increased biodiversity. Chromosomal rearrangements are known to facilitate reproductive isolation by hybrid sterility and favour speciation events. The genus Ipheion (Amaryllidaceae, Allioideae) is unique as its species exhibit a remarkable karyological variability but lack population-level genetic data. To unveil the diversification processes acting upon the formation of new lineages within Ipheion in the Pampas of South America, we combined morphology and karyology approaches with genotyping-by-sequencing. Our phylogenomic and population genomics results supported the taxonomic division of Ipheion into three morphological and genetically well-differentiated groups. The origin of Ipheion uniflorum was traced back to its current southern distribution area in the southern Pampean region (in Argentina), from where it had expanded to the north reaching Uruguay. Our results further suggested that chromosome rearrangements and ploidy shifts had triggered speciation events, first during the origin of I. uniflorum and later during its subsequent diversification into I. recurvifolium and I. tweedieanum, in both cases reinforced by extrinsic factors and biogeographical settings. The current study illustrates the analytical power of multidisciplinary approaches integrating phylo- and population genomics with classic analyses to reveal evolutionary processes in plants.Fil: Sassone, Agostina Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Hojsgaard, Diego H.. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Giussani, Liliana Mónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Brassac, Jonathan. Leibniz Institute of Plant Genetics and Crop Plant Research; AlemaniaFil: Blattner, Frank R.. Leibniz Institute of Plant Genetics and Crop Plant Research; Alemani

Annual report 2015

Accessions considered in the study. Overview of the material considered in this study. For all materials, the GenBank identifier, the accession and species name as used in this study (Species) as well as their species synonyms used in the donor seed banks or in the NCBI GenBank (Material source/Reference) are provided. The genome symbol, and the country of origin, where the material was originally collected are given. The ploidy level measured in the scope of this study and the information if a herbarium voucher could be deposited in the herbarium of IPK Gatersleben (GAT) is given. Genomic formulas of tetraploids and hexploids are given as “female x male parent”. The genomes of Aegilops taxa follow Kilian et al. [74] and Li et al. [84]. Genome denominations for Hordeum follow Blattner [107] and Bernhardt [12] for the remaining taxa. (XLS 84 kb

Unleashing floret fertility in wheat through the mutation of a homeobox gene

Floret fertility is a key determinant of the number of grains per inflorescence in cereals. During the evolution of wheat (Triticum sp.), floret fertility has increased, such that current bread wheat (Triticum aestivum) cultivars set three to five grains per spikelet. However, little is known regarding the genetic basis of floret fertility. The locus Grain Number Increase 1 (GNI1) is shown here to be an important contributor to floret fertility. GNI1 evolved in the Triticeae through gene duplication. The gene, which encodes a homeodomain leucine zipper class I (HD-Zip I) transcription factor, was expressed most abundantly in the most apical floret primordia and in parts of the rachilla, suggesting that it acts to inhibit rachilla growth and development. The level of GNI1 expression has decreased over the course of wheat evolution under domestication, leading to the production of spikes bearing more fertile florets and setting more grains per spikelet. Genetic analysis has revealed that the reduced-function allele GNI-A1 contributes to the increased number of fertile florets per spikelet. The RNAi-based knockdown of GNI1 led to an increase in the number of both fertile florets and grains in hexaploid wheat. Mutants carrying an impaired GNI-A1 allele out-yielded WT allele carriers under field conditions. The data show that gene duplication generated evolutionary novelty affecting floret fertility while mutations favoring increased grain production have been under selection during wheat evolution under domestication

Next generation breeding tools for chamomile: Evaluating genetic diversity, ploidy variation, and identifying marker-trait associations

Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous medicinally active compounds. Next generation sequencing (NGS) approaches are applied to exploit genetic resources in the major crop plants to develop genomic resources, and to enhance breeding. Genotyping-by-sequencing (GBS) has been used to evaluate the genetic structure of cultivated populations in the non-model crop chamomile using 6495 SNP markers, and to perform a genome wide association study (GWAS) identifying sequences significantly associated with the medicinally important alpha-bisabolol content. Ploidy variation in chamomile was investigated by high-throughput flow-cytometry. Di-, tri- and tetraploid plants were identified, and in field trials characterized. Since seeds are not needed in the harvested product of chamomile, triploidy could be a way to obtain a sterile chamomile variety, omitting the problems of chamomile seeds lying up to 15 years dormant in the soil and facilitating crop rotation in the fields.Die Nutzung von Kamille (Matricaria recutita L.) als Arzneipflanze hat eine lange Tradition und umfasst einen weiten Anwendungsbereich. Die Blütenköpfe von Kamille enthalten eine Vielzahl an medizinisch wirksamen Inhaltsstoffen. Next-Generation Sequenzierungsmethoden (NGS) werden bei den Hauptkulturpflanzen verwendet, um genetische Ressourcen zu erschließen und die Züchtung zu unterstützen. Genotypisierungdurch- Sequenzierung (GBS) wurde bei der Nicht-Modellpflanze Kamille zur Charakterisierung der genetischen Diversität angewandt. Unter Nutzung von den erhaltenen 6495 hochqualitativen SNP-Markern wurden mittels einer genomweiten Assoziationsstudie (GWAS) DNA-Sequenzen identifiziert, die signifikant mit dem pharmazeutisch wichtigen Alpha-Bisabolol-Gehalt assoziiert sind. Die Ploidievariation in der Art Echte Kamille wurde mittels Hochdurchsatz-Durchflusszytometrie untersucht. Di-, tri- und tetraploide Pflanzen wurden identifiziert und in Feldversuchen charakterisiert. Da für das Ernteprodukt bei Kamille keine Samen benötigt werden, könnte Triploidie ein Weg sein, eine sterile Kamillensorte zu erzeugen. Mit einer sterilen Sorte könnte so das Problem gelöst werden, dass Kamillensamen im Boden bis zu 15 Jahre lang nach dem Anbau auskeimen, was den Fruchtwechsel auf den Ackerböden erheblich erschwert und u.a. zur Akkumulation von Kamillenkrankheiten führt

Progenitor-Derivative Relationships of Hordeum Polyploids (Poaceae, Triticeae) Inferred from Sequences of TOPO6, a Nuclear Low-Copy Gene Region

Polyploidization is a major mechanism of speciation in plants. Within the barley genus Hordeum, approximately half of the taxa are polyploids. While for diploid species a good hypothesis of phylogenetic relationships exists, there is little information available for the polyploids (4×, 6×) of Hordeum. Relationships among all 33 diploid and polyploid Hordeum species were analyzed with the low-copy nuclear marker region TOPO6 for 341 Hordeum individuals and eight outgroup species. PCR products were either directly sequenced or cloned and on average 12 clones per individual were included in phylogenetic analyses. In most diploid Hordeum species TOPO6 is probably a single-copy locus. Most sequences found in polyploid individuals phylogenetically cluster together with sequences derived from diploid species and thus allow the identification of parental taxa of polyploids. Four groups of sequences occurring only in polyploid taxa are interpreted as footprints of extinct diploid taxa, which contributed to allopolyploid evolution. Our analysis identifies three key species involved in the evolution of the American polyploids of the genus. (i) All but one of the American tetraploids have a TOPO6 copy originating from the Central Asian diploid H. roshevitzii, the second copy clustering with different American diploid species. (ii) All hexaploid species from the New World have a copy of an extinct close relative of H. californicum and (iii) possess the TOPO6 sequence pattern of tetraploid H. jubatum, each with an additional copy derived from different American diploids. Tetraploid H. bulbosum is an autopolyploid, while the assumed autopolyploid H. brevisubulatum (4×, 6×) was identified as allopolyploid throughout most of its distribution area. The use of a proof-reading DNA polymerase in PCR reduced the proportion of chimerical sequences in polyploids in comparison to Taq polymerase

ARM1 and PUB15 coding sequences for phylogenetic tree

Data matrix for the tree, analyzed with RAxML 8.2.7, GTRGAMMA model and 100 bootstrap replicates.<br

Phylogenetic tree of PUB15 and ARM1, its partial duplicate in Triticeae grasses.

Phylogenetic tree of both proteins based on alignment of overlapping PUB15 and ARM1 coding sequences. A maximum likelihood tree with <i>OsPUB15 </i>as outgroup was calculated, and bootstrap values (in percent) based on 100 re-iterations are indicated along the branches and tree depth (in changes per nucleotide position) by scale bar

Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci

Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data